Cytocell Catalogue 2014/15 by Cytocell

Introduction

An Introduction to Cytocell Cytocell’s FISH business is now the oldest and most experienced in the world. The first products were developed over 23 years ago at Birmingham Heartlands Hospital, England, where, in 1991, the first of our directly labelled FISH probes were produced. These were also the first to employ a novel co-denaturation protocol that has now become universally adopted for FISH worldwide. These developments were followed by the first complete set of subtelomeric probes, along with a unique delivery device that enabled them all to be FISHed on a single slide, and the largest range of Microdeletion syndrome probes available. From these humble beginnings, our catalogue flourished so that today it contains around 430 different products, including an enviable range of Haematology and Solid Tumour probes, making it the largest FISH catalogue available. We are justifiably proud of our achievements over the last 23 years and equally as proud to have served you, our customers. Over the years, we have actively listened to and acted upon your needs and requirements leading to the development of our current portfolio of FISH probes, which are available in a convenient liquid format and packaged in kit sizes appropriate to your laboratory workload. Our success and enviable record for quality and service, along with our extensive distributor network throughout the world made Cytocell a clear partner for a similarly orientated company, Oxford Gene Technology, who, early in 2014, added Cytocell to their portfolio of products aimed at the Molecular Diagnostics market. Oxford Gene Technology was founded by Professor Sir Ed Southern to commercialise his oligonucleotide microarray technology. The Company has expanded its product offerings to now encompass both microarrays and Next Generation Sequencing through the company’s CytoSure™ and Genefficiency™ range of products and services. Together, both companies can now offer a comprehensive portfolio of diagnostic tests, delivering high-quality, high-throughput genetic analyses. This latest catalogue continues the trend of the last few years in that it is again our largest to date and contains the single largest collection of FISH probes available from one supplier. In addition, Cytocell is committed to the future development and expansion of our probe catalogue through the use of our proprietary sequence data and exclusive BAC collection. Under the banner of “myProbes®”, Cytocell is proud to offer our FISH expertise and services to our customers for the development of custom built probes. Using our myProbes® service and its website (www.myprobes.com), we can supply FISH probes tailored to your exact needs and specification, from establishing new diagnostic tests to research into genetic aberrations found in cancer.

Dr. Martin Lawrie Managing Director, Cytocell Ltd.

Cytocell FISH probes are developed and produced in the UK

Contents - Oncology and Constitutional FISH

Contents Haematology AML1 (RUNX1) Breakapart

TCL1 Breakapart

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion

TCRAD Breakapart

TCRB (TRB) Breakapart

ATM Deletion

BCR/ABL(ABL1) Translocation, Dual Fusion

TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion

BCR/ABL(ABL1) Plus Translocation, Dual Fusion

TLX1 Breakapart

BCL6 Breakapart

TLX3 Breakapart

CBFβ/MYH11 Translocation, Dual Fusion

CKS1B/CDKN2C(P18) Amplification, Deletion

CLL PROFILER Kit

CLL Plus Screening Panel

Chromoprobe Multiprobe® ALL

cMYC (MYC) Breakapart

Chromoprobe Multiprobe® CLL

CRLF2 Breakapart and P2RY8 Deletion

Chromoprobe Multiprobe® AML/MDS

Deletion 13q14.3, D13S319 Plus and D13S25

D13S319/13qter/12cen Deletion/Enumeration

Del(5q) Deletion

Del(7q) Deletion

Del(20q) Deletion

BCL6 Breakapart

E2A (TCF3) Breakapart

CCND1 Breakapart

E2A/PBX1 Translocation, Dual Fusion

IGH Breakapart

E2A/PBX1/HLF Translocation, Dual Fusion

IGH/BCL2 Translocation, Dual Fusion

EVI1 (MECOM) Breakapart

IGH/CCND1 Translocation, Dual Fusion

FIP1L1/CHIC2/PDGFRA Deletion/Fusion

IGH/MALT1 Translocation, Dual Fusion

IGH Plus Breakapart

IGH/MYC Translocation, Dual Fusion

IGH/BCL2 Plus Translocation, Dual Fusion

IGK Breakapart

IGH/CCND1 Plus Translocation, Dual Fusion

IGL Breakapart

IGH/CCND3 Plus Translocation, Dual Fusion

MYC Breakapart

IGH/cMYC(MYC) Plus Translocation, Dual Fusion

P16 (CDKN2A) Deletion

IGH/FGFR3 Plus Translocation, Dual Fusion

P53 (TP53) Deletion

IGH/MAF Plus Translocation, Dual Fusion

Haematopathology BCL2 Breakapart

Pathology

IGH/MAFB Plus Translocation, Dual Fusion

IGH/MYEOV Plus Translocation, Dual Fusion

IGK Breakapart

Tissue Pretreatment Kit

IGL Breakapart

100

ALK Breakapart

MLL (KMT2A) Breakapart

101

CHOP (DDIT3) Breakapart

MLL/AFF1 Translocation, Dual Fusion

102

C-MET (MET) Amplification

MLL/MLLT1, MLL/MLLT3 and MLL/MLLT4 Translocation, Dual Fusion

103

EGFR Amplification

104

EML4 Breakapart

MYB Deletion

105

EWSR1 Breakapart

P16 (CDKN2A) Deletion

106

EWSR1/ERG Translocation, Dual Fusion

P53 (TP53) Deletion

107

FLI1/EWSR1 Translocation, Dual Fusion

P53(TP53)/ATM Probe Combination

108

FGFR1 Breakapart/Amplification

PDGFRB Breakapart

109

HER2 (ERBB2) Amplification

110

MALT1 Breakapart

111

MDM2 Amplification

112

N-MYC (MYCN) Amplification

61 62 63

Multiprobe Haematology

FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion

RARα (RARA) Breakapart

113

PAX3 and PAX7 Breakapart

154

Satellite Enumeration Probes

114

RB1 Deletion

155

Dual Labelled Satellite Probe Sets

115

ROS1 Breakapart

155

Acro-P-Arm Probe

116

SRD (CHD5) Deletion

117

SYT (SS18) Breakapart

118

TMPRSS2/ERG Deletion/Breakapart

Subtelomere Specific Probes

119

TOP2A Amplification/Deletion

158

Subtelomere Specific Probes

120

ZNF217 Amplification

159

Aquarius® Subtelomere Specific Probes

160

Chromoprobe Multiprobe®-T Applications

161

Chromoprobe Multiprobe®-T Device

Prenatal 123

Aquarius® FAST FISH Prenatal Enumeration Kits

124

Aquarius® Prenatal Enumeration Kits

Microdeletion 127

Alagille (JAG1)

128

Angelman (UBE3A/D15S10)

129

CHARGE

130

Cri-Du-Chat and SOTOS Probe Combination

131

DiGeorge II (10p14)

132

DiGeorge and 22q13.3 Deletion Syndrome Probe Combinations

134

Kallmann (KAL1) and Steroid Sulphatase Deficiency (STS) Probe Combination

135

Langer-Giedion

136

Monosomy 1p36

137

Neurofibromatosis Type 1

138

Prader-Willi/Angelman (SNRPN)

139

Rubinstein-Taybi

140

Saethre-Chotzen/Williams-Beuren Combination

ZOO FISH 164

Aquarius® ZOO FISH Range

165

Murine Painting Probes

Accessories 168

Accessories

Indices 170

Haematology Probe Range Summary

171

Chromoprobe Multiprobe Range Summary

172

Tissue Pretreatment Kit Summary

172

Haematopathology Probe Range Summary

172

Pathology Probe Range Summary

173

FAST FISH Prenatal Probe Range Summary

173

Prenatal Probe Range Summary

174

Microdeletion Probe Range Summary

175

Painting Probe Range Summary

176

Satellite Probe Range Summary

177

Subtelomere Probe Range Summary

178

Murine Painting Probe Range Summary

141

SHOX

142

Smith-Magenis (RAI1 and FLII)/ Miller-Dieker Probe Combinations

144

SRY

179

Accessories Range Summary

145

Williams-Beuren

180

Index by Chromosome

146

Wolf-Hirschhorn

183

Index by Gene Name

XIST

187

Pathology Products by Disease State

188

Haematology Products by Disease State

147

Contents - Oncology and Constitutional FISH

Satellites

Pathology Continued

Paints 150

Painting Probes

151

Summary of Painting Probes

152

Chromoprobe Multiprobe® OctoChrome™

Our products

Our products Cytocell’s DNA diagnostic Fluorescence In Situ Hybridisation (FISH) kits are aimed at two disciplines; Constitutional cytogenetics and Oncology/Pathology cytogenetics.

We offer three key product ranges: Chromoprobe Multiprobe® Macroarray Range Using our unique Chromoprobe® process, multiple probes are reversibly bound to a glass slide providing a convenient screening tool for genetic abnormalities across multiple chromosomes. Key applications include detection of chromosomal rearrangements and as a diagnostic / prognostic tool in the detection of various Leukaemias.

Aquarius® Range Aquarius® probes are directly labelled liquid probes provided in hybridisation solution. The probes are accompanied by DAPI counterstain to provide a complete Fluorescence In Situ Hybridisation kit.

myProbes® myProbes® is a custom FISH probe design and manufacture service, which utilises Cytocell’s proprietary BAC clone collection. If a product you require does not appear in the catalogue, do not hesitate to contact Cytocell with your request.

Patents and Trademarks Aquarius, Chromoprobe, Cytocell, Chromoprobe Multiprobe and myProbes are registered trademarks of Cytocell Ltd. The Chromoprobe principle is covered by international patents WO9314223, EP0623177. The design of the Multiprobe is a registered design and is also covered by a Design Patent No. 420,745. Cytocell is registered with the MHRA (Medicines and Healthcare products Regulatory Agency) and all Cytocell products are CE marked in accordance with the In-Vitro Diagnostic Medical Devices Directive 98/79/EC, and the 2002 Regulations. Cytocell operates a Quality Management System that have been assessed and certified to both EN ISO 9001:2008 and EN ISO 13485:2003. Please check our website for the latest probe ranges available from Cytocell. www.cytocell.com

Disclaimer Every attempt has been made to ensure that the information in this catalogue is correct at time of going to print. Although every care has been taken in preparing this publication, no responsibility or liability will be accepted by Cytocell Ltd or its employees for its accuracy or completeness. v001/2014-06

Aquarius® Overview The Aquarius® range consists of directly labelled FISH probes for constitutional cytogenetic and oncology applications. All Aquarius® probes provide the benefits of: • Economical kit formats: 5 and 10 tests. Prenatal probes are also available in 30 or 50 test formats. • Liquid stable reagents premixed in hybridisation solution, provided with DAPI counterstain and full instructions for use. • Directly labelled probes allowing visualisation with standard (FITC, Texas Red® and DAPI) microscope filters. • Designed for FISH on interphase nuclei and metaphase chromosomes.

The procedure is simple: 1 Spot slide with cell sample and dehydrate.

2 Apply Aquarius® probe onto dehydrated cell sample.

3 Place coverslip onto slide and seal.

4 Denature on a hotplate and hybridise overnight.

5 Wash with rapid, formamide-free stringency washes.

6 Apply DAPI counterstain provided and view under a fluorescent microscope.

Multiprobe Overview The Chromoprobe Multiprobe® System is an extension of Cytocell's proprietary Chromoprobe® technology, whereby DNA FISH probes are reversibly bound to the surface of a glass device. These probes dissolve back into solution once in contact with the supplied hybridisation buffer, whilst denaturation of the probes and target DNA occurs simultaneously under the device once heated. This approach not only simplifies the whole FISH procedure but also renders it safer and quicker to use. This system allows multiple FISH probes to be hybridised on the same slide in a spatially separated manner allowing rapid screening of a patient sample for a number of different DNA sequences in a single FISH analysis. The assay is supplied in a kit format of 2, 5 or 10 devices and includes hybridisation solution, DAPI counterstain, template slides, a hybridisation chamber and full instructions for use. The kit even contains a unique liquid crystal display slide surface thermometer for accurate temperature measurement of the denaturation surface.

The procedure is simple:

Spot 2µl (or 4µl for an 8 square device) of cell sample onto alternate squares of the supplied slide.

Soak the slides in 100% methanol, then polish dry with a lint free cloth.

Carefully lower spotted slide onto the device.

Check the temperature of the hotplate using the slide surface thermometer provided. Denature the slide/device at 75°C for 2 minutes.

Once dry, fill in the remaining squares with the cell sample and check using phase contrast.

Place slides in 2xSSC for 2 minutes and then dehydrate through an ethanol series.

Place slide/device in hybridisation chamber supplied and float on the surface of a clean 37°C waterbath overnight.

Wash in 0.4xSSC at 72°C for 2 minutes, then 2xSSC/0.05% Tween at room temperature for 30 seconds.

Spot 1µl (or 2µl for an 8 square device) of supplied hybridisation solution onto each square of the device.

Apply DAPI counterstain provided and view under a fluorescence microscope.

Tissue Pretreatment Overview Introducing the first Pretreatment Kit capable of preparing slides for CISH and/or FISH analysis on Formalin-Fixed, Paraffin-Embedded (FFPE) tissue. Our ready-to-use Tissue Pretreatment Kit has been optimised to produce excellent visual results with our extensive AquariusÂŽ Pathology FISH range. To further extend the utility of the kit we have also validated its use with other commercially available CISH (Chromogeneic In Situ Hybridisation) and FISH (Fluorescence In Situ Hybridisation) DNA probes. With ease-of-use and convenience in mind, our simple two stage FFPE slide preparation protocol employs the use of ready-to-use reagents; which have been optimised to increase the permeabilisation of cell membranes and facilitate penetration of the desired FISH or CISH DNA probe.

The procedure is simple:

1 Deparaffinise slides and rehydrate through an ethanol series.

2 Place slides into Tissue Pretreatment Solution (Reagent 1), preheated to 100Â°C.

3 Rinse slides and apply Enzyme Reagent provided.

4 Dehydrate slides through an ethanol series and continue with FISH denaturation and hybridisation protocol.

Probe Maps Probe maps in this 2014/2015 version of the Cytocell catalogue have been updated to include information on gene orientation to allow the 3’ or 5’ positions of the probes to be seen in relation to the gene, or region, of interest. The arrows on the genes indicate the direction of transcription. Those with an arrow above, pointing to the right, are located on the plus, or sense, strand of the DNA. Those with an arrow below the gene, pointing to the left, are on the minus, antisense strand. In both cases, the 5’ end is that with the arrow as genes are transcribed in a 5’ to 3’ direction. Examples can be seen below.

Sense, Plus (+) strand 5’

3’

5’

Antisense, Minus (-) strand Example of a typical Cytocell product map.

5p15.31

5q31.2 EGR1 TAS2R1

CDC25C

D5S630

D5S1701 D5S500 D5S2415 D5S2542

D5S2064

184kb

310kb 100kb

HUGO Nomenclature Gene names have also been updated to reflect current HUGO Gene Nomenclature Committee (HGNC) approved symbols. Where this affects existing product names, the approved HGNC symbol is placed into brackets. All gene names were checked and updated according to the HGNC database1 as of November 2013.

RefeRenCes 1.

HGNC Database, HUGO Gene Nomenclature Committee (HGNC), EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. www.genenames.org

Common FISH

Signal Patterns

Haematology

Contents 18

AML1 (RUNX1) Breakapart

IGH/cMYC(MYC) Plus Translocation, Dual Fusion

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion

IGH/FGFR3 Plus Translocation, Dual Fusion

ATM Deletion

IGH/MAF Plus Translocation, Dual Fusion

BCR/ABL(ABL1) Translocation, Dual Fusion

IGH/MAFB Plus Translocation, Dual Fusion

BCR/ABL(ABL1) Plus Translocation, Dual Fusion

IGH/MYEOV Plus Translocation, Dual Fusion

BCL6 Breakapart

IGK Breakapart

CBFβ/MYH11 Translocation, Dual Fusion

IGL Breakapart

CKS1B/CDKN2C(P18) Amplification/Deletion

MLL (KMT2A) Breakapart

CLL PROFILER Kit

MLL/AFF1 Translocation, Dual Fusion

CLL Plus Screening Panel

cMYC (MYC) Breakapart

MLL/MLLT1, MLL/MLLT3 and MLL/MLLT4 Translocation, Dual Fusion

CRLF2 Breakapart and P2RY8 Deletion

MYB Deletion

Deletion 13q14.3, D13S319 Plus and D13S25

P16 (CDKN2A) Deletion

D13S319/13qter/12cen Deletion/Enumeration

P53 (TP53) Deletion

Del(5q) Deletion

P53(TP53)/ATM Probe Combination

Del(7q) Deletion

PDGFRB Breakapart

Del(20q) Deletion

E2A (TCF3) Breakapart

E2A/PBX1 Translocation, Dual Fusion

E2A/PBX1/HLF Translocation, Dual Fusion

TCL1 Breakapart

EVI1 (MECOM) Breakapart

TCRAD Breakapart

FIP1L1/CHIC2/PDGFRA Deletion/Fusion

TCRB (TRB) Breakapart

IGH Plus Breakapart

TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion

IGH/BCL2 Plus Translocation, Dual Fusion

TLX1 Breakapart

IGH/CCND1 Plus Translocation, Dual Fusion

TLX3 Breakapart

IGH/CCND3 Plus Translocation, Dual Fusion

FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion

RARα (RARA) Breakapart

Refer to our Haematology key to determine the most commonly associated disease state for each of our Haematology products. Haematology key: ALL

Acute Lymphoblastic Leukaemia

CML

Chronic Myeloid Leukaemia

AML

Acute Myeloid Leukaemia

HES

Hypereosinophilic Syndrome

APL

Acute Promyelocytic Leukaemia

CEL

Chronic Eosinophilic Leukaemia

CLL

Chronic Lymphocytic Leukaemia

Lymphoma Multiple Myeloma

Haematology

Haematology As long ago as the 19th Century, nuclear changes were recognised as being significant in cancer biology. Advances in cytogenetics and molecular cytogenetics in the last century showed that although a number of numerical and structural chromosome changes appeared to be random and non-specific, rearrangements involving individual chromosomes were shown to define specific abnormalities in individual tumour types. Fluorescence In Situ Hybridisation (FISH), using locus-specific probes that are capable of defining these stereotypic structural rearrangements, has now become a routine diagnostic test in the clinical laboratory and the technique has thus been shown to be useful in the management of cancer patients. Cytocell offers a range of FISH probes, specific for a number of haematological malignancies, which are available in the Aquarius速 liquid format. These probes are directly labelled, ready to use in hybridisation buffer and available in economical five, and larger ten, test kits. The protocol is rapid and simple and has been developed to allow co-denaturation of the FISH probe and target DNA simultaneously. The probe mixtures are designed for use on interphase nuclei and metaphase chromosomes from cultured peripheral blood cells or cultured bone marrow samples.

Haematology

Cat. No. LPH 027-s

(5 tests)

Cat. No. LPH 027

(10 tests)

AML1 (RUNX1) Breakapart The AML1 (RUNX1) gene is the most frequent target of chromosomal rearrangements observed in human acute leukaemia. The most common rearrangements are the TEL/AML1 and AML1/ETO fusions. The TEL(ETV6)/AML1 fusion is brought about by the t(12;21)(p13;q22) translocation, observed in around 21% of childhood B-ALL cases1, whilst the AML1/ETO(RUNX1T1) fusion is the result of the t(8;21)(q21;q22) translocation observed in ~40% of AML M2 cases and 5-12% of AML cases overall2. Both of these rearrangements provide for a favourable outcome3,4.

AML ALL RefeRenCes

The AML1 gene is also rearranged in many other rare translocations, with partners including chromosomes 1, 2, 3, 4, 6, 9, 16, 20 and X. The Cytocell AML1 breakapart product has been designed to allow the detection of rearrangements regardless of the partner gene. Rearrangements of AML1 are not restricted to translocations. Using FISH, amplifications of chromosome 21 (iAMP21), including the AML1 gene, have also been found in childhood ALL5,6. These amplifications have been associated with poor outcome7.

Jamil A et al., Cancer Genet Cytogenet 2000;122(2):73-8

Huret JL . t(8;21)(q22;q22). Atlas Genet Cytogenet Oncol

Haematol. September 1997 Shurtleff et al., Leukemia. 1995 Dec;9(12):1985-9

Cho et al., Korean J Intern Med. 2003 Mar;18(1):13-20

Niini T, Haematologica 2000;85(4):362-6

Harewood et al., Leukemia. 2003 Mar;17(3):547-53

Robinson HM et al., Leukemia 2003;17(11):2249-50

21q22.12

CLIC6

AML1 (RUNX1)

RCAN1

D21S326 D21S1706 D21S393 D21S1969 148kb

100kb

D21S1895 D21S1921 167kb

(5 tests)

Cat. No. LPH 026

(10 tests)

Haematology

Cat. No. LPH 026-s

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion AML1 (RUNX1 - Runt related Transcription Factor 1) is fused with ETO (RUNX1T1) in the t(8;21)(q21;q22) translocation, found most commonly in AML M2 patients and less frequently in subgroups M1 and M41. Overall, 7% of AML cases demonstrate the abnormality, the majority of which are de novo1. Additional abnormalities occur in around 80% of cases - these may be loss of a sex chromosome, del(9q), trisomy 8 or monosomy 71. Three-way variants of this rearrangement, along with the t(3;21) (AML1/EVI1, also known as RUNX1/MECOM) show that juxtaposition of AML1 to the derivative chromosome is consistent and therefore the critical part of the rearrangement2,3. AML1 is the most common target for translocations in acute myeloid leukaemia. The breakpoint mainly occurs in the intron between exons 5 and 6 just before the transactivation domain. The fusion proteins created contain the DNA-binding domain of AML1 fused to the transcription factors ETO or EVI1 (on chromosomes 8 and 3 respectively)1. These abnormalities can give rise to tumourigenic growth through a number of different mechanisms.

AML RefeRenCes 1. 2. 3.

Huret JL . t(8;21)(q22;q22). Atlas Genet Cytogenet Oncol Haematol. September 1997 Nucifora G et al., Blood 1995;86(1):1-14 Heim and Mitelman, Willey-Liss, Inc. 1995

21q22.12

CLIC6

AML1 (RUNX1)

RCAN1

D21S326 D21S1706 D21S393 D21S1969

D21S1895 D21S1921 167kb

148kb 100kb

8q21.3

ETO

(RUNX1T1)

D8S1950 D8S1952 D8S1648 D8S1603

D8S412 D8S2020

148kb

149kb 100kb

Haematology

Cat. No. LPH 011-s

(5 tests)

Cat. No. LPH 011

(10 tests)

ATM Deletion The protein kinase ATM (Ataxia-Telangiectasia Mutated) gene, located in 11q22.3, is frequently deleted in cases of B-CLL. ATM is an important checkpoint gene involved in the management of cell damage and its function is to assess the level of DNA damage in the cell and attempt repair by phosphorylating key substrates involved in the DNA damage response pathway. The ATM/P53 (also known as TP53) interaction in B-CLL has been shown to play an important role in the proliferation of lymphoid cancer1. It has been shown that ATM enhances the phosphorylation of P532, should the damage be so great that the cell requires destruction by apoptosis (which is mediated by P53). Deletion of ATM removes this checkpoint activity and hence activation of P53. Thus, there is no attempt made to repair, or apoptosis of, damaged cells, despite the presence of P53. In the absence of ATM, damaged cells are allowed to continue to proliferate.

CLL RefeRenCes 1. 2. 3.

Screening for deletions of ATM and/or P53 is vital to allow informed therapy choices for CLL patients, especially as deletions of P53 and ATM confer poor prognosis3.

D11Z1

11q22.3

ATM

NPAT

D11S3347

180kb 100kb

D11S2179

Stankovic et al., Blood 2004;103(1):291-300 Khanna et al., Nature Genetics 1998;20(4):398-400 Zent et al., Blood 2010;115(21):4154-4155

(5 tests)

Cat. No. LPH 007

(10 tests)

Haematology

Cat. No. LPH 007-s

BCR/ABL(ABL1) Translocation, Dual Fusion The presence of the Philadelphia chromosome (Ph) has important diagnostic and prognostic implications in a number of haematological disorders. The abnormality is characteristic of Chronic Myeloid Leukaemia (CML),

t(9:22) Patient

found in around 90% of cases, but also represents a significant abnormality in 30% of adult and 2 to 10% of childhood Acute Lymphoblastic Leukaemia (ALL) cases1,2,3,4,5. This rearrangement is also

ALL AML CML

seen in rare cases of Acute Myelogenous Leukaemia (AML)6. As a result of the Philadelphia translocation, t(9;22)(q34.12;q11.23), the ABL1 (Abelson) proto-oncogene and the BCR (Breakpoint Cluster

RefeRenCes 1.

Shteper et al., Leukemia 2001;15(4):575-582

Groffen et al., Cell 1984;36:93-9

Region) gene fuse, giving rise to the BCR/ABL1 fusion gene.

Shtivelman et al., Nature 1985;315:550-4

Hermans et al., Cell 1987;51:33-40

In ALL, the rearrangement is associated with an extremely poor

OMIM â&#x2122;Ż613065: http://www.omim.org/entry/613065

Soupir et al., Am J Clin Pathol 2007;127:642-650

outcome with only 20-30% of Philadelphia chromosome positive (Ph+) children being cured with chemotherapy alone7. Allogeneic bone

Koo et al., Korean J Pediatr 2011; 54(3):106-110

Van Rhee et al., Br j Haematol 1995;90:225-8

marrow transplantation is the only curative therapy for these patients. In a small number of cases of ALL, the translocation does not result in a cytogenetically visible Philadelphia chromosome. In these cases, FISH is essential for highlighting the fusion gene8. Ph+ Acute Myeloid Leukaemia (AML) is characterised by its resistance to conventional standard chemotherapy and poor prognosis6, so accurate and rapid identification of this chromosomal abnormality is vital.

22q11.22-q11.23

GNAZ

RAB36

BCR

IGLL1

D22S1027

D22S1002E D22S257

169kb

148kb 100kb

9q34.11-q34.12 ASS1

D9S2057

173kb

FUBP3 PRDM12

LAMC3

ABL1

D9S313

D9S1863

346kb 100kb

Haematology

Cat. No. LPH 038-s

(5 tests)

Cat. No. LPH 038

(10 tests)

BCR/ABL(ABL1) Plus Translocation, Dual Fusion The presence of the Philadelphia chromosome (Ph) has important diagnostic and prognostic implications in a number of haematological disorders.

ALL AML CML

The abnormality is characteristic of Chronic Myeloid Leukaemia (CML), found in around 90% of cases, but also represents a significant abnormality in 30% of adult and 2 to 10% of childhood Acute Lymphoblastic Leukaemia (ALL) cases1,2,3,4,5. This rearrangement is also seen in rare cases of Acute Myelogenous Leukaemia (AML)6. As a result of the Philadelphia translocation, t(9;22)(q34.12;q11.23), the ABL1 (Abelson) proto-oncogene and the BCR (Breakpoint Cluster Region) gene fuse, giving rise to the BCR/ABL1 fusion gene. The translocation between chromosomes 9 and 22 can be accompanied by loss of proximal sequences on the derivative chromosome 97. The deletion encompassing the ASS1 gene is associated with poor prognosis, though this may be partially abrogated by treatment with imatinib8. Therefore, the establishment of the atypical patterns in the BCR/ABL1 translocation may have clinical diagnostic and prognostic implications.

22q11.22-q11.23

GNAZ

RAB36

BCR

IGLL1

D22S1027

D22S1002E D22S257

169kb

148kb 100kb

9q34.11-q34.12 ASS1

D9S2057

173kb

FUBP3 PRDM12

LAMC3

ABL1

D9S1863

D9S313

346kb 100kb

RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8.

Shteper et al., Leukemia 2001;15(4):575-582 Groffen et al., Cell 1984;36:93-9 Shtivelman et al., Nature 1985;315:550-4 Hermans et al., Cell 1987;51:33-40 OMIM â&#x2122;Ż613065: http://www.omim.org/entry/613065 Soupir et al., Am J Clin Pathol 2007;127:642-650 Robinson et al., Leukemia 2005;19(4):564-71 Siu et al., BMC Blood Disorders 2009;9:4

(5 tests)

Cat. No. LPH 035

(10 tests)

Haematology

Cat. No. LPH 035-s

BCL6 Breakapart* Rearrangements of the BCL6 gene have been observed in 28.6-35.5% of Diffuse Large B-Cell Lymphoma (DLBCL) and in 6.4-14.3% of Follicular Lymphoma (FL)1. This translocation results in the dysregulation of BCL6 and may involve the IGH, IGK and IGL genes, although other non-Ig partner genes have also been identified2,3. BCL6 encodes a 95kD nuclear phosphoprotein belonging to the pox virus zinc finger (POZ)/zinc finger (ZF) family of transcription factors4. BCL6 functions as a transcriptional repressor and plays an important regulatory role in lymphoid cell development and function. In the B-cell lineage, the BCL6 protein is expressed only in germinal centre B cells5. Translocations involving band 3q27.3 affect a 4kb major breakpoint region of BCL6 in the first non-coding exon and 5' region of the first intron, and are common in diffuse large B-cell lymphomas. Recently, an alternative breakpoint cluster region located between 245 and 285kb 5' of BCL6 was identified in Non-Hodgkin Lymphoma (NHL) and may be preferentially associated with follicular lymphoma6.

L RefeRenCes 1.

Ohno H et al., Leuk Lymphoma 1997;27:53-63

Ueda C et al., Leuk Lymphoma 2002;43:1375-81

Akasaka H et al., Cancer Res 2000;60:2335-41

Chang CC et al., PNAS 1996;93:6947-52

Cattoretti G et al., Blood 1995;86:45-53

Bosga-Bouwer AG et al., Genes Chrom Cancer 2005;44:301-4

3q27.3 BCL6 SST RTP2

G67157

165kb

D3S4344

100kb

170kb

* A similar product is also available within the Haematopathology range, refer to page 84.

Haematology

Cat. No. LPH 022-s

(5 tests)

Cat. No. LPH 022

(10 tests)

CBFÎ˛/MYH11 Translocation, Dual Fusion The fusion gene CBFÎ˛ (CBFB)/MYH11, created by the inversion inv(16)(p13.11q22.1), is found in 20% of AML M4 cases - in particular M4 with marked eosinophilia (M4eo) - and rarely, in M2, M5 and M4 without eosinophilia1. Overall, abnormalities involving 16q22 are seen in 5-10% of AML1,2,3. Frequently, Central Nervous System (CNS) involvement develops, particularly in relapse. However, the complete remission rate is high and the prognosis is better than most of the AML associated abnormalities3. The inversion may be missed in poor cytogenetic preparations. FISH probes for 16p13 often show a deletion within 16p13 in addition to the 16p13.11/16q22.1 rearrangement (~20% cases). In these patients, the split signal may be lost. Variant rearrangements are the (16;16)(p13;q22) and del(16)(q22). The latter is associated with previous MDS, older age, a complex karyotype and a worse prognosis. Additional abnormalities include +8, +22, del(7q) and +2, which confer no change to the prognosis1. The breakpoints occur in intron 5 of CBFB and intron 5 of MYH11. The N-terminal of CBFB fuses to the C-terminal of MYH11 with its multimerisation domain. The resultant chimaeric protein reduces the amount of active CBF. An accumulation of CBFB-MYH11/CBFA multimers in the nucleus also occurs. CBFB regulates expression of certain ADP-Ribosylation Factors (ARFs) and other tumour suppressor genes (TSGs) and therefore the fusion protein is thought to repress TSG expression3. MYH11 D16S3302 D16S3060

D16S2853 D16S3286 D16S2803 D16S405 D16S3127

D16S3292

610kb

16p13.11

16q22.1 CBFB

D16S3308 D16S2584E D16S2846

D16S301 D16S324 D16S3339 D16S3323 606kb

100kb

AML RefeRenCes 1. 2. 3.

Huret, inv(16)(p13q22); t(16;16)(p13;q22); del(16)(q22). Atlas Genet Cytogenet Oncol Haematol 1999 Heim and Mitelman, Wiley-Liss Inc. 1995 Monreno-Miralles et al., J Biol Chem 2005;280(48):40097-103

(5 tests)

Cat. No. LPH 039

(10 tests)

Haematology

Cat. No. LPH 039-s

CKS1B/CDKN2C(P18) Amplification/Deletion Structural abnormalities of chromosome 1 are frequently detected in multiple myeloma and have been correlated with more advanced disease1. Amplification of 1q21 (CKS1B) is one of the most recurrent chromosomal aberrations in multiple myeloma3. Over-expression of the CKS1B gene up-regulates cell cycle progression, resulting in a more proliferative disease2. This is related to the advanced phenotype of multiple myeloma and may therefore be associated with poor prognosis and disease progression3. Gain of 1q21 has been linked to inferior survival and further amplification is observed in disease relapse. It has been shown that gain of 1q21 copy number is not an independent prognostic factor in multiple myeloma and it is often associated with other chromosomal aberrations, most commonly t(4:14)(p16;q32) (IGH-FGFR3) and chromosome 13 deletion2. The association of 1q21 gain and loss of chromosome 13 has been linked to the risk of conversion to overt disease2. In a case study of multiple myeloma patients, it was discovered that 30% of chromosomal abnormalities mapped to chromosome 1, that most up-regulated genes mapped to chromosome 1q and down-regulated genes to chromosome 1p4. Gains of the long arm 1q are one of the most common genetic abnormalities in multiple myeloma5 and duplications of chromosome band 1q are frequently associated with disease progression3,6,7.

MM RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8. 9.

Tasaka et al., Br J Haematology 1997;96(1):98-102 Fonseca et al., Leukemia 2006;20(11):2034-40 Hanamura I, Blood 2006;108(5):1724-32 Shaughnessy JD, Blood 2007;109(6):2276-84 Avet-Loiseau H, Genes Chromosomes Cancer 1997;19(2):124-33 Sawyer JR, Blood 1998;91(5):1732-41 Le Baccon P et al., Genes Chromosomes Cancer 2001;32(3):250-64 Leone et al., Clin Cancer Res. 2008;14(19):6033-41 Kulkarni et al., Leukemia 2006;16:127-34

CDKN2C (P18), in band 1p32.3, is a tumour suppressor gene responsible for inducing apoptotic cell death and DNA fragmentation8. It is up-regulated by the expression of the cytokine IL-6 in multiple myeloma and homozygous deletion of the gene is associated with a more proliferative disease8. Although CDKN2C deletions have been reported to be rare in human malignancy, cytogenetic analyses have shown that abnormalities of 1p32-36 occur in around 16% of human multiple myeloma9.

1p32.3

1q21.3

CKS1B

FAF1

CDKN2C

PYGO2

ZBTB7B

D1S1661

168kb

180kb 100kb

Haematology

Cat. No. LPH 067-s

(2x5 tests)

Cat. No. LPH 067

(2x10 tests)

CLL PROFILER Kit The Cytocell CLL PROFILER Kit is intended to detect deletions of P53, ATM and D13S319, and gains of the chromosome 12 centromere sequence in peripheral blood or bone marrow samples from patients with B-cell Chronic Lymphocytic Leukaemia (B-CLL).

P53(TP53)/ATM Probe Combination P53 is a tumour suppressor gene that mediates the apoptosis of damaged cells. It has been found that approximately 17% of B-CLL patients have deletions of the P53 gene1. Patients exhibiting this genotype are associated with a poor prognosis2 as they harbour a proliferating population of damaged cells. The ATM gene is an important regulatory candidate in cell damage management. When it is deleted damaged cells are neither repaired nor apoptosed and are allowed to proliferate. The detection of the ATM deletion in CLL is important as it indicates poor prognosis and can define a patient's therapy3. Deletions of ATM and P53 are the most serious rearrangements involved in CLL and detection of deletions of these genes provides very important information as to the therapy choices for such patients especially since deletions of P53 and ATM provide a poor prognosis4,5.

D13S319/13qter/12cen Deletion/Enumeration Deletions affecting the 13q14 band are the most frequent genetic abnormalities of B-cell Chronic Lymphocytic Leukaemia (B-CLL)6. This region is found deleted heterozygously in 30-60% and homozygously in 10-20% of CLL patients7. Recently though, the survival rate has been shown to be similar8. Two non-coding RNA genes, DLEU1 and DLEU2, and the genetic marker D13S319, span the pathogenic critical region 13q14.39. DLEU1 is considered to be the most likely CLL-associated candidate tumour suppressor gene within the 13q14 region10. Trisomy of chromosome 12 is the most common chromosome abnormality in B-CLL11,12,13,14 and is now thought to have strong prognostic significance15. The molecular consequences of the additional chromosome are not clear, though it has been shown to be more common in the non-dividing cells rather than mitoses which are frequently found to be cytogenetically normal. This was deduced from FISH studies using centromeric probes for chromosome 1211.

RefeRenCes 1. 2. 3. 4. 5.

Döhner et al., J Mol Med 1999;77:266-81 Döhner et al., Blood 1995; 85(6):1580-1589 Tsimberidou et al., Cancer 2009; 115:373–380 Guarini et al., Haematol. 2012;97(1):47-55 Stilgenbauer and Zenz ASH Education Book

2010 1:481-488 Juliusson G et al., N Eng J Med 1990;323:720-4

Hammarsund M et al., FEBS Letters 2004;556:75-80

Van Dyke DL et al., Br J Haematology 2009;148:544-50

Liu Y et al., Oncogene 1997;15:2463-73 9. 10. Wolf S et al., Hum Mol Genet 2001;10:1275-85 11. Anastasi J et al., Blood 1992;79(7):1796-801 12. Aoun P et al., Leuk Lymphoma 2004;45(8):1595-603 13. Bienz N et al., Br J Haematol 1993;85(4):819-22 14. Escudier SM et al., Blood 1993;81(10):2702-7 15.

Chiorazzi. ASH Education Book; 2012: 2012(1):76-87

(5x5 tests)

Cat. No. LPH 087

(5x10 tests)

Haematology

Cat. No. LPH 087-s

CLL Plus Screening Panel A selection of haematology probes and an alpha-satellite probe for Chronic Lymphocytic Leukaemia (CLL).

Alpha Satellite 12 Plus for CLL Trisomy of chromosome 12 is a relatively common chromosome abnormality in B- CLL, being present in around 16% of patients, when evaluated by FISH on interphase and metaphase cells1 and is now thought to have strong prognostic significance2. This product is also available in 5 (LPH 069-S) and 10 (LPH 069) test kit sizes and has been optimised for overnight hybridisation.

13q14.3 Deletions of 13q14 are a common event in CLL. This region is found to be heterozygously deleted in 30-60% and homozygously deleted in 10-20% of CLL patients3.

RefeRenCes 1. 2. 3. 4. 5.

Dรถhner et al., N Engl J Med 2000;343(26):1910-1916 Chiorazzi. ASH Education Book; 2012: 2012(1):76-87 Hammarsund M et al., FEBS Letters 2004;556:75-80 Dรถhner et al., J Mol Med 1999;77:266-81 Foรก et al., Haematol 2013; 98(5):675-685

Brigaudeau and Bilhou-Nabera . del(6q) abnormalities in lymphoid malignancies. Atlas Genet Cytogenet Oncol Haematol. December 1998

P53 (TP53) (17p13.1) P53 (TP53) is a tumour suppressor gene that mediates the apoptosis of damaged cells. It has been found that approximately 17% of B-CLL patients have deletions of the P53 gene4. Patients exhibiting this genotype are associated with a poor prognosis5 as they harbour a proliferating population of damaged cells.

ATM (11q22.3) The ATM gene is an important regulatory candidate in cell damage management. When it is deleted, damaged cells are neither repaired nor apoptosed and are allowed to proliferate. Screening for deletions of ATM is important to allow informed therapy choices for CLL patients, especially as deletions confer poor prognosis5.

MYB (6q23.3) Deletions of chromosome 6q are found in B-CLL, with breakpoints being reported in bands 6q13, q15 or q21. The MYB gene is essential in haematopoietic cell proliferation and differentiation. It is located in band 6q23.3 and is provided as a marker for 6q deletion as it is distal to reported deletion breakpoints (6q13, 6q15 and 6q21)6.

Haematology

Cat. No. LPH 010-s

(5 tests)

Cat. No. LPH 010

(10 tests)

cMYC (MYC) Breakapart* Translocations involving the MYC (cMYC) oncogene (Avian Myelocytomatosis Viral Oncogene Homologue) are a molecular feature of Burkitt lymphoma and occur in almost every case. These rearrangements can also be found in 5 to 10% of diffuse large B-cell lymphoma (DLBCL)1. The majority of rearrangements result in the juxtaposition of MYC to IGH, IGL or IGK in the t(8;14), t(8;22) or t(2;8) respectively. In each case, this results in dysregulation of MYC (as a result of being close to the constitutively active immunoglobulin locus), increased transcription and neoplastic growth2. The breakpoints involved are widely scattered throughout the gene but the t(8;14) translocation always spares the protein coding exons which become attached to the derived 14. In the t(2;8) and t(8;22), MYC remains on chromosome 8 and the immunoglobulin locus joins it, resulting in close positioning of the MYC and immunoglobulin loci. Rare cases of translocations not involving immunoglobulin partners have also been reported3.

L RefeRenCes 1. 2. 3. 4.

Savage et al., Blood. 2009 Oct 22;114(17):3533-7 Robertson. Nature. 1983 Apr 7;302(5908):474-5 Seo et al., Ann Lab Med. 2012 Jul;32(4):289-93 Hoelzer et al., Blood. 1996 Jan 15;87(2):495-508

Patients with MYC rearrangements, in isolation of a confirmed diagnosis of Burkitt lymphoma, were originally thought to have poor prognoses but they do respond well to intensive chemotherapy affording them an increased survival rate. This shows that cytogenetic confirmation of the rearrangement is necessary to manage the patient effectively4.

8q24.21

POU5F1B CASC8 D8S1153

MYC PVT1

D8S1128 D8S1980

173kb

D8S1644 D8S1720 186kb

100kb

* A similar product is also available within the Haematopathology range, refer to page 93.

Cat. No. RU-LPH 086-s* (50µl)

Cat. No. RU-LPH 085*

Cat. No. RU-LPH 086*

(100µl)

Haematology

Cat. No. RU-LPH 085-s* (50µl)

(100µl)

CRLF2 Breakapart* and P2RY8 Deletion* Overexpression of Cytokine Receptor-Like Factor 2 (CRLF2) has been shown to occur in Acute Lymphoblastic Leukaemia (ALL), particularly that associated with Down Syndrome (DS-ALL)1,2. Overexpression of this protein has been associated with activation of the JAK/STAT5 pathway in transduced primary B-cell progenitors1,3 and various groups have attempted to characterise the biochemical consequences of these genetic lesions, with the goal of identifying targets for new therapies2,3. CRLF2 overexpression has been shown to be caused by chromosomal rearrangements including the t(X;14) or t(Y;14) translocations or interstitial deletions of the pseudoautosomal region 1 (PAR1) of chromosomes X and Y. These place CRLF2 under control of an IGH enhancer1 or juxtapose the first non-coding exon of P2RY8 to the coding region of CRLF22, respectively. All of these CRLF2 rearrangements are cytogenetically cryptic and cannot be detected by conventional G-banded analysis1, making FISH a powerful detection tool for these abnormalities and an aid to furthering this research. Our CRLF2 Breakapart probe will detect rearrangements of the CRLF2 gene, whilst the P2RY8 Deletion probe allows detection of deletions between CRLF2 and P2RY8, causing the fusion gene.

CRLF2

CRLF2 Breakapart

ALL RefeRenCes 1.

Russell et al., Blood. 2009 Sep 24;114(13):2688-98

Mullighan et al., Nat Genet 2009; 41(11): 1243–6

Tasian et al., Blood 2012; 120(4):833-842

Cat. No. RU-LPH 085*

Xp22.33

CRLF2 G66170

IL3RA ASMTL

131kb

P2RY8

SHGC-64134

SHGC-1094

G66032

71kb

CSF2RA

243kb 100kb

P2RY8

Cat. No. RU-LPH 086*

Xp22.33

CSF2RA CRLF2

IL3RA ASMTL

SHGC-1094

100kb

P2RY8

SHGC-64134

243kb

AKAP17A ASMT SHGC-151117

DXYS144

290kb

*For research use only, not for use in diagnostic procedures.

Haematology

Cat. No. LPH 006-s

(5 tests)

Cat. No. LPH 006

(10 tests)

Deletion 13q14.3, D13S319 Plus and D13S25 Chromosome 13q abnormalities occur in 16-40% of multiple myeloma cases and are associated with poor prognosis1,2. A case study has shown that in 90% of patients, the 13q14 region was affected and 68% also showed involvement of the 13q21 region - the critical region in all but 8 patients was narrowed down to 13q143. Deletions affecting 13q14 are also the most frequent structural genetic abnormalities in B-cell Chronic Lymphocytic Leukaemia (B-CLL)4. This region is found to be heterozygously deleted in 30-60% and homozygously deleted in 10-20% of CLL patients5. Recently though, the survival rate has been shown to be similar for the two groups6. Two non-coding RNA genes, DLEU1 and DLEU2, and the genetic marker D13S319, span the pathogenic critical region of 13q147. DLEU1 is considered to be the most likely CLL-associated candidate tumour suppressor gene within the 13q14 region8. Subsequently, D13S319, located between the RB1 gene and D13S25 and within the DLEU1 locus, was found to be deleted in 44% of CLL cases9. It has also been postulated that a gene telomeric to the D13S319 region, encompassing D13S25, may be important in cases with hemizygous deletions and that this gene is a putative tumour suppressor gene10.

13q14.3 Deletion

CLL MM RefeRenCes 1. 2.

Bullrich F et al., Cancer Res 2001;61:6640-8 Zojer et al., Blood 2000;95(6 ):1925-1930

3. 4. 5. 6. 7. 8. 9. 10.

Shaughnessy J et al., Blood 2000;96:1505-11 Juliusson G et al., N Eng J Med 1990;323:720-4 Hammarsund M et al., FEBS Letters 2004;556:75-80 Van Dyke DL et al., Br J Haematology 2009;148:544-50 Liu Y et al., Oncogene 1997;15:2463-73 Wolf S et al., Hum Mol Genet 2001;10:1275-85 Liu Y et al., Blood 1995;86:1911-5 Bullrich F et al., Blood 1996;88(8):3109-15

(5 tests)

Cat. No. LPH 043-s

(5 tests)

Cat. No. LPH 068

(10 tests)

Cat. No. LPH 043

(10 tests)

Haematology

13q14.3

Cat. No. LPH 068-s

Cat. No. LPH 006

13qter

13q14.2-q14.3

TRIM13 DLEU1 DLEU2 D13S1477

D13S311

D13S319

215kb

RH44686 D13S25

100kb

D13S319 Plus

93kb

Cat. No. LPH 068

13qter

13q14.2 TRIM13 DLEU1 DLEU2 RH47934

D13S272 D13S319 156kb

D13S25

100kb

Cat. No. LPH 043

13qter

13q14.3 DLEU7

D13S25

D13S294

306kb

100kb

Haematology

Cat. No. LPH 066-s

(5 tests)

Cat. No. LPH 066

(10 tests)

D13S319/13qter/12cen Deletion/Enumeration Deletions affecting band 13q14 and trisomy of chromosome 12 are common events in B-cell Chronic Lymphocytic Leukaemia (B-CLL). Deletions affecting the 13q14 band are the most frequent genetic abnormalities of B-CLL1. This region is found to be deleted heterozygously in 30-60%, and homozygously in 10-20%, of CLL patients2. Recently, the survival rate has been shown to be similar3. Two non-coding RNA genes, DLEU1 and DLEU2, and the genetic marker D13S319, span the pathogenic critical region 13q14.34. DLEU1 is considered to be the most likely CLL-associated candidate tumour suppressor gene within the 13q14 region5. Trisomy of chromosome 12 is the most common chromosome abnormality in B-CLL6,7,8,9 and is now thought to have strong prognostic significance10. The molecular consequences of the additional chromosome are not clear, though it has been shown to be more common in non-dividing cells rather than mitoses, which are frequently found to be cytogenetically normal. This was deduced from FISH studies using centromeric probes for chromosome 126.

D12Z3

13qter

13q14.2

TRIM13 DLEU1 DLEU2 RH47934

D13S272 D13S319

156kb

100kb

CLL MM RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8. 9. 10.

Juliusson G et al., N Eng J Med 1990;323:720-4 Hammarsund M et al., FEBS Letters 2004;556:75-80 Van Dyke DL et al., Br J Haematology 2009;148:544-50 Liu Y et al., Oncogene 1997;15:2463-73 Wolf S et al., Hum Mol Genet 2001;10:1275-85 Anastasi J et al., Blood 1992;79(7):1796-801 Aoun P et al., Leuk Lymphoma 2004;45(8):1595-603 Bienz N et al., Br J Haematol 1993;85(4):819-22 Escudier SM et al., Blood 1993;81(10):2702-7 Chiorazzi. ASH Education Book; 2012: 2012(1):76-87

(5 tests)

Cat. No. LPH 024

(10 tests)

Haematology

Cat. No. LPH 024-s

Del(5q) Deletion Deletion of a region of chromosome 5q, which includes the EGR1 gene, is one of the most common rearrangements in AML and MDS1,2. The deletions are large, with breakpoints occurring between bands 5q11 and 5q35, and are usually interstitial. Two regions, 5q12-14 and 5q31-33, are hot spots for breakpoints but the common deleted region (CDR) in AML and aggressive MDS cases is within 5q31.12,3.

AML

Early Growth Response 1 (EGR1) maps to this band3 and loss of this gene may cause tumourigenesis in at least two ways: Firstly, EGR1 directly controls the expression of fibronectin (FN1) through pathways that involve TGFB1 and plasminogen activator inhibitor-1 (SERPINE1 or PAI1). EGR1 dependent expression of TGFB1 inhibits human cancer cell growth in model cells4. In addition, EGR1 is required for p53-dependent apoptosis through the mediation of Retinoblastoma

RefeRenCes 1. 2. 3. 4.

Boultwood J et al., Blood 2002;99(12):4638-41 Charrin C, Atlas Genet Cytogenet Oncol Haematol 1998;2(3):302-6 OMIM :http://omim.org/entry/153550 Liu C et al., Proc Natl Acad Sci USA 1996;93:11831-6

Das et al., J. Biol. Chem. 2001 276: 3279-3286

(RB1) protein5.

5p15.31

5q31.2 EGR1 TAS2R1

CDC25C

D5S630

D5S1701 D5S500 D5S2415 D5S2542

D5S2064

184kb

310kb 100kb

Haematology

Cat. No. LPH 025-s

(5 tests)

Cat. No. LPH 025

(10 tests)

Del(7q) Deletion Abnormalities of chromosome 7 are very common in myeloid malignancies, such as adult and paediatric MDS and treatment related AML/MDS. In children, it is often associated with juvenile Chronic Myeloid Leukaemia (jCML)1,2,3,4. There is also a predominance in leukaemias associated with a constitutional predisposition, caused by disorders including neurofibromatosis 1 (NF1), Fanconi Anaemia and possibly Down syndrome, which produces a distinct clinical picture known as Monosomy 7 syndrome. Another rearrangement, -5/del(5q), is found as an additional abnormality in 40-60% of secondary MDS cases. +8 is less frequently seen4. Studies of myeloid disorders involving -7/del(7q) have found that signalling pathways involving RAS proteins are affected. There are two commonly deleted regions (CDR): one at 7q22, the other at 7q31-342,3,5,6,7. RELN (7q22) encodes a large secreted protein related to extracellular matrix proteins, a family of proteins that contains multiple epidermal growth factor (EGF)-like proteins.

7q22.1-q22.2

AML RefeRenCes 1. 2. 3. 4. 5. 6. 7.

Heim and Mittelman, Willey-Liss, Inc. 1995 Emerling BM et al., Oncogene 2002;21:4849-54 Kratz CP et al., Genomics 2001;77(3):171-80 Desangles F, -7/del(7q) in adults. Atlas Genet Cytogenet Oncol Haematol 1999 Le Beau MM et al., Blood 1996;88(6):1930-5 Fischer K et al., Blood 1997;89(6):2036-41 Koike M et al., Leukemia Res 1999;23:307-10

7q31.2

TES RELN

ORC5 D7S796

D7S658

D7S2886 D7S486

203Kb 203kb

396kb 100kb

D7S2543

(5 tests)

Cat. No. LPH 020

(10 tests)

Haematology

Cat. No. LPH 020-s

Del(20q) Deletion Deletions of the long arm of chromosome 20 are a common chromosomal abnormality associated with myeloid malignancies, in particular myeloproliferative disorders (MPD), myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML)1. The deletions are predominantly interstitial2. Often other cytogenetic abnormalities are present such as del(5q), -7/del(7q), +8, del(18q), +21 and rearrangements of 13q. Due to the

AML

relatively small size of the deletion and the lack of banding features on chromosome 20, FISH is particularly useful in detecting this abnormality. The prognosis for MDS cases where del(20q) is the sole abnormality is good. However if secondary abnormalities are present, a poor outcome is indicated3. AML patients respond poorly to treatment and have reduced survival rates. The clinical outcome for MPD patients remains unchanged in the presence of the abnormality4.

RefeRenCes 1. 2. 3. 4.

BĹ&#x2122;ezinovĂĄ et al., 2005:160(2):188-192 MacKinnon et al., Cancer Genet. 2011 Mar;204(3):153-61 Liu et al., Cancer Genet Cytogenet. 2006 Nov;171(1):9-16 Bilhou-Nabera, del(20q) in myeloid malignancies. Atlas Genet Cytogenet Oncol Haematol 2000

5. 6. 7.

Bench et al., Oncogene 2000;19(34):3902-13 Li J et al., PNAS 2004;101:7341-6 Wang et al., Genomics 1999;59:275-81

The mechanism of leukaemogenesis associated with del(20q) is unknown, however, deletion of a tumour suppressor gene (TSG) is thought to cause the increased proliferation of the cancer cells4. Using RT-PCR analysis, Bench et al identified potential target genes in the region of overlap between the AML/MDS and MPD CDR at band 20q12. Five genes were expressed in both bone marrow and CD34 positive cells. Of the three previously identified genes, L(3)MBT regulates chromatin structure during mitosis, SFRS6 encodes a serine rich protein important to regulation of alternative splicing of mRNA, and MYBL2, a member of the MYB transcription factor family, is involved in cell cycle control5,6,7.

20q12

20q13.12

MYBL2

PTPRT D20S591E

D20S108

D20S858

D20S43

331kb

D20S150

139kb

174kb

100kb

Haematology

Cat. No. LPH 019-s

(5 tests)

Cat. No. LPH 019

(10 tests)

E2A (TCF3) Breakapart Translocations involving the E2A (TCF3: Transcription Factor 3) gene are some of the most common rearrangements in childhood B-ALL, specifically B-cell precursor ALL1. The two main partner genes are PBX1 and HLF (on chromosomes 1 and 17 respectively) which become fused to E2A as a result of the t(1;19) and t(17;19) translocations, forming the E2A/PBX1 and E2A/HLF fusion proteins. Other translocation partners have also been detected. The t(1;19) is the most common E2A rearrangement, being present in around 5% of B-ALL and 20% of pre B-ALL2, whilst the t(17;19) is present in around 1% of all ALL cases3. Both are historically associated with a poor outcome, though treatment therapies have overcome this in the case of the t(1;19)4. Detection of the t(1;19) is best carried out using molecular methods, such as FISH, as the fusion has been shown to be missed in 20 to 25% of patients by standard cytogenetics5. Similarly, other E2A translocations have been shown to be cytogenetically cryptic6.

ALL RefeRenCes 1.

Barber et al., Genes Chromosomes Cancer. 2007

May;46(5):478-86 Alonso CN. t(1;19)(q23;p13) TCF3/PBX1. Atlas Genet

Cytogenet Oncol Haematol. July 2012 ViguiĂŠ F . t(17;19)(q22;p13). Atlas Genet Cytogenet Oncol

4. 5. 6.

Haematol. May 1999 Felice et al., Leuk Lymphoma. 2011 Jul;52(7):1215-21 Izraeli et al., Leukemia 1993;7(5):671-8 Huret JL. TCF3 (transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)). Atlas Genet Cytogenet Oncol Haematol. January 2012

19p13.3

MEX3D D19S883

E2A (TCF3)

MBD3

163kb

189kb 100kb

RH98588

(5 tests)

Cat. No. LPH 079

(10 tests)

Haematology

Cat. No. LPH 079-s

E2A/PBX1 Translocation, Dual Fusion The E2A (TCF3) gene is involved in recurrent rearrangements in childhood Acute Lymphoblastic Leukaemia (ALL)1. Two known partner genes are the Pre-B-cell Leukaemia Homeobox 1 gene (PBX1, chromosome 1q23.3) and the Hepatic Leukaemia Factor gene (HLF, chromosome 17q22), which become fused to E2A as a result of translocations, forming the E2A/PBX12 and E2A/HLF fusion proteins, respectively3. The 2011 Acute Lymphoblastic Leukaemia Best Practice Guidelines

ALL RefeRenCes

state that “when TCF3 ‘breakapart’ FISH identifies a rearrangement, it

1. 2.

important

distinguish

between

t(17;19)(q22;p13)

and

t(1;19)(q23;p13), the former translocation being associated with adverse prognosis”4.

Cytocell provides a range of probes that allow flexibility in screening

LeBrun. Front Biosci. 2003 May 1;8:s206-22 Alonso CN. t(1;19)(q23;p13) TCF3/PBX1. Atlas Genet Cytogenet Oncol Haematol. July 2012 Viguié F. t(17;19)(q22;p13). Atlas Genet Cytogenet Oncol Haematol. May 1999 Professional Guidelines for Clinical Cytogenetics: ACUTE LYMPHOBLASTIC LEUKAEMIA BEST PRACTICE GUIDELINES (2011) V1.00. www.cytogenetics.org.uk

for E2A (TCF3) rearrangements: the E2A (TCF3) Breakapart probe (LPH 019), the E2A/PBX1 Translocation, Dual Fusion probe (LPH 079) and the E2A/PBX1/HLF Translocation, Dual Fusion probe (LPH 080), a 3 colour probe that allows both E2A/PBX1 and E2A/HLF fusions to be detected.

19p13.3 E2A (TCF3)

DAZAP1 PLK5 C19orf25

ATP8B3

KLF16

GAMT

ABHD17A PCSK4 MEX3D ADAMTSL5 MBD3 RH15936

110kb

REXO1

RH93415

RH91108

146kb

321kb 100kb

1q23.3

PBX1

SGHC-141870

SHGC-36037

147kb

110kb

SHGC-81010

100kb

AL010113

117kb

Haematology

Cat. No. LPH 080-s

(5 tests)

Cat. No. LPH 080

(10 tests)

E2A/PBX1/HLF Translocation, Dual Fusion The E2A (TCF3) gene is involved in recurrent rearrangements in childhood Acute Lymphoblastic Leukaemia (ALL)1. Two known partner genes are the Pre-B-cell Leukaemia Homeobox 1 gene (PBX1, chromosome 1q23.3) and the Hepatic Leukaemia Factor gene (HLF, chromosome 17q22), which become fused to E2A as a result of translocations, forming the E2A/PBX12 and E2A/HLF fusion proteins, respectively3. The 2011 Acute Lymphoblastic Leukaemia Best Practice Guidelines

ALL RefeRenCes

state that “when TCF3 ‘breakapart’ FISH identifies a rearrangement, it

1. 2.

important

distinguish

between

t(17;19)(q22;p13)

and

t(1;19)(q23;p13), the former translocation being associated with adverse prognosis”4.

Cytocell provides a range of probes that allow flexibility in screening

19p13.3

1q23.3 E2A (TCF3)

DAZAP1 PLK5 C19orf25

ATP8B3

PBX1

KLF16

GAMT

ABHD17A PCSK4 MEX3D ADAMTSL5 MBD3

REXO1

RH93415

SGHC-141870

SHGC-36037 RH15936

110kb

SHGC-81010

AL010113

RH91108

146kb

321kb

147kb

100kb

110kb

100kb

117kb

17q22 HLF

TOM1L1

MMD

STXBP4 RH91952

STS-D63113

D17S2188

RH118584

482kb

323kb 100kb

SHGC-142062

D17S591

RH41992

166kb

(5 tests)

Cat. No. LPH 036

(10 tests)

Haematology

Cat. No. LPH 036-s

EVI1 (MECOM) Breakapart Chromosome rearrangements involving band 3q26.2 are associated with myeloid malignancies, aberrant expression of the human ecotropic virus integration site 1 (EVI1) gene, an unfavourable prognosis and an aggressive clinical course1. The EVI1 gene encodes a 1051 amino acid zinc finger protein that is inappropriately expressed in the leukaemic cells of between 2-5% of AML and MDS patients . EVI1 activation often follows a chromosomal

AML

rearrangement involving 3q26.2 and the two most common aberrations are the t(3;3)(q21;q26.2) and inv(3)(q21q26.2). EVI1 also exists as a longer protein, named MDS1/EVI1, created by splicing of the MDS1 and EVI1 mRNAs. This includes 188 additional amino acid

RefeRenCes 1. 2.

Bobadilla D et al., Br J Haematol 2007;136:806-13 Soderholm J et al., Leukemia 1997;11:352-8

residues at the N-terminus2. The breakpoints for the translocations and inversions vary considerably. Inv(3) breakpoints are found centromeric to, and including, the EVI1 gene and cover about 600kb. The majority of breakpoints in 3q26.2 translocations are telomeric to the EVI1 gene and cover a region including the telomeric end of the MDS1 gene and the MYNN gene1.

3q26.2 EVI1 (MECOM) D3S3364

559kb

D3S1614 D3S3809

MYNN LRRC34

D3S3523 D3S1282

D3S4415

156kb

179kb 100kb

Haematology

Cat. No. LPH 032-s

(5 tests)

Cat. No. LPH 032

(10 tests)

FIP1L1/CHIC2/PDGFRA Deletion/Fusion Deletion of CHIC2 in patients with idiopathic hypereosinophilic syndrome (HES) and chronic eosinophilic leukaemia (CEL) results in the fusion of FIP1L1 (FIP1-like 1) with PDGFRA (platelet derived growth factor receptor alpha) producing a tyrosine kinase which transforms haematopoietic cells.

CEL HES

In such patients, this activity is inhibited by imatinib mesylate (Gleevec), which is a tyrosine kinase inhibitor. The diagnosis of the fusion gene can therefore lead to therapeutic choices for the patient1,2.

RefeRenCes 1. 2.

Cools J et al., N Eng J Med 2003;348:1201-14 GrifďŹ n JH et al., PNAS 2003;100:7830-5

4q12 FIP1L1 SCFD2

CHIC2 PDGFRA LNX1 D4S1394

D4S1514 D4S1036 D4S461

177kb

D4S1594

D4S956 D4S1630

174kb

174kb 100kb

KIT

D4S643

(5 tests)

Cat. No. LPH 070

(10 tests)

Haematology

Cat. No. LPH 070-s

IGH Plus Breakapart* In Burkittâ&#x20AC;&#x2122;s Lymphoma, IGH is most notably involved in rearrangements involving the MYC oncogene as a result of the t(8;14)(q24.21;q32.33) translocation1. However, other rearrangements of the IGH gene are also seen in a number of different malignancies, including T-ALL, Chronic Lymphocytic Leukaemia (CLL) and Acute Lymphpblastic Leukaemia (ALL).

ALL CLL MM

There are a number of stereotypical translocations involved in each of the diseases and more are being described regularly. In T-ALL for example, IGH is observed in the t(14;14)(q11;q32) translocation

RefeRenCes

(or inv(14)(q11q32) rearrangement)2 that is found in T-cell leukaemia

associated with ataxia-telangiectasia (AT). However, rare reports have indicated that this abnormality also occurs in B-ALL. The recurrent t(14;19)(q32;q13) translocation associated with chronic B-cell lymphoproliferative disorders, such as atypical CLL, has also been shown to occur in B-ALL and results in the juxtaposition of the IGH and BCL3 genes and subsequent over expression of BCL33. More recently, a report suggested the involvement of IGH in a novel

2. 3. 4. 5.

Hoffman, Ronald (2009). Hematology : basic principles and practice (5th ed. ed.). Philadelphia, PA: Churchill Livingstone/Elsevier. pp. 1304â&#x20AC;&#x201C;1305 Liu et al., Cancer Genet Cytogenet 2004;152:141-5 Robinson et al., Genes Chromosomes Cancer 2004;39(1):88-92 van Zutven et al., Haematologica 2004;89(6):671-8 Huret JL . t(14;18)(q32;q21) (IgH/BCL2); t(2;18)(p11;q21); t(18;22)(q21;q11). Atlas Genet Cytogenet Oncol Haematol. May 1998 Huret JL . t(11;14)(q13;q32). Atlas Genet Cytogenet Oncol Haematol. May 1998

cryptic translocation in paediatric T-ALL, which also involved TLX3 (HOX11L2) or NKX2-5 (CSX) on 5q35 brought about by a t(5;14)(q35;q32) translocation4. IGH is involved in a large number of different rearrangements with fusion partners on almost every other chromosome. Many of these rearrangements have been reported in only one or a few cases but some are more common, such as IGH/BCL2, caused by the t(14;18) translocation5, and IGH/CCND1, a result of the t(11;14) translocation6. All these rearrangements do, however, have breakpoints within the IGH gene. We have designed a split probe set for IGH, which allows the detection of rearrangements, regardless of the partner gene involved.

14q32.33

Constant Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

Variable Segment

SHGC-36156

SHGC-170017

359kb

617kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 86.

Haematology

Cat. No. LPH 071-s

(5 tests)

Cat. No. LPH 071

(10 tests)

IGH/BCL2 Plus Translocation, Dual Fusion* This is a recurrent rearrangement of IGH in CLL1 and is cytogenetically indistinguishable from the t(14;18) translocation observed in follicular lymphoma. The translocation (t(14;18)(q32.33;q21.33)) is thought to be brought about by an error in the joining function of the IGH gene, mediated by the observation that both IGH and BCL2 are arranged next to each other in 3D space in normal B lymphocytes2. The translocation breakpoint at the end of the Joining (J) segment, and the subsequent fusion of the BCL2 gene to this region, results in the BCL2 gene coming under the regulatory control of those processes normally involved in maintenance of IGH gene activity. The protein encoded by the BCL2 gene has been shown to be involved in the regulation of apoptosis.

CLL

RefeRenCes 1. 2.

Baseggio et al., Br J Haematol. 2012 Aug;158(4):489-98 Roix et al., Nature Genetics 2003;34(3):287-91

14q32.33

Constant Segment G36213

Variable Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

SHGC-36156

SHGC-170017

359kb

617kb 100kb

18q21.33

BCL2 D18S91

D18S1264

KDSR D18S51

D18S87 D18S1366

585kb

100kb

* A similar product is also available within the Haematopathology range, refer to page 87.

(5 tests)

Cat. No. LPH 072

(10 tests)

Haematology

Cat. No. LPH 072-s

IGH/CCND1 Plus Translocation, Dual Fusion* Although translocations involving IGH and CCND1 (BCL1) were initially reported in B-CLL patients, the rearrangement is now considered to be a hallmark of mantle cell lymphoma (MCL). Reciprocal translocations involving the IGH and CCND1 (previously known as BCL1) loci, t(11;14)(q13;q32), have been reported in B-CLL patients1. The CCND1/IGH probe for detection of t(11;14) has been recommended by the British Committee for Standards in Haematology to enable atypical B-CLL patients to be distinguished from possible MCL patients2.

CLL

RefeRenCes 1. 2.

Brizard et al., Leuk Lymphoma 1997;25(5-6):539-43 Parker et al., Best Practice in Lymphoma Diagnosis and Reporting; Specific disease appendix 2010, p5

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

SHGC-36156

SHGC-170017

359kb

617kb 100kb

11q13.3 CCND1

MYEOV

D11S2663 D11S1100

FGF19 ORAOV1

D11S4095 D11S1076

FGF4 FGF3

D11S4381

155kb

D11S2927

162kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 88.

Haematology

Cat. No. LPH 075-s

(5 tests)

Cat. No. LPH 075

(10 tests)

IGH/CCND3 Plus Translocation, Dual Fusion Approximately 40-60% of Multiple Myeloma cases are associated with translocations involving the IgH locus at chromosome 14q32 and one of several partners including CCND1, WHSC1 (MMSET), CCND3, MAF or MAFB. Cases lacking an IgH translocation are associated with a hyperdiploid phenotype1. The CCND3/IGH translocation, t(6;14)(p21;q32), has been reported in 4% of multiple myeloma tumours2. However, it is also characteristic of a variety of other B-cell malignancies, including plasma cell leukaemia, diffuse large B-cell non-Hodgkin lymphoma (DLBCL) and Splenic Lymphomas with Villous Lymphocytes (SLVLs)3. CCND3 has been identified as a putative oncogene that is dysregulated as a consequence of the translocation2. The translocation appears to be mediated by an error in IgH switch recombination as it has been shown that in KMM-1 cell lines, the translocation disrupts a switch sequence in this region and results in juxtaposition of CCND3 with the IGH promoter, thus elevating the levels of CCND3 expression2. It is thought that this mechanism is similar in all cases of IgH translocation. Most breakpoints appear to be clustered in a region that is fewer than 200kb centromeric to CCND32 and this region is flanked by the Cytocell probe.

CLL MM RefeRenCes 1. 2. 3.

Fonseca et al., Cancer Res 2004;64:1546-58 Shaughnessy et al., Blood 2001;98(1):217-23 Soniki et al., Blood 2001;98(9):2837-44

14q32.33

Constant Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

Variable Segment

SHGC-36156

SHGC-170017

359kb

617kb 100kb

6p21

TFEB

USP49 D6S1017

TAF8

GUCA1A C6orf132 D6S400

TRERF1 D6S1463

244kb

158kb 100kb

CCND3

(5 tests)

Cat. No. LPH 076

(10 tests)

Haematology

Cat. No. LPH 076-s

IGH/cMYC(MYC) Plus Translocation, Dual Fusion* The cMYC(MYC)/IGH translocation t(8;14), and the variant forms t(2;8)(p13;q24) and t(8;22)(q24;q11), are found in Burkitt's lymphoma and mature B-cell or Burkitt's type Acute Lymphoblastic Leukaemia (ALL)1. The t(8;14) is the most common and is found in approximately 85% of patients with Burkitt's lymphoma2. While translocation breakpoints on chromosome 14 are clustered to a narrow region 5' to the intron enhancer of the immunoglobulin heavy chain, the breakpoints on chromosome 8 can occur more than 340kb upstream of MYC, with no preferential site3. The translocation brings MYC into close proximity to the IgH enhancer and results in the up-regulation of MYC4. Over expression of the transcription factor stimulates gene amplification resulting in uncontrolled cell proliferation, which usually occurs in the late event of tumour progression5.

ALL

RefeRenCes 1. 2.

Berger R, Bernheim A, Cancer Genet Cytogenet 1982;7(3):231-44 Hoffman, Ronald (2009). Hematology : basic principles and practice (5th ed. ed.). Philadelphia, PA: Churchill Livingstone/Elsevier. pp. 1304â&#x20AC;&#x201C;1305 Joos et al., Human Molecular Genetics 1992;1(8):625-32

Erikson J et al., Proc Natl Acad Sci USA 1983;80(3):820-4

Shou et al., PNAS 2000;97(1):228-33

14q32.33

Constant Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

Variable Segment

SHGC-36156

SHGC-170017

359kb

617kb 100kb

8q24.21 POU5F1B CASC8

MYC PVT1

D8S490 D8S1087 D8S1153 D8S1128 D8S1980 D8S1720

220kb

D8S1644

186kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 90.

Haematology

Cat. No. LPH 074-s

(5 tests)

Cat. No. LPH 074

(10 tests)

IGH/FGFR3 Plus Translocation, Dual Fusion The t(4;14)(p16.3;q32.3) translocation is found in 15-20% of multiple myeloma patients and results in the known dysregulation of two genes, one on each derivative chromosome: MMSET (Multiple Myeloma SET domain containing protein, also known as WHSC1) on the der(4) and FGFR3 (fibroblast growth factor receptor 3) on the der(14)1. The majority of the breakpoints on chromosome 4 occur within the MMSET locus resulting in a fusion gene where the 5' exons of MMSET are replaced with the VDJ region of the heavy chain locus. This results in MMSET being brought under the influence of the enhancer Eµ on the der(4)1, FGFR3 lies at least 50kb from the breakpoints after translocation to chromosome 14 and FGFR3 expression is upregulated via proximity to the strong enhancer elements (particularly the Ea enhancer) in the immunoglobulin heavy chain2. Other studies state that the breakpoints on chromosome 4 lie in a 113kb region between FGFR3 and MMSET exon 53.

MM RefeRenCes 1.

Viguié F t(4;14)(p16;q32). Atlas Genet Cytogenet

Oncol Haematol. May 2005 Sibley K et al., Oncogene. 2001 Feb 8;20(6):686-91

Keats JJ et al., Blood 2003;101(4):1520-9

The breakpoint on chromosome 14 is almost exclusively in or near the switch region of the IGH locus. This t(4;14) translocation is often cytogenetically cryptic and was poorly described before the advent of FISH techniques.

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

359kb

617kb 100kb

4p16.3 FGFR3

D4S168

NELFA (WHSC2) MMSET

D4S2561E LETM1 (WHSC1)

D4S573 D4S166 D4S1182

118kb

126kb 100kb

SHGC-36156

SHGC-170017

D4S43

(5 tests)

Cat. No. LPH 073

(10 tests)

Haematology

Cat. No. LPH 073-s

IGH/MAF Plus Translocation, Dual Fusion The translocation t(14;16)(q32.3;q23) involving MAF and IGH is present in 25% of myeloma cell lines1, in 5% of primary Multiple Myeloma samples2,3 and results in high levels of MAF expression. Patients harbouring the t(14;16) appear to have a worse outcome3,4.

The majority of the breakpoints are dispersed over a region of approximately 500kb, centromeric to the MAF proto-oncogene at

RefeRenCes

16q23. Another breakpoint has been observed that is telomeric to

Chesi M et al., Blood 1998;91(12):4457-63

MAF1. Translocations with the centromeric breakpoints place MAF

Avet-Loiseau H et al., Blood 2002;99(6):2185-91

under the control of strong 3' IGH enhancers. Recent gene expression

Fonseca R et al., Blood 2003;101(11):4569-75

Chang H et al., Leukemia 2007;21:1572-4

Nunez MI et al., BMC Cancer 2005;5:64

profiling of myeloma cell lines revealed that MAF caused transactivation of cyclin D2 (a promoter of cell cycle progression), thus enhancing proliferation of myeloma cells4. Within or near to the MAF/IGH breakpoint region lies the putative tumour suppressor gene, WWOX, which spans the common chromosomal fragile site 16D (FRA16D) at chromosome 16q23.3-24.1 â&#x20AC;&#x201C; a region that is a frequent target for both loss of heterozygosity and chromosomal rearrangements in ovarian, breast, hepatocellular and prostate carcinomas as well as other neoplasias5.

14q32.33

Constant Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

Variable Segment

SHGC-36156

SHGC-170017

359kb

617kb 100kb

16q23.1-q23.2

WWOX D16S2793

D16S518

D16S3213 D16S3029 D16S3324 145kb 91kb

MAF RH69965 D16S3073

119kb 125kb 100kb

Haematology

Cat. No. LPH 077-s

(5 tests)

Cat. No. LPH 077

(10 tests)

IGH/MAFB Plus Translocation, Dual Fusion The t(14;20) translocation is one of seven recurrent IGH translocations that are referred to as primary oncogenic events in around 73% of Multiple Myeloma (MM) cases1. These translocations result in a transcription product that dysregulates further genes, such as the cyclin family of cell cycle control genes, which then disrupts normal cell division. In the case of the t(14;20) translocation, the reciprocal rearrangement brings a truncated form of the IGH Îź-Enhancer (EÎź, located between the Joining (J) segments and the constant region of the IGH gene) in close contact with the MAFB gene2. The resultant fusion and the up-regulated transcription product has been shown to cause dysregulation of Cyclin D2 in around 7% of tumours3. Of the seven translocation partners of IGH in multiple myeloma (including CCND1, CCND2, CCND3, MAF, MAFA and FGFR3/MMSET), MAFB has a prevalence of around 2%4. Involvement of any of the three MAF genes provides equally poor prognoses and a similar phenotype for patients5, but the MAFB translocation shows a different prevalence in multiple myeloma patients (2%) compared to Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM) cases (7%)5.

MM RefeRenCes 1. 2. 3. 4. 5.

Avet-Loiseau et al., Blood 2002;99(6):2185-91 Boersma-Vreugdenhil et al., Br J Haematol 2004;126:355-63 Bergsagel et al., Blood 2005;106(1):296-303 Zhan et al., Blood 2007;109(4):1692-700 Chng et al., Best Pract Res Clin Haematol 2007;20:571-96

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

SHGC-36156

SHGC-170017

359kb

617kb 100kb

20q12

MAFB

PP1R16B

195kb

161kb

289kb 100kb

TOP1 PLCG1

(5 tests)

Cat. No. LPH 078

(10 tests)

Haematology

Cat. No. LPH 078-s

IGH/MYEOV Plus Translocation, Dual Fusion The most common translocation in Multiple Myeloma (MM) is the t(11;14)(q13;q32)1, which accounts for 15-20% of cases as identified by FISH2. Unlike Mantle Cell Lymphoma (MCL), where the breakpoints are clustered in a 1kb region that is 120kb centromeric to the CCND1 gene3, the breakpoints in Multiple Myeloma cases are dispersed within a 360kb region between CCND1 and MYEOV (MYEloma OVerexpressed) in band 11q134. MYEOV is a putative oncogene, located 360kb away from CCND1, which is thought to be activated in the translocation by becoming closely associated with IGH enhancers. In contrast to IGH rearrangements in other neoplasms, those found in Multiple Myeloma have IGH breakpoints predominantly in the C/J region, which, in the case of MYEOV, brings the MYEOV gene under the control of the 3' Eα1 enhancer4. In CCND1 translocations by contrast, the Eμ enhancer controls CCND1 expression. MYEOV overexpression is a possible prognostic factor in MM5.

MM RefeRenCes 1.

Fonseca et al., Br J Haematol 1998;101(2):296-301

Bergsagel et al., Oncogene 2001;20(40):5611-5622

Ronchetti et al., Blood 1999 93(4):1330-1337

Janssen et al., Blood. 2000 15;95(8):2691-8

Moreaux et al., Exp Haematol 2010;38(12):1189-1198

14q32.33

Constant Segment

IGHA2 IGHM IGHG3 IGHE IGHG4 IGHG1 IGHG2 IGHA1 IGHGP G35395

G36213

Variable Segment

SHGC-36156

SHGC-170017

359kb

617kb 100kb

11q13.3

TPCN2

D11S4113

CCND1

MYEOV

D11S2663 D11S1100

155kb

FGF19 ORAOV1

D11S4095 D11S1076

FGF4 FGF3

D11S4381

162kb 100kb

Haematology

Cat. No. LPH 034-s

(5 tests)

Cat. No. LPH 034

(10 tests)

IGK Breakapart* Translocations involving the immunoglobulin loci are recurring events in various subtypes of B-cell lymphomas. In addition to translocations involving the IGH locus, variant translocations have been described in 5-10% of B-cell neoplasms involving either the immunoglobulin kappa (IGK) light chain locus at 2p11.2 or the lambda light chain (IGL) at 22q11.21,2. The best known translocations involving IG light chain loci are the variant Burkitt's translocations t(2;8)(p12;q24) and t(8;22)(q24;q11), which are present in up to 21% of all Burkitt's lymphomas3. Other translocations involve the BCL6 oncogene, the t(2;3)(p12;q27) and t(3;22)(q27;q11)4, and BCL2 locus, the t(2;18)(p12;q21) and t(18;22)(q21;q11)5. Translocations involving the IG light chain loci usually lead to breakage within the joining region of the respective locus2. IGK has a largely duplicated structure with duplicate gene regions being 96-100% identical. The IGK proximal copy is located within a 542kb contig with 22 potentially functional variable (IGKV) gene segments and 18 pseudogenes, plus five joining (J)-segments and one IGK constant (IGKC) gene segment. The distal copy is a within a 433kb contig with 21 potentially functional IGKV gene segments and 15 pseudogenes. The two contigs are separated by a DNA sequence of around 800kb that does not contain any IGKV segments1.

L RefeRenCes 1.

Poulseu TS et al., Leukemia 2002;16:2148-55

Martin-Subero JI et al., Int J Cancer 2002;98:470-4

Kornblau SM et al., Hematol Oncol 1991;9:63-78

Chaganti SR et al., Genes Chromosomes Cancer

1998;23:323-7 Tashiro S et al., Oncogene 1992;7:573-7

2p11.2 IGK Variable Regions CJ D2S2216 D2S2610

Proximal

Distal D21S1241

D2S1994 D2S2510

606kb

183kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 91.

(5 tests)

Cat. No. LPH 033

(10 tests)

Haematology

Cat. No. LPH 033-s

IGL Breakapart* Translocations involving the immunoglobulin loci are recurring events in various subtypes of B-cell lymphomas. In addition to translocations involving the IGH locus, variant translocations have been described in 5-10% of B-cell neoplasms involving either the immunoglobulin kappa (IGK) light chain locus at 2p11.2 or the lambda light chain (IGL) at 22q11.21,2. The best known translocations involving IG light chain loci are the variant Burkitt's translocations t(2;8)(p12;q24) and t(8;22)(q24;q11), which are present in up to 21% of all Burkitt's lymphomas3. Other translocations involve the BCL6 oncogene, the t(2;3)(p12;q27) and t(3;22)(q27;q11)4, and BCL2 locus, the t(2;18)(p12;q21) and t(18;22)(q21;q11)5. Translocations involving the IG light chain loci usually lead to breakage within the joining region of the respective locus2. IGL consists of 38 potentially active variable (IGLV) gene segments, 35 pseudogenes and seven IGL constant gene segments, each with a joining (J)-segment IGL (J-C)1.

L RefeRenCes 1. 2. 3. 4. 5.

Poulseu TS et al., Leukemia 2002;16:2148-55 Martin-Subero JI et al., Int J Cancer 2002;98:470-4 Kornblau SM et al., Hematol Oncol 1991;9:63-78 Chaganti SR et al., Genes Chromosomes Cancer 1998;23:323-7 Tashiro S et al., Oncogene 1992;7:573-7

22q11.21-q11.23

IGLV

MAPK1

IGLC

BCR

D22S446 D22S1264 D22S1003E

307kb

278kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 92.

Haematology

Cat. No. LPH 013-s

(5 tests)

Cat. No. LPH 013

(10 tests)

MLL (KMT2A) Breakapart Rearrangement of the MLL (KMT2A: lysine (K)-specific methyltransferase 2A) gene on chromosome 11q23.3 can be detected in the leukaemic cells of approximately 85% of infants with B-ALL1,2,3. They can also be found in 3% of de novo and 10% of therapy related AML cases4. Translocations involving the MLL gene are generally associated with increased risk of treatment failure5. In infant ALL, the most frequent of these translocations is the t(4;11)(q21;q23.3) translocation involving MLL and the AFF1 (AF4) gene on chromosome 46,7. A poor outcome for infants with ALL is strongly associated with the presence of this rearrangement in particular6. The discovery that a single YAC spanned breakpoints in four of the more common translocations led to the naming of the candidate gene MLL (Myeloid/Lymphoid or Mixed Lineage Leukaemia). The gene has homology with a drosophila gene ('trithorax'), which is highly conserved in humans and gives rise to a protein that can be folded to give six zinc finger domains and is a developmental regulator. The zinc finger domains are translocated to the AFF1, MLLT3 and MLLT1 genes on the partner chromosomes in the aforementioned t(4;11), t(9;11)(p22;q23.3) and t(11;19)(q23.3;p13.3) translocations, respectively. Each of the genes involved in these translocations have been shown to have high sequence homology. There have been over 85 recurrent translocations involving the MLL gene reported, with 66 partner genes so far identified8.

11q23.3 CD3G UBE4A

D11S1374 D11S1933 D11S3222

MLL (KMT2A) D11S3207

168kb

87kb 100kb

PHLDB1

ALL AML RefeRenCes 1.

Rubnitz et al., Blood 1994;84(2):570-3

Secker-Walker et al., Leukaemia 1998;12(5):840-4

Rowley, Annu Rev Genet 1998;32:495-519

Grossman et al., Leukemia 28 March 2013; doi10.1038/leu.2013.90

5. 6. 7. 8.

Pui and Evans, New Engl J Med 1998;339(9):605-15 Felix and Lange, Oncologist 1999;4(3):225-40 Heerema et al., Leukemia 1999;13(5):679-86 Huret JL. KMT2A (myeloid/lymphoid or mixed lineage leukemia). Atlas Genet Cytogenet Oncol Haematol. October 2005

(5 tests)

Cat. No. LPH 081

(10 tests)

Haematology

Cat. No. LPH 081-s

MLL/AFF1 Translocation, Dual Fusion The t(4;11)(q21;q23) translocation that involves the MLL (KMT2A) gene, on chromosome 11q23.3, and the AFF1 gene, on chromosome 4q21.3-q22.1, is the most frequently observed translocation involving the MLL gene in Acute Lymphoblastic Leukaemia (ALL)1.

ALL

The t(4:11) translocation results in the generation of two reciprocal fusion genes: MLL/AFF1 and AFF1/MLL – the leukaemic properties of the first have been documented but the role of the AFF1/MLL fusion protein is still under debate2,3,4.

RefeRenCes 1. 2. 3. 4. 5.

The 2011 Acute Lymphoblastic Leukaemia Best Practice Guidelines5 state that: “The t(4;11)(q21;q23) is associated with a poor prognosis, and patients with this translocation may be treated on the high risk arm of MRC protocols”…“If chromosome analysis is unsuccessful but FISH indicates a rearrangement of MLL, then further attempts to identify the t(4;11) must be made.”

Meyer et al., Leukemia 2009;23(8):1490-9 Smith et al., Genes Dev. 2011;25(7): 661–72 Kumar et al., Leuk Res. 2011;35(3):305-9 Bursen et al., Blood. 2010; 29;115(17):3570-9 Professional Guidelines for Clinical Cytogenetics: ACUTE LYMPHOBLASTIC LEUKAEMIA BEST PRACTICE GUIDELINES (2011) V1.00. www.cytogenetics.org.uk

The MLL/AFF1 Translocation, Dual Fusion probe allows both fusion genes, generated by the t(4;11)(q21;q23) translocation, to be detected.

11q23.3 ATP5L UBE4A

MLL

(KMT2A) TMEM25

CD3G

ARCN1 RH122609

SHGC-80669

200kb 100kb

4q21.3-q22.1

PTPN13

AFF1

SLC10A6 C4orf36

D4S824

KLHL8

SHGC-79180

SHGC-50512

220kb

61kb

110kb

HSD17B13 HSD17B11

RH36051

211kb

100kb

Haematology

Cat. No. RU-LPH 082-s* (50µl) Cat. No. RU-LPH 082*

(100µl)

MLL/MLLT1*, MLL/MLLT3* and MLL/MLLT4* Translocation, Dual Fusion Translocations involving chromosome 11q23 frequently occur in both acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL). In most cases, the MLL gene is involved but translocation partners are extremely variable, with 79 direct translocation partners having been molecularly characterised so far. The most common MLL rearrangement in both AML and ALL involves fusion of the MLL and AFF1 (AF4) genes via a t(4;11)(q21;q23) translocation. Three of the other more common translocations involve the MLLT3 (AF9) gene on chromosome 9, the MLLT1 (ENL) gene on chromosome 19 or the MLLT4 (AF6) gene on chromosome 6. • MLL/MLLT3(AF9) - t(9;11)(p22;q23) • MLL/MLLT1(ENL) - t(11;19)(q23;p13.3) • MLL/MLLT4(AF6) - t(6;11)(q27;q23) We now have a range of Research Use Only (RUO) Translocation, Dual Fusion probes to allow specific detection of these MLL rearrangements.

MLL/MLLT1

Cat. No. RU-LPH 082*

11q23.3 ATP5L UBE4A

MLL

(KMT2A) TMEM25

CD3G

ARCN1 RH122609

SHGC-80669

200kb 100kb

19p13.3

FUT5

RANBP3

SHGC-110515

ACSBG2

RH41878

203kb

RFX2

MLLT1

ACER1

GTF2F1 SLC25A41 TUBB4A

SHGC-31644

100kb

SLC25A23

226kb

SHGC-35317

ALL AML RefeRenCes •

Meyer et al., Leukemia 2013;27(11):2165-76

Cat. No. RU-LPH 084-s* (50µl)

Cat. No. RU-LPH 083*

Cat. No. RU-LPH 084*

(100µl)

Haematology

MLL/MLLT3

Cat. No. RU-LPH 083-s* (50µl)

(100µl)

Cat. No. RU-LPH 083*

11q23.3 ATP5L UBE4A

MLL

(KMT2A) TMEM25

CD3G

ARCN1 RH122609

SHGC-80669

200kb 100kb

9p21.3

MLLT3

FOCAD

SHGC-155125

G15985

167kb

140kb

100kb

MLL/MLLT4

SHGC-14450

186kb

Cat. No. RU-LPH 084*

11q23.3 ATP5L UBE4A

MLL

(KMT2A) TMEM25

CD3G

ARCN1 RH122609

SHGC-80669

200kb 100kb

6q27

C6orf123

FRMD1

RH80394

RH37393

187kb

KIF25

MLLT4

100kb

SHGC-145679

136kb

*For research use only, not for use in diagnostic procedures.

Haematology

Cat. No. LPH 016-s

(5 tests)

Cat. No. LPH 016

(10 tests)

MYB Deletion Deletions of chromosome 6q are found in B-CLL, with breakpoints being reported in bands 6q13, q15 and q21. The MYB gene (Avian Myeloblastosis Viral Oncogene Homolog) is a homologue of the avian v-myb oncogene and has been shown to be highly expressed in all immature lymphoid and myeloid T-cells, but becomes down regulated in mature T or B-cells1. The MYB gene is located in band 6q23.3 and is provided as a marker for 6q deletion as it is distal to reported deletion breakpoints (6q13, 6q15 and 6q21).

ALL CLL RefeRenCes 1.

D6Z1

6q23.3

MYB AHI1 D6S1837

AFMA074ZG9

D6S1431

183kb 100kb

Oh and Reddy. Oncogene. 1999 May 13;18(19):3017-33

(5 tests)

Cat. No. LPH 009

(10 tests)

Haematology

Cat. No. LPH 009-s

P16 (CDKN2A) Deletion* Deletions of chromosome 9p21 are implicated in a wide variety of tumours including approximately 10% of paediatric ALL patients1, though the incidence is higher in T-ALL2. The region has been the subject of much study but deletion of the potential tumour suppressor gene P16 (Cyclin-Dependent Kinase Inhibitor 2A (CDKN2A)) was found to take place in 90% of newly diagnosed cases of paediatric ALL showing cytogenetic deletions of 9p21 by FISH3. This study showed that deletion of P16 only (rather than both P16 (CDKN2A) and P15 (CDKN2B)) was the critical step as one case was found to be deleted for P16 but P15 was present. The deletion is usually homozygous (81% compared to 9% hemizygous) in cases of T-ALL whilst homozygous and hemizygous deletions are roughly equal in B-ALL (23% vs. 20% for homozygous and hemizygous respectively).

ALL

RefeRenCes 1. 2. 3. 4.

Heerema et al., Blood 1999; 94:1537-1544 Secker-Walker et al., Br J Haematol 1997;96(3):601-10 Okuda et al., Blood 1995;85(9):2321-30 Fry et al., Mol Cancer Ther. 2004 Nov;3(11):1427-38

The gene product inhibits the Cyclin Dependent Kinases CDK4 and CDK6, which are important in controlling cell cycle progression from G1 to S phase4. Disruptions of this process are therefore likely to result in the proliferation of mutated cells.

D9Z3

9p21.3

P16 (CDKN2A) CDKN2B D9S1605 D9S1604 D9S1748

D9S2060 D9S974

193kb

100kb

* A similar product is also available within the Haematopathology range, refer to page 94.

Haematology

Cat. No. LPH 017-s

(5 tests)

Cat. No. LPH 017

(10 tests)

P53 (TP53) Deletion* Although previously difficult to detect, the advent of FISH analysis of interphase cells from patients with B-CLL showed that around 17% of patients with the disease have deletions of the P53 (TP53) gene1. As with ATM, deletions of P53 have important therapeutic implications for patients with B-CLL2. Knowledge of the P53 deletion status in the patient should mediate the choice of therapy. P53 is a tumour suppressor gene and its protein product is responsible for the death of cells that contain damaged DNA. This is thought to be brought about by phosphorylation of P53 and the subsequent prevention of its repression by MDM2 (Mouse Double Minute 2 Homolog). This phosphorylation is mediated by ATM. In the absence of P53 activity, cells that cannot be repaired by ATM will continue to proliferate in their damaged state. Patients deleted for P53 may be rendered resistant to alkylating chemotherapeutic agents3 and purine analogues4 as these are designed to damage DNA in the cells that P53 would have destroyed. In the absence of P53, therefore, patients treated with these agents will harbour a proliferating population of damaged cells.

AML CLL

RefeRenCes 1. 2. 3. 4.

Dรถhner et al., J Mol Med 1999;77:266-81 Foรก et al., Haematol 2013; 98(5):675-685 Sturm et al., Cell Death Differ. 2003 Apr;10(4):477-84 Dรถhner et al., Blood. 1995 Mar 15;85(6):1580-9

D17Z1

17p13.1 P53 (TP53) SHBG ATP1B2

WRAP53 EFNB3

D17S1678

D17S1353 D17S655

159kb 100kb

* A similar product is also available within the Haematopathology range, refer to page 95.

(5 tests)

Cat. No. LPH 052

(10 tests)

Haematology

Cat. No. LPH 052-s

P53(TP53)/ATM Probe Combination Although previously difficult to detect, the advent of FISH analysis of interphase cells from patients with B-CLL showed that around 17% of patients with the disease have deletions of the P53 (TP53) gene1. As with ATM, deletions of P53 have important therapeutic implications for patients with B-CLL2.

CLL

Knowledge of the P53 deletion status in the patient should

RefeRenCes

mediate the choice of therapy. P53 is a tumour suppressor gene

Dรถhner et al., J Mol Med 1999;77:266-81

Foรก et al., Haematol 2013; 98(5):675-685

contain damaged DNA. This is thought to be brought about by

Sturm et al., Cell Death Differ. 2003 Apr;10(4):477-84

Dรถhner et al., Blood. 1995 Mar 15;85(6):1580-9

phosphorylation of P53 and the subsequent prevention of its

Stankovic et al., Blood 2004;103(1):291-300

Khanna et al., Nature Genetics 1998;20(4):398-400

and its protein product is responsible for the death of cells that

repression by MDM2 (Mouse Double Minute 2 Homolog). This phosphorylation is mediated by ATM. In the absence of P53 activity, cells that cannot be repaired by ATM will continue to proliferate in their damaged state. Patients deleted for P53 may be rendered resistant to alkylating chemotherapeutic agents3 and purine analogues4 as these are designed to damage DNA in the cells that P53 would have destroyed. In the absence of P53, therefore, patients treated with these agents will harbour a proliferating population of damaged cells. The protein kinase ATM (Ataxia-Telangiectasia Mutated) gene,

17p13.1

located in 11q22.3, is frequently deleted in cases of B-CLL.

P53 (TP53)

ATM is an important checkpoint gene involved in the

WRAP53

SHBG ATP1B2

management of cell damage and its function is to assess the

EFNB3

level of DNA damage in the cell and attempt repair by

D17S1678

D17S1353 D17S655

phosphorylating key substrates involved in the DNA damage response pathway. The ATM/P53 interaction in B-CLL has been

159kb 100kb

shown to play an important role in the proliferation of lymphoid cancer5. It has been shown that ATM concurrently enhances the phosphorylation of P536, should the damage be so great that the cell requires destruction by apoptosis (which is mediated by P53). Deletion of ATM removes this checkpoint activity and hence activation of P53. Thus, there is no attempt made to

11q22.3

repair or to apoptose damaged cells, despite the presence of P53. In the absence of ATM, damaged cells are allowed to continue to proliferate.

ATM

NPAT

D11S3347

Screening for deletions of ATM and/or P53 is vital to allow informed therapy choices for CLL patients, especially as deletions of P53 and ATM confer poor prognosis2.

D11S2179

180kb 100kb

Haematology

Cat. No. LPH 031-s

(5 tests)

Cat. No. LPH 031

(10 tests)

PDGFRB Breakapart Some cases of Chronic Myelomonocytic Leukaemia (CMML) have constitutive activation of the gene for PDGFRB (platelet derived growth factor receptor beta) which encodes a receptor tyrosine kinase1. The activation is usually caused by a t(5;12)(q32;p13) translocation which results in the ETV6 (TEL)-PDGFRB fusion gene. Patients with this fusion have reportedly been shown to be responsive to the drug imatinib mesylate (Gleevec)1, which specifically inhibits the kinase activity of PDGFRB. The breakpoint in PDGFRB is characteristically located in intron 102,3.

CML RefeRenCes 1.

Apperley JF et al., N Engl J Med 2002;347:481-7

Tokita K et al., Leukemia 2007;21:190-2

Levine et al., Leukemia 2005;19:27-30

5q32

HMGXB3 D5S2618

CSF1R

PDGFRB

D5S2619

CAMK2A D5S2015

107kb

154kb 100kb

CDX1 SLC6A7 ARSI

(5 tests)

Cat. No. LPH 064

(10 tests)

Haematology

Cat. No. LPH 064-s

FAST PML/RARÎą(RARA) Translocation, Dual Fusion Immediate treatment of patients carrying the t(15;17) (PML/RARA) translocation is critical due to the risk of early death2. This FAST PML/RARA FISH probe allows rapid detection of the rearrangement, with only one hour of hybridisation required.

AML APL

The fusion gene PML/RARA is created by the t(15;17)(q24.1;q21.2) translocation, found in 98% of AML M3 Acute hypergranular

RefeRenCes

promyelocytic leukaemia and 9% of AML overall1,2,3. The PML protein

Licht, Sternberg, The Molecular Pathway of AML ASH

Education Book 2005;137-42 Huret and Chomienne. t(15;17)(q24;q21). Atlas Genet

Cytogenet Oncol Haematol 1998;2(3):329-34 Heim and Mitelman, Willey-Liss, Inc. 1995

Greaves, BMJ 2002;324(7332):283-7

is a transcription factor and RARA encodes a nuclear receptor. The fusion protein generated, PML-RARA, is a chimaeric transcription factor that operates as a dominant negative form of RARA and results in cells that are blocked at the promyelocytic stage of differentiation and then proliferate. Gain of function mutation allows repression of multiple genes and recruitment of DNA methyltransferases to promoters, allowing prolonged suppression. PML-RARA also activates components of the WNT signalling pathway, promoting stem cell renewal. Immediate treatment of PML/RARA positive patients is critical as intravascular coagulation causes early death in 10-40% of cases2. Terminal differentiation is induced by the use of all-trans-retinoic-acid (ATRA), which reactivates the RARA gene and degrades the PML-RARA fusion product and 80-90% of treated patients achieve complete remission1,2,4. Despite the efficacy of ATRA, the death rate remains around 15-20%, but 70% of patients will achieve 3 year survival2.

Additional

abnormalities

found

with

PML/RARA

translocations include trisomy 8, seen in one third of cases, del(7q) and del(9q)2.

15q24.1

17q21.1-q21.2

PML STOML1 LOXL1 TBC1D21 D15S188

RAPGEFL1 CASC3

ISLR2 STRA6

MSL1

D15S160 D15S818 D15S1326 D15S965 D15S169 D15S624E D15S1281

RARA CDC6 WIPF2

100kb

174kb

IGFBP4 TNS4

D17S1423E D17S1984

167kb

151kb

TOP2A

164kb 100kb

Haematology

Cat. No. LPH 023-s

(5 tests)

Cat. No. LPH 023

(10 tests)

PML/RARÎą(RARA) Translocation, Dual Fusion The fusion gene PML/RARA is created by the t(15;17)(q24.1;q21.2) translocation, found in 98% of AML M3 acute hypergranular promyelocytic leukaemia and 9% of AML overall1,2,3.

AML APL

Breakpoints in the PML gene vary between intron 3 and exon 7a, which is in contrast to the RARA breakpoint, which remains constant in intron 2. Variant translocations include partner breakpoints in

RefeRenCes

11q23, 5q32 and 11q13. The presence of three-way translocations

Licht, Sternberg, The Molecular Pathway of AML. ASH

Education Book 2005;137-42 Huret and Chomienne. t(15;17)(q24;q21). Atlas Genet

Cytogenet Oncol Haematol 1998;2(3):329-34 Heim and Mitelman, Willey-Liss, Inc. 1995

Greaves, BMJ 2002;324(7332):283-7

indicate that the critical event occurs on the der(15), which always receives the distal end of chromosome 17. The PML protein is a transcription factor and RARA encodes a nuclear receptor. The fusion protein generated, PML-RARA, is a chimaeric transcription factor that operates as a dominant negative form of RARA and results in cells that are blocked at the promyelocytic stage of differentiation and then proliferate. Gain of function mutation allows repression

multiple

genes

and

recruitment

DNA

methyltransferases to promoters, allowing prolonged suppression. PML-RARA also activates components of the WNT signalling pathway, promoting stem cell renewal. Immediate treatment of PML/RARA positive patients is critical as intravascular coagulation causes early death in 10-40% of cases2. Terminal differentiation is induced by the use of all-trans-retinoic-acid (ATRA), which reactivates the RARA gene and degrades the PML-RARA fusion product and 80-90% of treated patients achieve complete remission1,2,4. Despite the efficacy of ATRA, the death rate remains around 15-20%, but 70% of patients will achieve 3 year survival2.

Additional

abnormalities

found

with

PML/RARA

translocations include trisomy 8, seen in one third of cases, del(7q) and del(9q)2.

17q21.1-q21.2

15q24.1 PML STOML1 LOXL1 TBC1D21 D15S188

RAPGEFL1 CASC3

ISLR2 STRA6

MSL1

RARA CDC6 WIPF2

167kb

100kb

174kb

IGFBP4 TNS4

D17S1423E D17S1984

D15S160 D15S818 D15S1326 D15S965 D15S169 D15S624E D15S1281 151kb

TOP2A

164kb 100kb

(5 tests)

Cat. No. LPH 065

(10 tests)

Haematology

Cat. No. LPH 065-s

RARα (RARA) Breakapart Acute Promyelocytic Leukaemia (APL) is associated with chromosomal rearrangements involving the retinoic acid receptor α (RARA) gene, on chromosome 17q21.1-q21.2, and various partner genes situated on different chromosomes2. In the vast majority of APL cases, the RARA gene fuses with the Promyelocytic Leukaemia (PML) gene located on chromosome 15q24, as a result of a t(15;17) translocation, but RARA fusions with Promyelocytic Leukemia Zinc Finger (PLZF (now known as ZBTB16), 11q23.2), Nucleophosmin (NPM1, 5q35.1), Nuclear Mitotic Apparatus protein 1 (NUMA1, 11q13.4), Myeloid/lymphoid or Mixed Lineage Leukaemia (MLL (KMT2A), 11q23.3) and FIP1-like-1 (FIP1L1, 4q12) genes have also been described1,2,3. The RARAα (RARA) Breakapart probe will detect rearrangements of the RARA gene, irrespective of partner genes or chromosomes involved.

AML APL RefeRenCes 1.

Melnick A, Licht JD, Blood 1999;93(10):3167-215

http://atlasgeneticsoncology.org/Genes/RARAID46.html

Rohr et al., Med Oncol 2011;29(4):2345-7

17q21.1-q21.2 RAPGEFL1 CASC3 MSL1

RARA CDC6 WIPF2

TOP2A

IGFBP4 TNS4

D17S1423E D17S1984

167kb

164kb 100kb

Haematology

Cat. No. LPH 046-s

(5 tests)

Cat. No. LPH 046

(10 tests)

TCL1 Breakapart Dysregulation of normal transcription is a feature of all acute leukaemias. In T-cell neoplasms, this is brought about by altered expression of normal transcription factor proteins, often as a consequence of chromosomal translocations or inversions placing these genes into close proximity of the promoter and enhancer elements of the T-cell receptor genes, TRA@ (TCRA), TRB@ (TCRB), TRG@ (TCRG) and TRD@ (TCRD)1,2. In T-PLL (a form of mature T-cell proliferation in patients with Ataxia Telangiectasia (AT)3), the (T-cell Leukaemia 1A/1B) gene cluster on chromosome 14q32 has been shown to be involved in a number of different chromosomal rearrangements, including the t(14;14)(q11;q32) and inv(14)(q11;q32), which bring elements of the cluster into close juxtaposition to, and under the control of, the TCR gene promoters and enhancers. There are two breakpoint regions in the gene cluster, each of which are observed in different neoplasms, though both are involved in either the inv(14) or t(14;14). Breakpoints are concentrated in regions centromeric and telomeric to the TCL1A, TCL6 and TCL1B genes4.

ALL RefeRenCes 1. 2. 3. 4.

Korsmeyer SJ, Annual Rev Immunol 1992;10:785-807 Virgilio et al., PNAS 1994;91:12530-12534 Brito-Babpulle V, Catovsky D, Cancer Genet Cytogenet 1991;55:1-9 Saitou et al., Oncogene 2000;19:2796-802

14q32.13-q32.2

GLRX5

TCL1A TCL1B

TCL6

D14S62

D14S131

124kb

138kb 100kb

(5 tests)

Cat. No. LPH 047

(10 tests)

Haematology

Cat. No. LPH 047-s

TCRAD Breakapart Dysregulation of normal transcription is a feature of all types of acute leukaemia. In T-ALL, this is brought about by altered expression of normal transcription factor proteins, which is in contrast with AML and B-ALL, where chimaeric proteins are expressed and provide the drivers for the malignancy.

ALL

T-ALL composes around 12-15% of childhood ALL1. In about 30% of these cases, chromosomal rearrangements involving the T-cell receptor genes TRA@ (TCRA), TRB@ (TCRB), TRG@ (TCRG) and TRD@ (TCRD) have been described2. It has been suggested that a number of developmentally important transcription factor genes are dysregulated as a result of being brought into close proximity with the promoter and enhancer elements of one of these T-cell receptor genes3. These can be more clearly demonstrated by FISH than by using conventional cytogenetics4.

RefeRenCes

The TCRAD complex, on chromosome 14q11.2 has been shown to be involved in a number of different translocations in T-ALL. These include the t(10;14)(q24;q11) involving TLX1 (HOX11); the t(1;14)(p32;q11) involving TAL1; the t(11;14)(p15;q11) involving LMO1 and the t(11;14)(p13;q11) involving LMO2. The relative frequencies for these rearrangements in children have been estimated to be 7, 3, 2 and 3% respectively5.

Schneider NR et al., Blood 2000;96:2543-9

Secker-Walker LM, Chromosomes and Genes in Acute

Lymphoblastic Leukaemia. New York: Chapman and Hall 1997 Raimondi SC. T-lineage acute lymphoblastic leukemia (T-ALL)

Atlas Genet Cytogenet Oncol Haematol. May 2007 Gesk S et al., Leukemia 2003;17:738-45

Graux C et al., Leukemia 2006;20:1496-510

14q11.2

TOX4

TRAC

SALL2 IGV Region

G36107

DAD1 IGD

IGJ IGC Region

OXA1L ABHD4 G35927 143kb

225kb

100kb

Haematology

Cat. No. LPH 048-s

(5 tests)

Cat. No. LPH 048

(10 tests)

TCRB (TRB) Breakapart Dysregulation of normal transcription is a feature of all types of acute leukaemia. In T-ALL, this is brought about by altered expression of normal transcription factor proteins, which is in contrast with AML and B-ALL, where chimaeric proteins are expressed and provide the drivers for the malignancy. T-ALL composes around 12-15% of childhood ALL1. In about 30% of these cases, chromosomal rearrangements involving the T-cell receptor genes TRA@ (TCRA), TRB@ (TCRB), TRG@ (TCRG) and TRD@ (TCRD) have been described2. It has been suggested that a number of developmentally important transcription factor genes are dysregulated as a result of being brought into close proximity with the promoter and enhancer elements of one of these T-cell receptor genes3. These can be more clearly demonstrated by FISH than by using conventional cytogenetics4. The TCRB T-cell Receptor gene on chromosome 7q34 is rearranged with the genes TLX1, HOX@, LYL1, TAL2, LCK and NOTCH1 following the t(7;10)(q34;q24); t(7;7)(p15;q34); t(7;19)(q34;p13); t(7;9)(q34;q32); t(1;7)(p34;q34) and t(7;9)(q34;q34) translocations respectively. The frequency of rearrangements varies between 7% (for the TLX1 rearrangement) to less than 1% (for TAL2, LYL1, LCK and NOTCH1)5.

ALL RefeRenCes 1. 2. 3. 4. 5.

Schneider NR et al., Blood 2000;96:2543-9 Secker-Walker LM, Chromosomes and Genes in Acute Lymphoblastic Leukaemia. New York: Chapman and Hall 1997 Raimondi SC. T-lineage acute lymphoblastic leukemia (T-ALL) Atlas Genet Cytogenet Oncol Haematol. May 2007 Gesk S et al., Leukemia 2003;17:738-45 Graux C et al., Leukemia 2006;20:1496-510

7q34

PRSS1

EPHB6

TRB D7S2473

IGV Region

177kb

SHGC-81465

133kb 100kb

IGJ IGC Region

(5 tests)

Cat. No. LPH 012

(10 tests)

Haematology

Cat. No. LPH 012-s

TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion The TEL (or ETV6 - Erythroblastosis Variant Gene 6 translocation, ETS) / AML1 (or RUNX1 - Runt-Related Transcription Factor 1) fusion is brought about by the cytogenetically invisible t(12;21) translocation. This is the most common rearrangement in childhood B-ALL and has been detected using FISH in around 17% of cases1, compared to a pick-up rate of 0.05% by conventional cytogenetics2. The translocation is associated with a favourable outcome and has been associated with late relapse3. TEL has also been shown to be deleted in some children with ALL with loss of heterozygosity (LOH) of chromosome 12p12-13 and this deletion is often associated with a TEL/AML1 translocation4. Both the TEL and AML1 genes encode transcription factors and TEL has been shown to be required for proper transcription during haematopoiesis within the bone marrow5.

ALL RefeRenCes 1. 2. 3. 4. 5.

Jamil et al., Cancer Genet Cytogenet 2000;122(2):73-8 Borkhardt et al., Blood. 1997 Jul 15;90(2):571-7 Mosad et al., Journal of Hematology & Oncology 2008;1:17 Raynaud et al., Blood 1996;87(7):2891-9 Wang et al., Genes Dev. 1998 Aug 1;12(15):2392-402

12p13.2

TEL (ETV6) D12S827 D12S845

D12S1095 D12S1697

D12S98 D12S850

D12S89 D12S1898

180kb

168kb 100kb

21q22.12

RCAN1

AML1 (RUNX1)

CLIC6

D21S326

D21S1706 D21S1895

D21S1969 D21S393

148kb

100kb

D21S1921

167kb

Haematology

Cat. No. LPH 049-s

(5 tests)

Cat. No. LPH 049

(10 tests)

TLX1 Breakapart Dysregulation of normal transcription is a feature of all acute leukaemias. In T-cell neoplasms, this is brought about by altered expression of normal transcription factor proteins, often as a consequence of chromosomal translocations or inversions placing these genes into close proximity of the promoter and enhancer elements of the T-cell receptor genes, TRA@ (TCRA), TRB@ (TCRB), TRG@ (TCRG) and TRD@ (TCRD)1. Murine studies show that expression of mouse homologues of TLX1 (T-Cell Leukaemia Homeobox 1 or HOX11) can immortalise haematopoietic cells in vitro as the first of a potential two-hit mechanism leading to full malignancy2. This work suggests that TLX1, which is aberrantly expressed in 30% of adult and 5-10% of childhood T-ALL cases3, is an oncogene that can become dysregulated through the translocations t(10;14)(q24;q11) and t(7;10)(q35;q24), placing it into close proximity to TCRA/D and TCRB elements respectively4. Breakpoints are clustered within a region 10kb centromeric to and immediately adjacent to TLX1.

10q24.31 SFXN3 PDZD7 KAZALD1 LZTS2

TLX1 LBX1

D10S1629

WI-19473

179kb

124kb 100kb

RH92279

ALL RefeRenCes 1.

Korsmeyer SJ, Annual Rev Immunol 1992;10:785-807

Hawley RG et al., Oncogene 1994;9:1-12

Riz et al., Oncogene (2005) 24, 5561â&#x20AC;&#x201C;5575

DubĂŠ ID et al., Blood 1991;78(11):2996-3003

(5 tests)

Cat. No. LPH 050

(10 tests)

Haematology

Cat. No. LPH 050-s

TLX3 Breakapart In common with other factors involved in T-ALL, the normal expression of TLX3 (T-Cell Leukaemia Homeobox 3, previously known as HOX11L2) can be disrupted by a chromosomal translocation1. Unlike TLX1 (HOX11), however, the dysregulation of TLX3 is not brought about by close juxtaposition with T-cell receptor genes, instead, it is brought into contact with another gene which is highly expressed in normal T-cell differentiation, BCL11B (B-Cell Lymphoma 11B, or CTIP2) on chromosome 14q32.11. The translocation t(5;14)(q35;q32) is generally cryptic and the breakpoint does not actually disrupt TLX3 but, in the majority of cases, occurs within or downstream of the RANBP17 (Ran-Binding Protein 17) gene2. However, this gene is very close to TLX3 and though RANBP17 expression is not affected by the translocation, TLX3 expression is. Dysregulated expression of TLX3 is observed in around 20% of paediatric cases and around 13% of adult T-ALL patients3,4.

ALL RefeRenCes 1. 2. 3. 4.

Bernard OA et al., Leukaemia 2001;15:1495-504 Van Zutven et al., Haematologica 2004;89:671-8 Van Vlierberghe et al., Leukemia. 2008 Apr;22(4):762-70 Borghini et al., Mol Cancer Res. 2006 Sep;4(9):635-43

5q35.1

TLX3

NPM1 FGF18

RANBP17 RH80894

D5S653

162kb

173kb 100kb

Haematology

Multiprobe Haematology

Contents 74

Chromoprobe Multiprobe速 ALL

Chromoprobe Multiprobe速 CLL

Chromoprobe Multiprobe速 AML/MDS

Multiprobe Haematology As long ago as the 19th Century, nuclear changes were recognised as being significant in cancer biology. Advances in cytogenetics and molecular cytogenetics in the last century showed that although a number of numerical and structural chromosome changes appeared to be random and non-specific, rearrangements involving individual chromosomes were shown to define specific abnormalities in individual tumour types. Fluorescence In Situ Hybridisation (FISH), using locus-specific probes that are capable of defining these stereotypic structural rearrangements, has now become a routine diagnostic test in the clinical laboratory and the technique has thus been shown to be useful in the management of cancer patients. The Chromoprobe Multiprobe速 haematology devices are designed for use on interphase nuclei and metaphase chromosomes from cultured peripheral blood cells or cultured bone marrow samples.

Multiprobe Haematology

The procedure is simple:

Spot 2µl (or 4µl for an 8 square device) of cell sample onto alternate squares of the supplied slide.

Soak the slides in 100% methanol, then polish dry with a lint free cloth.

Carefully lower spotted slide onto the device.

Check the temperature of the hotplate using the slide surface thermometer provided. Denature the slide/device at 75°C for 2 minutes.

Once dry, fill in the remaining squares with the cell sample and check using phase contrast.

Place slides in 2xSSC for 2 minutes and then dehydrate through an ethanol series.

Place slide/device in hybridisation chamber supplied and float on the surface of a clean 37°C waterbath overnight.

Wash in 0.4xSSC at 72°C for 2 minutes, then 2xSSC/0.05% Tween at room temperature for 30 seconds.

Spot 1µl (or 2µl for an 8 square device) of supplied hybridisation solution onto each square of the device.

Apply DAPI counterstain provided and view under a fluorescence microscope.

Cat. No. PMP 030

(2 devices)

Cat. No. PMP 032

(10 devices)

Cat. No. PMP 031

(5 devices)

Cat. No. PMP 033

(20 devices)

Multiprobe Haematology

Chromoprobe Multiprobe速 ALL cMYC (MYC) Breakapart

P16 (CDKN2A) Deletion

Translocations involving the cMYC (MYC) oncogene are a molecular feature of Burkitt Lymphoma (former FAB L3 subtype ALL) and occur in almost every case. These rearrangements can also be found very rarely (approximately 0.1% of cases) in paediatric ALL with the precursor B-cell phenotype.

Deletions of chromosome 9p21 are implicated in a wide variety of tumours including approximately 10% of paediatric ALL patients, though the incidence is higher in T-ALL. 90% of patients with a deletion in 9p21 are deleted for P16.

TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion

MLL (KMT2A) Breakapart

This is the most common rearrangement in childhood B-ALL and has been detected using FISH in around 17% of cases, compared to a pick-up rate of 0.05% by conventional cytogenetics. The translocation is associated with a favourable outcome and has been associated with late relapse.

Rearrangement of the MLL (KMT2A) gene on chromosome 11q23.3 can be detected in the leukaemic cells of approximately 85% of infants with B-ALL. Translocations involving the MLL gene are generally associated with increased risk of treatment failure.

2 D9Z3

9p21.3

8q24.21

D8S1153

P16 (CDKN2A) CDKN2B

MYC

POU5F1B CASC8

PVT1

D8S1128 D8S1980

D9S1605 D9S1604 D9S1748

D9S2060 D9S974

D8S1644 D8S1720

193kb

173kb

186kb 100kb

100kb

P16 (CDKN2A) Deletion

cMYC (MYC) Breakapart

6 12p13.2

TEL (ETV6) D12S827 D12S845

D12S1095 D12S1697

D12S89

D12S98 D12S850 D12S1898

180kb

11q23.3

168kb 100kb

CD3G UBE4A

MLL (KMT2A)

21q22.12 D11S1374 D11S1933 D11S3222 RCAN1

D21S326

D21S1706 D21S1895

D21S1969 D21S393

148kb

100kb

TEL/AML1 (EVT6/RUNX1) Translocation, Dual Fusion

D11S3207

AML1 (RUNX1)

CLIC6

D21S1921

168kb

87kb 100kb

167kb

MLL (KMT2A) Breakapart

PHLDB1

Multiprobe Haematology

E2A (TCF3) Breakapart

Hyperdiploidy

Translocations involving the E2A (TCF3) gene are relatively common in childhood B-ALL, specifically B-cell precursor ALL, with the t(1;19) being the most common. Detection of the t(1;19) is best carried out using molecular methods, such as FISH, as this and other E2A translocations have been shown to be cytogenetically cryptic.

Approximately 30% of childhood ALL cases have cells exhibiting a chromosome number between 51 and 67. Within this group are prognostically significant subsets, with individuals possessing 51 to 55 chromosomes having a poorer prognosis than those with 56 to 67. The chromosomes that are more readily hyperdiploid are chromosomes 4, 6, 10, 14, 17, 18, 21 and X, with gains of chromosomes 4, 10 and 17 leading to a relatively better prognosis.

BCR/ABL(ABL1) Translocation, Dual Fusion

IGH Breakapart

The stereotypical Philadelphia chromosome forming translocation, t(9;22), represents a significant abnormality in ALL and is associated with an extremely poor outcome. In a small number of cases, the translocation does not result in a cytogenetically visible Philadelphia chromosome. In these cases, FISH is essential for highlighting the fusion gene.

In ALL, IGH is involved in rearrangements with a number of different partner chromosomes. In T-ALL associated with Ataxia Telangiectasia (AT), for example, IGH is observed in the t(14;14)(q11;q32) translocation. This abnormality also, very rarely, occurs in B-ALL. The IGH Breakapart probe allows the detection of rearrangements, regardless of the partner gene/chromosome involved.

4 D10Z1

D17Z1 19p13.3 E2A (TCF3)

MEX3D D19S883

4q12

RH98588

MBD3

163kb

CHIC2

189kb 100kb

D4S1594

174kb 100kb

E2A (TCF3) Breakapart

Hyperdiploidy

8 22q11.22-q11.23

GNAZ

RAB36

BCR D22S1002E

IGLL1

D22S1027 D22S257

14q32.33 148kb

169kb 100kb

Constant Segment D14S1007

9q34.11-q34.12

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP

D14S1420 D14S1419 D14S308

124kb

FUBP3 PRDM12

LAMC3

ABL1

D9S1863

617kb 100kb

D9S313

346kb 100kb

BCR/ABL(ABL1) Translocation, Dual Fusion

IGH Breakapart For more information please see individual product pages.

Cat. No. PMP 018

(2 devices)

Cat. No. PMP 016

(10 devices)

Cat. No. PMP 017

(5 devices)

Cat. No. PMP 020

(20 devices)

Multiprobe Haematology

Chromoprobe Multiprobe速 CLL MYB Deletion

Chromosome 12 Enumeration

Deletions of chromosome 6q are found in B-CLL, with breakpoints being reported in bands 6q13, q15 and q21. The MYB gene is located in band 6q23.3 and is provided as a marker for 6q deletion as it is distal to the reported deletion breakpoints.

The chromosome 12 probe on the CLL Panel is a repeat sequence probe, labelled in red, which recognises the centromeric repeat sequence D12Z3. This probe will allow detection of trisomy 12, a recurrent abnormality in CLL.

IGH Breakapart

P53 (TP53) Deletion

Around 20% of cytogenetically abnormal CLL patients have a detectable 14q+ marker chromosome. The markers are derived from reciprocal translocations involving a number of fusion partners from different chromosomes that fuse with the IGH gene at 14q32.33. The two most common translocations are IGH/BCL2, caused by the t(14;18) translocation, and IGH/CCND1, a result of the t(11;14) translocation.

Along with ATM, P53 (TP53) deletions are the most serious aberrations in CLL. Since the interaction between ATM and P53 during apoptosis of damaged cells is disrupted by deletion of one or other of these genes, damaged cells can proliferate in the patient unchecked, leading to a poor prognosis. Knowledge of the P53 deletion status in patients should mediate their choice of therapy as those deleted for P53 may be rendered resistant to alkylating chemotherapeutic agents and purine analogues.

2 D6Z1

6q23.3

D12Z3 MYB AHI1 D6S1837

AFMA074ZG9

D6S1431

183kb 100kb

Chromosome 12 Enumeration

MYB Deletion

6 D17Z1

14q32.33

Constant Segment D14S1007

17p13.1

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP

D14S1420 D14S1419 D14S308

P53 (TP53) SHBG ATP1B2

WRAP53 EFNB3

124kb

617kb

D17S1678

100kb

D17S1353 D17S655

159kb 100kb

IGH Breakapart

P53 Deletion

IGH/BCL2 Translocation, Dual Fusion

Deletions of ATM (and P53) are the most serious aberrations involved in B-CLL. The two genes have an important interaction in checkpoint control of patients with the disease. In the absence of ATM, damaged cells are allowed to escape P53-mediated apoptosis and proliferate, leading to poor prognosis for the patient.

This is the second most common rearrangement of IGH in CLL. The translocation (t(14;18)(q32.33;q21.33)) results in the BCL2 gene coming under the regulatory control of those processes normally involved in maintenance of IGH gene activity. The BCL2 gene has been shown to be involved in the regulation of apoptosis.

IGH/CCND1 Translocation, Dual Fusion

13q14.3 Deletion

The IGH/CCND1 probe, for the detection of t(11;14), has been recommended by the British Committee for Standards in Haematology to enable atypical B-CLL patients to be distinguished from possible Mantle Cell Lymphoma (MCL) patients.

Deletions affecting 13q14 are the most frequent genetic abnormalities in B-cell Chronic Lymphocytic Leukaemia (B-CLL). This region is found to be heterozygously deleted in 30-60% and homozygously deleted in 10-20% of CLL patients.

Multiprobe Haematology

ATM Deletion

14q32.33

Constant Segment D14S1007

11q12.1

11q22.3

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP 124kb

D14S1420 D14S1419 D14S308

168kb

617kb 100kb

SHGC-154780

ATM

NPAT

OR5G5P SHGC-110550

122kb

D11S3347 D11S2179

130kb

18q21.33

180kb

BCL2

100kb

D18S91

D18S1264

KDSR D18S51

D18S87 D18S1366

585kb

100kb

ATM Deletion

IGH/BCL2 Translocation, Dual Fusion

7 14q32.33

Constant Segment D14S1007

124kb

13qter

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP

D14S1420 D14S1419 D14S308

13q14.2-q14.3

617kb

168kb 100kb

TRIM13 DLEU1 DLEU2 D13S1477

11q13.3

D13S311

RH44686 D13S25

100kb

93kb

CCND1

MYEOV

D11S2663 D11S1100

D13S319

215kb

FGF19 ORAOV1

D11S4095 D11S1076

FGF4 FGF3

D11S4381

D11S2927

162kb

155kb 100kb

IGH/CCND1 Translocation, Dual Fusion

13q14.3 Deletion For more information please see individual product pages.

Cat. No. PMP 025

(2 devices)

Cat. No. PMP 027

(10 devices)

Cat. No. PMP 026

(5 devices)

Cat. No. PMP 028

(20 devices)

Multiprobe Haematology

Chromoprobe Multiprobe® AML/MDS Del(5q) Deletion Deletion of a region of 5q is the most common rearrangement in AML and MDS. The common deleted region (CDR) is within 5q31.1, which includes the EGR1 gene. Loss of this gene has been implicated in tumourigenesis.

PML/RARα(RARA) Translocation, Dual Fusion The fusion gene PML/RARA is created by the t(15;17)(q24.1;q21.2) translocation, found in 98% of AML M3 Acute hypergranular promyelocytic leukaemia and 9% of AML overall. Immediate treatment of PML/RARA positive patients is critical as intravascular coagulation causes early death in 10-40% of cases. 80-90% of treated patients achieve complete remission.

MLL (KMT2A) Breakapart

Del(7q) Deletion

Translocations involving the MLL (11q23) gene are generally associated with increased risk for treatment failure, and are found in 3% of de novo and 10% of therapy related cases of AML. The MLL gene is necessary to maintain HOX gene expression, which is an important gene involved in development.

Abnormalities of chromosome 7 are very common in myeloid malignancies, such as adult and paediatric MDS and treatment related AML/MDS. Studies of myeloid disorders involving -7/del(7q) have found that signalling pathways involving RAS proteins are affected.

2 15q24.1 PML STOML1 LOXL1

ISLR2

TBC1D21

5p15.31

5q31.2

STRA6

D15S160 D15S818 D15S1326 D15S965 D15S169 D15S624E D15S1281

D15S188

151kb

174kb

100kb

EGR1 TAS2R1

CDC25C

D5S630

D5S1701 D5S500 D5S2415 D5S2542

D5S2064

17q21.1-q21.2 RAPGEFL1 CASC3

184kb

310kb

MSL1

RARA CDC6 WIPF2

IGFBP4 TOP2A TNS4

100kb D17S1423E D17S1984

167kb

164kb 100kb

PML/RARα(RARA) Translocation, Dual Fusion

Del(5q) Deletion

11q23.3 7q22.1-q22.2

CD3G UBE4A

D11S1374 D11S1933 D11S3222

MLL (KMT2A)

7q31.2

PHLDB1

TES RELN

ORC5 D7S796

D7S658

D11S3207

100kb

87kb 100kb

MLL (KMT2A) Breakapart

Del(7q) Deletion

D7S2886 D7S486

203Kb 203kb

396kb

168kb

D7S2543

Knowledge of the P53 deletion status in patients should mediate their choice of therapy as those deleted for P53 may be rendered resistant to alkylating chemotherapeutic agents and purine analogues.

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion AML1 (or RUNX1 - Runt related Transcription Factor 1) is fused with ETO (or RUNX1T1) in the t(8;21)(q21;q22) translocation, found most commonly in AML M2 patients and less frequently in subgroups M1 and M4. Overall 7% of AML cases demonstrate the abnormality, the majority of which are de novo.

CBFβ/MYH11 Translocation, Dual Fusion

Del(20q) Deletion

The fusion gene CBFß(CBFB)/MYH11, created by the inversion inv(16)(p13.11q22.1), is found in 20% of AML M4 cases and abnormalities involving 16q22 are seen in 5-10% of AML overall. Frequently, Central Nervous System (CNS) involvement develops, particularly in relapse. However, the complete remission rate is high and the prognosis is better than most of the AML associated abnormalities.

Deletions of the long arm of chromosome 20 are a common chromosomal abnormality associated with myeloid malignancies, including AML. The prognosis for MDS cases where del(20q) is the sole abnormality is good. However if secondary abnormalities are present, a poor outcome is indicated. AML patients respond poorly to treatment and have reduced survival rates.

Multiprobe Haematology

P53 (TP53) Deletion

4 21q22.12

D17Z1 CLIC6

AML1 (RUNX1)

RCAN1

17p13.1

D21S326 D21S1706 D21S393 D21S1969

SHBG ATP1B2

D21S1895 D21S1921 167kb

148kb

P53 (TP53)

100kb

WRAP53 EFNB3

D17S1678

D17S1353 D17S655 8q21.3

159kb

ETO

100kb

(RUNX1T1)

D8S1950 D8S1952 D8S1648 D8S1603

D8S412 D8S2020

148kb

149kb 100kb

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion

P53 (TP53) Deletion

8 MYH11 D16S3302 D16S3060

D16S2853 D16S3286 D16S2803 D16S405 D16S3127

D16S3292

610kb

20q12

20q13.12

16p13.11 MYBL2

PTPRT

16q22.1 CBFB

D20S591E

D20S108

D20S858

D20S43

331kb

D20S150

139kb

174kb

100kb

D16S3308 D16S2584E D16S2846

D16S301 D16S324 D16S3339 D16S3323 606kb

100kb

CBFβ/MYH11 Translocation, Dual Fusion

Del(20q) Deletion

For more information please see individual product pages.

Multiprobe Haematology

HaematoPathology

Haematopathology

HaematoPathology

Contents 83

BCL2 Breakapart

BCL6 Breakapart

CCND1 Breakapart

IGH Breakapart

IGH/BCL2 Translocation, Dual Fusion

IGH/CCND1 Translocation, Dual Fusion

IGH/MALT1 Translocation, Dual Fusion

IGH/MYC Translocation, Dual Fusion

IGK Breakapart

IGL Breakapart

MYC Breakapart

P16 (CDKN2A) Deletion

P53 (TP53) Deletion

Haematopathology The assessment of genetic changes in tissue biopsies can provide important information for prediction of tumour progression. The majority of these changes are either amplifications, deletions or other chromosomal rearrangements that can be detected using FISH. Current methodologies, namely immunohistochemistry or Southern blotting can provide information at the gene expression level but, when carried out on tissue sections (either cryostat or paraffin embedded), FISH can provide information at the DNA level, in situ, at the precise site within the tumour. This can reveal cell-to-cell heterogeneity and enable the detection of small clones of genetically distinct cells. This analysis can be made even more efficient through the use of automated image analysis systems and software.

Cat. No. LPs 028-s

(5 tests)

Cat. No. LPs 028

(10 tests)

BCL2 Breakapart HaematoPathology

The B-cell CLL/Lymphoma 2 (BCL2) gene located at 18q21.33 encodes one of a large protein family that regulates and contributes to programmed cell death, or apoptosis, by controlling mitochondrial membrane permeability1. Translocations of the BCL2 gene result in constant expression of the BCL2 protein. BCL2 usually translocates to the immunoglobulin (IG) heavy chain (IGH) gene via a t(14;18)(q32;q21.3) and rarely to IG light chain (IGK or IGL) loci via t(2;18)(p11;q21.3) or t(18;22)(q21.3;q11)2. The translocation (t(14;18)(q32.33;q21.33)) is thought to be brought about by an error in the joining function of the IGH gene, mediated by the observation that both IGH and BCL2 are arranged next to each other in 3D space in normal B lymphocytes3. The translocation breakpoint at the end of the Joining (J) segment, and the subsequent fusion of the BCL2 gene to this region, results in the BCL2 gene coming under the regulatory control of those processes normally involved in maintenance of IGH gene activity4.

RefeRenCes 1. 2. 3. 4.

Sharpe et al., Biochim Biophys Acta. 2004;1644(2-3):107-13 Tomita N., J Clin Exp Hematop 2011;51(1):7-12 Roix et al., Nat Genet 2003;34(3):287-91 Stoos-VeiÄ&#x2021; et al., Coll Antropol. 2010 Jun;34(2):425-9

5. 6.

Barrans et al., Clin Cancer Res 2003; 9; 2133 Bassegio L et al., Br J Haematol 2012;158(4):489-98

The t(14;18) is observed in 70-95% of Follicular Lymphoma (FL) cases and 20-30% of Diffuse Large B-cell Lymphoma (DLBCL)2. Presence of the t(14;18) translocation in DLBCL is a predictor of outcome and has a poor prognostic effect5. BCL2 translocations have also been implicated in Chronic B-cell Lymphoproliverative Disease (CLPD) and occur frequently in Chronic Lymphocytic Leukaemia (CLL)6.

18q21.33-q22.1

BCL2

PHLPP1

RH123414

D18S91

161kb

D18S51

CLADE B SERPIN CLUSTER

KDSR VPS4B

D18S87

304kb

196kb

176kb

100kb

Cat. No. LPs 029-s

(5 tests)

Cat. No. LPs 029

(10 tests)

BCL6 Breakapart* Rearrangements of the BCL6 gene have been observed in 28.6-35.5% of Diffuse Large B-Cell Lymphoma (DLBCL) and in 6.4-14.3% of Follicular Lymphoma (FL)1. HaematoPathology

This translocation results in the dysregulation of BCL6 and may involve the IGH, IGK and IGL genes, although other non-Ig partner genes have also been identified2,3. BCL6 encodes a 95kD nuclear phosphoprotein belonging to the pox virus zinc finger (POZ)/zinc finger (ZF) family of transcription factors4. BCL6 functions as a transcriptional repressor and plays an important regulatory role in lymphoid cell development

RefeRenCes

and function. In the B-cell lineage, the BCL6 protein is expressed only

in germinal centre B cells5. Translocations involving band 3q27.3 affect

Ohno H et al., Leuk Lymphoma 1997;27: 53-63

Ueda C et al., Leuk Lymphoma 2002;43: 1375-81

a 4kb major breakpoint region of BCL6 in the first non-coding exon

Akasaka H et al., Cancer Res 2000; 60: 2335-41

Chang CC et al., PNAS 1996;93: 6947-52

and 5' region of the first intron, and are common in diffuse large B-cell

Cattoretti G et al., Blood 1995;85:45-53

Bosga-Bouwer AG et al., Genes Chrom Cancer

lymphomas. Recently, an alternative breakpoint cluster region located

2005;44: 301-304

between 245 and 285kb 5' of BCL6 was identified in Non-Hodgkin Lymphoma (NHL) and may be preferentially associated with follicular lymphoma6.

3q27.3-q28 BCL6 MASP1 RH16625

RTP2 SST SHGC-142900

366 kb

D3S4141

SHGC-110014

461 kb

165 kb 100kb

* A similar product is also available within the Haematology range, refer to page 23.

Cat. No. LPs 030-s

(5 tests)

Cat. No. LPs 030

(10 tests)

CCND1 Breakapart

Cyclins function as regulators of cyclin dependent kinases (CDKs). CCND1 forms a complex with, and functions as a regulatory subunit of, CDK4 or CDK8, whose activity is required for the G1/S transition through the cell cycle1. The translocation t(11;14)(q13;q32) between CCND1 and Immunoglobulin Heavy chain (IGH) has been described as the molecular hallmark for Mantle Cell Lymphoma (MCL)2,5, a subtype of B-cell non-Hodgkin Lymphoma, and results in overexpression of cyclin D1. This translocation is estimated to occur in 53-93% of MCL cases3 and has also been implicated in 10-25% of Multiple Myeloma patients with abnormal cytogenetics4.

HaematoPathology

The Cyclin D1 (CCND1) gene located at 11q13.3 encodes a protein that belongs to the highly conserved cyclin family. Mutations, amplifications and overexpression of this gene, which alters cell cycle progression, are observed frequently in a variety of tumours and may contribute to tumourigenesis1.

RefeRenCes 1.

RefSeq, Jul 2008

Vose JM, et al., Am J Hematol 2012;87(6):604-9

Rahman K et al., Indian J Pathol 2012;55:66-71

Hoyer JD et al., Am J Clin Pathol 2000;113(6):831-7

Avet-Loiseau et al., Genes Chromosomes Cancer. 1998; 23(2):175-82

11q13.3 CCND1 IGHMBP2 TPCN2 CPT1A

D11S1138

MYEOV

ORAOV1 FGF4 FGF19 FGF3

SHGC-154860

D11S1919 SHGC-146763

154kb

159kb

289kb

373kb

100kb

Cat. No. LPs 032-s

(5 tests)

Cat. No. LPs 032

(10 tests)

IGH Breakapart*

HaematoPathology

Rearrangements involving the IGH gene have been identified in numerous different tumour types. There are a number of stereotypical translocations involved in each of the diseases and more are being described regularly. The t(8;14)(q24;q32), involving IGH and the MYC gene, is the most common rearrangement in Burkitt's lymphoma and occurs in around 85% of cases1. IGH rearrangements have also been noted in 50% of non-Hodgkin B-cell lymphomas (NHLs) and have been correlated to clinically relevant subgroups2. One study showed that the t(14;18)(q32;q21) (IGH-BCL2) was found in 88.1% of follicular lymphomas and the t(11;14)(q13;q32) (IGH-CCND1) in 85.7% of mantle cell lymphomas2. IGH rearrangements were also identified in 52.5% of diffuse large B-cell lymphomas (DLBCL)1.

RefeRenCes 1.

Hoffman, Ronald (2009). Hematology : basic principles and practice (5th ed. ed.). Philadelphia, PA: Churchill Livingstone/Elsevier. pp. 1304â&#x20AC;&#x201C;1305 Bernicot et al., Cytogenet Genome Res. 2007;118(2-4):345-52

IGH is commonly rearranged in lymphomas and has many different translocation partners. We have, therefore, designed a split probe set for IGH, which allows the detection of rearrangements of the IGH gene, regardless of partner gene or chromosome involved.

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 D14S1007 IGHA1 IGHG2 IGHGP

D14S1420 D14S1419 D14S308

124kb

617kb 100kb

* A similar product is also available within the Haematology range, refer to page 41.

Cat. No. LPs 033-s

(5 tests)

Cat. No. LPs 033

(10 tests)

IGH/BCL2 Translocation, Dual Fusion*

The translocation is thought to be brought about by an error in the joining function of the IGH gene, mediated by the recent observation that both IGH and BCL2 are arranged next to each other in 3D space in the normal B lymphocytes2. The translocation breakpoint at the end of the Joining (J) segment, and the subsequent fusion of the BCL2 gene to this region, results in the BCL2 gene coming under the regulatory control of those processes normally involved in maintenance of IGH gene activity3. The BCL2 gene itself has been shown to be involved in the regulation of apoptosis4.

HaematoPathology

The IGH/BCL2 fusion gene is brought about by a t(14;18)(q32;q21) translocation and is found in over 88% of follicular lymphoma cases1,2.

RefeRenCes 1.

Bernicot et al., Cytogenet Genome Res.

2007;118(2-4):345-52 Roix et al., Nature Genetics 2003;34(3):287-91

Stoos-VeiÄ&#x2021; et al., Coll Antropol. 2010 Jun;34(2):425-9

Sharpe et al., Biochim Biophys Acta. 20041644(2-3):107-13

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHG3 D14S1007 IGHE IGHG4 IGHG1 IGHA1 IGHG2 IGHGP 124kb

D14S1420 D14S1419 D14S308

168kb

617kb 100kb

18q21.33-q22.1

BCL2

PHLPP1

RH123414

D18S91

161kb

196kb

D18S51

CLADE B SERPIN CLUSTER

KDSR VPS4B D18S87

304kb

176kb

100kb

* A similar product is also available within the Haematology range, refer to page 42.

Cat. No. LPs 031-s

(5 tests)

Cat. No. LPs 031

(10 tests)

IGH/CCND1 Translocation, Dual Fusion* HaematoPathology

Although translocations involving IGH and CCND1 (BCL1) were initially reported in B-CLL patients, the rearrangement is now considered to be a hallmark of mantle cell lymphoma (MCL). Reciprocal translocations involving the IGH and CCND1 (previously known as BCL1) loci, t(11;14)(q13;q32), were frequently reported in B-CLL patients1. The involvement of the CCND1 (Cyclin D1) gene was initially reported from a cloning study looking at the breakpoints of the translocation. However, it is likely that the initial diagnosis on the samples used for the study should have been MCL. The IGH/CCND1 probe for detection of t(11;14) has been recommended by the British Committee for Standards in Haematology to enable atypical B-CLL patients to be distinguished from possible MCL patients2.

RefeRenCes 1.

Brizard et al., Leuk Lymphoma 1997;25(5-6):539-43

Parker et al., Best Practice in Lymphoma Diagnosis and Reporting; Specific disease appendix 2010, p5

14q32.33

Constant Segment D14S1007

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP 124kb

D14S1420 D14S1419 D14S308

168kb

617kb 100kb

11q13.3 CCND1 ORAOV1 FGF19 FGF4 FGF3

MYEOV

D11S1100

D11S2927 D11S4381

D11S4095

223kb

267kb 100kb

* A similar product is also available within the Haematology range, refer to page 43.

Cat. No. LPs 034-s

(5 tests)

Cat. No. LPs 034

(10 tests)

IGH/MALT1 Translocation, Dual Fusion

Extranodal marginal zone B-cell lymphoma of the mucosa-associated lymphoid tissue is listed as a distinct clinicopathologic entity. MALT lymphomas comprise 7.6% of all non-Hodgkin lymphoma's (NHLs) and represents 1 of the 6 most common NHLs2. MALT lymphomas are characterised by a proliferation of neoplastic marginal zone-related cells that invade the epithelial structures to generate lymphoepithelial lesions and colonise reactive lymphoid follicles3. t(14;18)/IGH-MALT1positive MALT lymphomas originate in sites such as the liver, skin, ocular adnexa, or salivary glands1. The molecular characteristics of the t(14;18) resemble those found in the t(14;18)/IGH-BCL2 (follicular lymphoma) and t(11;14)/MALT1-IGH (mantle cell lymphoma), suggesting that these translocations could be generated by common pathomechanisms involving illegitimate V(D)J-mediated recombination of IGH as well as non-homologous end joining (NHEJ) or alternative NHEJ repair pathways1.

HaematoPathology

The t(14;18)(q32;q21) involving the Immunoglobulin heavy chain locus (IGH) at 14q32 and the Mucosa Associated Lymphoid Tissue Lymphoma Translocation gene 1 (MALT1) at 18q21 is a recurrent abnormality in MALT lymphoma1.

RefeRenCes 1.

Murga Penas EM et al., Blood 2010;115(11):2214-9

Streubel B et al., Blood 2003;101:2335-2339

Bacon et al., J Clin Pathol 2007;60:361â&#x20AC;&#x201C;372

14q32.33

Constant Segment

Variable Segment

IGHA2 IGHM IGHG3 D14S1007 IGHE IGHG4 IGHG1 IGHA1 IGHG2 IGHGP 124kb

D14S1420 D14S1419 D14S308

168kb

617kb 100kb

18q21.31-q21.32 MALT1 NEDD4L D18S887

ALPK2

GRP

D18S881

D18S1117

D18S1333 171kb

OACYLP ZNF532 SEC11C

D18S531 D18S1265

D18S1129 132kb

228kb

306kb

100kb

Cat. No. LPs 035-s

(5 tests)

Cat. No. LPs 035

(10 tests)

IGH/MYC Translocation, Dual Fusion* HaematoPathology

The cMYC/IGH translocation, t(8;14)(q24;q32), and the variant forms t(2;8)(p13;q24) and t(8;22)(q24;q11) are found in Burkitt's lymphoma and mature B-cell or Burkitt's type Acute Lymphoblastic Leukaemia (ALL)1. The t(8;14) is the most common and is found in approximately 85% of patients with Burkitt's lymphoma2. While translocation breakpoints on chromosome 14 are clustered to a narrow region 5' to the intron enhancer of the immunoglobulin heavy chain, the breakpoints on chromosome 8 can occur more than 340kb upstream of MYC, with no preferential site3. The translocation brings MYC into close proximity to the IgH enhancer and results in the up-regulation of MYC4. Over expression of the transcription factor stimulates gene amplification resulting in uncontrolled cell proliferation, which usually occurs in the late event of tumour progression5.

RefeRenCes 1. 2.

3. 4. 5.

Berger R, Bernheim A, Cancer Genet Cytogenet 1982;7(3):231-44 Hoffman, Ronald (2009). Hematology : basic principles and practice (5th ed. ed.). Philadelphia, PA: Churchill Living stone/Elsevier. pp. 1304â&#x20AC;&#x201C;1305 Joos et al., Human Molecular Genetics 1992;1(8):625-32 Erikson J et al., Proc Natl Acad Sci USA 1983;80(3):820-4 Shou et al., PNAS 2000;97(1):228-33

14q32.33

Constant Segment D14S1007

Variable Segment

IGHA2 IGHM IGHE IGHG3 IGHG4 IGHG1 IGHA1 IGHG2 IGHGP 124kb

D14S1420 D14S1419 D14S308

168kb

617kb 100kb

8q24.21

CASC8

MYC PVT1

POU5F1B D8S1153

197kb

277kb

D8S1980

100kb

D8S1644

186kb

D8S1017

297kb

* A similar product is also available within the Haematology range, refer to page 45.

Cat. No. LPs 038-s

(5 tests)

Cat. No. LPs 038

(10 tests)

IGK Breakapart* Translocations involving the immunoglobulin loci are recurring events in various subtypes of B-cell lymphomas.

Translocations involving the IG light chain loci usually lead to breakage within the joining region of the respective locus2. IGK has a largely duplicated structure with duplicate gene regions being 96-100% identical. The IGK proximal copy is present in a 542kb contig with 22 potentially functional variable (IGKV) gene segments and 18 pseudogenes plus five joining (J)- segments and one IGK constant (IGKC) gene segment. The distal copy is a 433kb contig with 21 potentially functional IGKV gene segments and 15 pseudogenes. The two contigs are separated by a DNA sequence of 800kb without any IGKV segments1.

HaematoPathology

RefeRenCes 1. 2. 3. 4. 5.

2p11.2 IGK Variable Regions CJ D2S2216 D2S2610

Proximal

Distal D21S1241

D2S1994 D2S2510

606kb

183kb 100kb

* A similar product is also available within the Haematology range, refer to page 50.

Cat. No. LPs 039-s

(5 tests)

Cat. No. LPs 039

(10 tests)

IGL Breakapart* Translocations involving the immunoglobulin loci are recurring events in various subtypes of B-cell lymphomas.

HaematoPathology

In addition to translocations involving the IGH locus, variant translocations have been described in 5-10% of B-cell neoplasms involving either the immunoglobulin kappa (IGK) light chain locus at 2p11.2 or the lambda light chain (IGL) at 22q111,2. The best known translocations involving IG light chain loci are the variant Burkitt's translocations t(2;8)(p12;q24) and t(8;22)(q24;q11) present in up to 21% of all Burkitt's lymphomas3. Other translocations involve the BCL6 oncogene, the t(2;3)(p12;q27) and t(3;22)(q27;q11) and BCL2 locus, t(2;18)(p12;q21) and t(18;22)(q21;q11)4,5. Translocations involving the IG light chain loci usually lead to breakage within the joining region of the respective locus2. IGL consists of 38 potentially active variable (IGLV) gene segments, 35 pseudogenes and seven IGL constant gene segments, each with a joining (J)-segment IGL (J-C)1.

RefeRenCes 1. 2. 3. 4. 5.

22q11.21-q11.23

IGLV

MAPK1

IGLC

BCR

D22S446 D22S1264 D22S1003E

307kb

278kb 100kb

* A similar product is also available within the Haematology range, refer to page 51.

Cat. No. LPs 027-s

(5 tests)

Cat. No. LPs 027

(10 tests)

MYC Breakapart*

The majority of rearrangements result in the juxtaposition of MYC to IGH, IGL or IGK in the t(8;14), t(8;22) or t(2;8) respectively. In each case, this results in dysregulation of MYC (as a result of being close to the constitutively active immunoglobulin locus), increased transcription and neoplastic growth2. The breakpoints involved are widely scattered throughout the gene but the t(8;14) translocation always spares the protein coding exons which become attached to the derived 14. In the t(2;8) and t(8;22), MYC remains on chromosome 8 and the immunoglobulin locus joins it, resulting in close positioning of the MYC and immunoglobulin loci. Rare cases of translocations not involving immunoglobulin partners have also been reported3.

HaematoPathology

Translocations involving the MYC (cMYC) oncogene (Avian Myelocytomatosis Viral Oncogene Homologue) are a molecular feature of Burkitt lymphoma and occur in almost every case. These rearrangements can also be found in 5 to 10% of diffuse large B-cell lymphoma (DLBCL)1.

RefeRenCes 1.

Savage et al., Blood. 2009 Oct 22;114(17):3533-7

Robertson. Nature. 1983 Apr 7;302(5908):474-5

Seo et al., Ann Lab Med. 2012 Jul;32(4):289-93

Hoelzer et al., Blood. 1996 Jan 15;87(2):495-508

8q24.21 MYC

CASC8 POU5F1B D8S1153

396kb

PVT1

GSDMC D8S1207

D8S1980

100kb

D8S1732

148kb 297kb

* A similar product is also available within the Haematology range, refer to page 28.

Cat. No. LPs 036-s

(5 tests)

Cat. No. LPs 036

(10 tests)

P16 (CDKN2A) Deletion*

HaematoPathology

Diffuse large B-cell lymphoma (DLBCL) is the most frequent form of aggressive lymphoma and deletions of the P16 (now known as CDKN2A) locus occur in approximately one-third of DLBCL patients1. The CDKN2A gene encodes a cyclin dependent kinase inhibitor that functions in the control of phosphorylation of Retinoblastoma (RB), a protein that is frequently hypermethylated in lymphomas2. There are two proteins produced by the CDKN2A gene, P16 and P14ARF, the latter being an alternate reading frame product. These protein products have been linked to two tumour suppressor pathways, the RB pathway and the p53 pathway. P16 inhibits phosphorylation of RB, whereas P14ARF targets MDM2, a P53 inhibitory protein, for degradation. A deletion of the CDKN2A gene would therefore disturb both pathways3.

RefeRenCes 1.

Guney et al., Genes Chromosomes Cancer.

2012 Sep;51(9):858-67 Chim et al., Hum Pathol. 2007 Dec;38(12):1849-57

MĂ¸ller et al., Leukemia. 1999 Mar;13(3):453-9

Jardin et al., Blood. 2010 Aug 19;116(7):1092-104

Losses of CDKN2A are significantly associated with a shorter survival after treatment4.

D9Z3

9p21.3

P16 (CDKN2A) CDKN2B D9S2060 D9S974

D9S1605 D9S1604 D9S1748

193kb

100kb

* A similar product is also available within the Haematology range, refer to page 57.

Cat. No. LPs 037-s

(5 tests)

Cat. No. LPs 037

(10 tests)

P53 (TP53) Deletion*

Knowledge of the P53 deletion status in the patient should mediate the choice of therapy3. P53 is a tumour suppressor gene and its protein product is responsible for the death of cells that contain damaged DNA. This is thought to be brought about by phosphorylation of P53 and the subsequent prevention of its repression by MDM2 (Mouse Double Minute 2 Homolog). This phosphorylation is mediated by ATM. In the absence of P53 activity, cells that cannot be repaired by ATM will continue to proliferate in their damaged state. Patients deleted for P53 may be rendered resistant to alkylating chemotherapeutic agents3 and purine analogues4 as these are designed to damage DNA in the cells that P53 would have destroyed. In the absence of P53, therefore, patients treated with these agents will harbour a proliferating population of damaged cells.

HaematoPathology

Although previously difficult to detect, the advent of FISH analysis of interphase cells from patients with B-CLL showed that around 17% of patients with the disease have deletions of the P53 (TP53) gene1. As with ATM, deletions of P53 have important therapeutic implications for patients with B-CLL2.

RefeRenCes 1. 2. 3. 4.

Dรถhner et al., J Mol Med 1999;77:266-81 Foรก et al., Haematol 2013; 98(5):675-685 Sturm et al., Cell Death Differ. 2003 Apr;10(4):477-84 Dรถhner et al., Blood. 1995 Mar 15;85(6):1580-9

D17Z1

17p13.1 P53 (TP53) SHBG ATP1B2

WRAP53 EFNB3

D17S1678

D17S1353 D17S655

159kb 100kb

* A similar product is also available within the Haematology range, refer to page 58.

HaematoPathology

Pathology

Contents 99

Tissue Pretreatment Kit

100

ALK Breakapart

101

CHOP (DDIT3) Breakapart

102

C-MET (MET) Amplification

103

EGFR Amplification

104

EML4 Breakapart

105

EWSR1 Breakapart

106

EWSR1/ERG Translocation, Dual Fusion

107

FLI1/EWSR1 Translocation, Dual Fusion

108

FGFR1 Breakapart/Amplification

109

HER2 (ERBB2) Amplification

110

MALT1 Breakapart

111

MDM2 Amplification

112

N-MYC (MYCN) Amplification

113

PAX3 and PAX7 Breakapart

114

RB1 Deletion

115

ROS1 Breakapart

116

SRD (CHD5) Deletion

117

SYT (SS18) Breakapart

118

TMPRSS2/ERG Deletion/Breakapart

119

TOP2A Amplification/Deletion

120

ZNF217 Amplification

Pathology The assessment of genetic changes in tissue biopsies can provide important information for prediction of tumour progression. The majority of these changes are either amplifications, deletions or other chromosomal rearrangements that can be detected using FISH. Current methodologies, namely immunohistochemistry or Southern blotting, can provide information at the gene expression level but, when carried out on tissue sections (either cryostat or paraffin embedded), FISH can provide information at the DNA level, in situ, at the precise site within the tumour. This can reveal cell-to-cell heterogeneity and enable the detection of small clones of genetically distinct cells. This analysis can be made even more efficient through the use of automated image analysis systems and software.

Cat. No. LPs 100

Tissue Pretreatment Kit Introducing the first Pretreatment kit capable of preparing slides for CISH and/or FISH analysis on Formalin-Fixed, Paraffin-Embedded (FFPE) tissue.

Pathology

Our ready-to-use Tissue Pretreatment Kit has been optimised to produce excellent visual results with our extensive Aquarius速 Pathology FISH range. To further extend the utility of the kit we have also validated its use with other commercially available CISH (Chromogenic In Situ Hybridisation) and FISH (Fluorescence In Situ Hybridisation) DNA probes*. With ease-of-use and convenience in mind, our simple two stage FFPE slide preparation protocol employs the use of ready-to-use reagents; which have been optimised to increase the permeabilisation of cell membranes and facilitate penetration of the desired FISH or CISH DNA probe.

Product Information

Kit Components

Aquarius速 Tissue Pretreatment Kit**

Reagent 1 (1x1L) Reagent 2 (1x10mL)

*A list of manufacturers is available upon request. **This product is provided under an agreement between Life Technologies Corporation and Cytocell Ltd and is available for life science use only.

Cat. No. LPs 019-s

(5 tests)

Cat. No. LPs 019

(10 tests)

ALK Breakapart Transforming rearrangements of the Anaplastic Lymphoma Receptor Tyrosine Kinase (ALK) gene at 2p23 have been recognised in a subset of human haematological and solid malignancies1.

Pathology

ALK fuses with Nucleophosmin (NPM1) in anaplastic lymphoma, resulting in constitutive kinase activity, which inhibits apoptosis and promotes cellular proliferation2. The rearrangement of ALK has now also been implicated in the development of Non-Small Cell Lung Cancer (NSCLC) as a result of an inversion involving chromosome 2, inv(2)(p21p23), causing ALK to fuse with the EML4 gene2. The ALK gene is frequently involved in translocations of chromosome 2 that lead to gene fusions in a variety of different malignancies, including neuroblastomas and myofibroblastic tumours3.

RefeRenCes 1. 2. 3.

Marileila Varella-Garcia et al., Association of molecular pathology: Solid Tumour Review. 2010 Takeuchi K et al., Clin Cancer Res. 2008;14(20):6618-6624 Lin et al., Mol Cancer Res. 2009;7(9):1466-1476

2p23.2-p23.1 SPDYA FAM179A CLIP4 PPP1CB WDR43

D2S2312

TRMT61B

D2S2383

D2S2934 D2S405

420kb

486kb 100kb

100

ALK

Cat. No. LPs 015-s

(5 tests)

Cat. No. LPs 015

(10 tests)

CHOP (DDIT3) Breakapart Myxoid liposarcoma (MLS) is the most common subtype of liposarcoma1. The TLS-CHOP (FUS-DDIT3) t(12;16)(q13.3;p11) fusion gene, firstly described by Turc-Carel et al. in 19862, is now well established and is present in at least 95% of MLS3. In rare cases, an EWS-CHOP (EWSR1-DDIT3) t(12;22)(q13;q12) translocation has been described4. The transcription factor gene, CHOP (DDIT3) (CREBP-homologous protein/DNA damage inducible transcript 3), is a negative regulator of adipocyte differentiation5. RefeRenCes 1.

Enzinger and Weiss, Soft Tissue Tumors 3rd Ed. St Louis; MO:Mosby, 1995 Turc-Carel et al., Can Genet Cytogenet 1986;23:291-9 Mitelman, Catalog of chromosome aberrations in cancer. 5th Ed. 1995 New York: WileyLiss, Inc. 1994

2. 3. 4. 5. 6. 7.

Antonescu et al., Clin Canc Res 2001;7:3977-87 Hunag et al., Biol Open. 2012 Aug 15;1(8):705-10 Crozat et al., Nature 1993;363:640-4 Rabbitts et al., Nat Genet 1993;4:175-80

12q13.3

CHOP (DDIT3) R3HDM2 D12S1266

ARHGAP9 MARS GLI1

D12S1934

DCTN2 MBD6

D12S1943

Pathology

The TLS (Translocated in Liposarcoma)6 or FUS7 gene is a nuclear RNA-binding protein with extensive sequence similarity to EWS. The TLS-CHOP protein interferes with adipocyte differentiation and favours proliferation over terminal differentiation4.

KIF5A

D12S2159 D12S1889

D12S1969

145kb

146kb 100kb

101

Cat. No. LPs 004-s

(5 tests)

Cat. No. LPs 004

(10 tests)

C-MET (MET) Amplification The C-MET (MET - Mesenchymal-Epithelial Transition factor) encodes a transmembrane tyrosine kinase1, which is an oncoprotein. The MET gene regulates both cell motility and cell growth2, so normal C-MET expression allows stem cells and progenitor cells to grow invasively. This invasive growth is required to generate new tissues in an embryo, or in an adult in regenerating tissue, such as the liver, or during wound repair3.

Pathology

MET has been shown to be overexpressed in many tumours including ovarian4, breast5, lung6, thyroid7, stomach8, pancreatic9,10 and colon11,12. This overexpression correlates with a poor prognosis4,13,14. In breast cancers, MET was only shown to be co-expressed with HER2 (ERBB2) in 50% of patients, indicating that it has a significant impact on tumour aggressiveness independently of HER213.

RefeRenCes 1. 2. 3. 4.

Dean M et al., Nature 1985;318:385-8 Gherardi E, Stoker M, Cancer Cells 1991;3(6):227-32 Boccaccio C, Comoglio PM, Nat Rev Cancer 2006;6(8):637-45 Sawada K et al., Cancer Res 2007;67(4):1670-9

5. 6. 7. 8. 9. 10. 11. 12. 13. 14.

Carracedo A et al., Breast Cancer Res 2009;11(2):402 Zucali PA et al., Ann Oncol 2008;19(9):1605-12 Di Renzo MF et al., Oncogene 1992;7:2549-53 Kuniyasu H et al., Int J Cancer 1993;55(1):72-5 Ebert M et al., Cancer Res 1994;54:5775-8 Di Renzo MF et al., Cancer Res 1995;55:1129-38 Liu C et al., Oncogene 1992;7(1):181-5 Di Renzo MF et al., Clin Cancer Res 1995;1:147-54 Miyamoto et al., Br J Cancer. 2011 Jun 28;105(1):131-8 Lengyel E et al., Int J Canc 2005;113:678-82

D7Z1

7q31.2

MET D7S1402

D7S2877

CAPZA2 D7S2460 D7S1764 D7S2863

278kb 100kb

102

D7S1599

Cat. No. LPs 003-s

(5 tests)

Cat. No. LPs 003

(10 tests)

EGFR Amplification The EGFR (previously known as HER1), Epidermal Growth Factor Receptor, gene on chromosome band 7p11.2, is a type 1 tyrosine kinase receptor for members of the epidermal growth factor family. Binding of the EGFR and epidermal growth factor proteins leads to cell proliferation1.

There are three small molecule EGFR kinase inhibitor drugs in clinical use (gefitinib, erlotinib and lapatinib) and several others that are currently undergoing clinical development4. Approximately 10% of lung cancer patients show a rapid and dramatic response to these Tyrosine Kinase Inhibitors (TKIs)5,6. FISH has proven to be useful for determining the amplification status of EGFR in NSCLC and has therefore aided in the selection of patients for treatment with EGFR TKIs7.

Pathology

Abnormally elevated EGFR kinase activity can lead to proliferative diseases such as non-small-cell lung carcinoma (NSCLC), which accounts for 80-85% of all lung cancers2, and less frequently breast cancer3, amongst others. RefeRenCes 1.

Voldborg et al., Annals of Oncology 8: 1197-1206,1997

Jemal A et al., CA Cancer J Clin 2006;56:106-30

Bhargava R et al., Modern Path 2005;18:1027-33

Hegymegi-Barakonyi B, Curr Opin Mol Ther

2009;11(3):308-21 Lynch TJ et al., N E J Med 2004;350:2129-39

Pao W et al., Proc Natl Acad Sci USA

2004;101(36):13306-11 Hirsch FR et al., JCO 2008;26(20): 3351-7

D7Z1

7p11.2

EGFR D7S793

D7S2357

D7S1988

D7S2935

295kb 100kb

103

Cat. No. LPs 020-s

(5 tests)

Cat. No. LPs 020

(10 tests)

EML4 Breakapart The protein encoded by the Echinoderm Microtubule Associated Protein-like 4 (EML4) gene is involved in microtubule formation and stabilisation1. A novel gene fusion of EML4 and Anaplastic Lymphoma Kinase (ALK) was recently identified in Non-Small Cell Lung Cancer (NSCLC). The EML4-ALK fusion was shown to result from an inversion within chromosome 2p, inv(2)(p21p23), and was detected in approximately 7% of NSCLC cases2,3. Pathology

RefeRenCes 1. 2. 3.

Xuchao Zhang et al., Mol Cancer Res 2010;9:188 Lin et al., Mol Cancer Res 2009;7(9):1466-1476 Martelli et al., AJP 2009;174(2):661-670

2p21

C2orf91 SHGC-106023

PKDCC

EML4 RH120737

MTA3

D2S2306

RH94235

406kb

353kb 100kb

104

KCNG3

Cat. No. LPs 006-s

(5 tests)

Cat. No. LPs 006

(10 tests)

EWSR1 Breakapart Ewing's sarcoma (EWS) is the second most frequent primary bone cancer in patients under 20 years of age1.

RefeRenCes

EWSR1 is also involved in translocations in desmoplasmic small round cell tumours, a subset of angiomatoid fibrous histocytomas, and possibly in myxoid liposarcoma4,5.

1. 2.

The EWSR1 breakapart probe can also be used to distinguish rare soft tissue sarcoma, a clear cell sarcoma, from malignant myeloma, a distinction that is difficult to make via either histology or immunohistology. The EWS-ATF1 (Activating Transcription Factor 1) translocation, t(12;22) (q13;q12), has been identified in 70-90% of clear cell sarcoma yet has not been observed in malignant myeloma6. This translocation can be detected using the EWSR1 breakapart probe.

3. 4.

Sandberg AA, Bridge JA, Cancer Genet Cytogenet

2000;123(1):1-26 Patel RM et al., Modern Path 2005;18:1585-90

Bridge RS et al., Modern Path 2006;19:1-8

FISH has been shown to be a more sensitive and reliable method than RT-PCR for the diagnosis of EWS in solid tissues7.

22q12.1-q12.2 EWSR1 KREMEN1 RH47619

EMID1 AP1B1 D22S991E RASL10A D22S448

392kb

NEFH RFPL1 THOC5

D22S590

NF2

ZMAT5

NIPSNAP1

MTMR3 ASCC2

D22S973E

631kb 100kb

105

Pathology

Cat. No. LPs 008-s

(5 tests)

Cat. No. LPs 008

(10 tests)

EWSR1/ERG Translocation, Dual Fusion Ewing's sarcoma (EWS) is the second most frequent primary bone cancer in patients under 20 years of age1.

Pathology

It is mainly characterised by a translocation between the two genes - EWSR1 (Ewing's Sarcoma Region 1) and FLI1 (Friend Leukaemia virus Integration 1) - in the t(11;22)(q24;q12) translocation, found in 83% of such tumours2. 10% of the remaining cases have a variant translocation involving EWSR1 and ERG, t(21;22)(q22;q12), and less than 1% carry one of the 7p22 (ETV1), 17q12 (E1AF) or 2q36 (FEV) translocations with EWSR13. EWSR1 is also involved in translocations in desmoplasmic small round cell tumours, a subset of angiomatoid fibrous histocytomas, and possibly in myxoid liposarcoma4,5. The EWSR1 breakapart probe can also be used to distinguish rare soft tissue sarcoma, a clear cell sarcoma, from malignant myeloma, a distinction that is difficult to make via either histology or immunohistology. The EWS-ATF1 (Activating Transcription Factor 1) translocation, t(12;22) (q13;q12), has been identified in 70-90% of clear cell sarcoma yet has not been observed in malignant myeloma6. This translocation can be detected using the EWSR1 breakapart probe. FISH has been shown to be a more sensitive and reliable method than RT-PCR for the diagnosis of EWS in solid tissues7.

22q12.1-q12.2 EWSR1 EMID1 AP1B1 D22S991E RASL10A D22S448

NEFH RFPL1 THOC5 D22S590

139kb

NIPSNAP1

151kb 100kb

21q22.13-q22.2

ERG

KCNJ15 D21S339

D21S1809 D21S338

215kb

D21S1836

D21S1959 D21S1956

154kb 100kb

106

ETS2

RefeRenCes 1. 2. 3. 4. 5. 6. 7.

Bernstein M et al., Oncologist 2006;11(5):503-19 Turc-Carel C et al., Cancer Genet Cytogenet 1988;32:229-38 Suรกrez Antelo et al., Arch Bronconeumol. 2010;46(01):44-6 Borden EC et al., Clin Canc Res 2003;9:1941-56 Sandberg AA, Bridge JA, Cancer Genet Cytogenet 2000;123(1):1-26 Patel RM et al., Modern Path 2005;18:1585-90 Bridge RS et al., Modern Path 2006;19:1-8

Cat. No. LPs 007-s

(5 tests)

Cat. No. LPs 007

(10 tests)

FLI1/EWSR1 Translocation, Dual Fusion Ewing's sarcoma (EWS) is the second most frequent primary bone cancer in patients under 20 years of age1.

EWSR1 is also involved in translocations in desmoplasmic small round cell tumours, a subset of angiomatoid fibrous histocytomas, and possibly in myxoid liposarcoma4,5. The EWSR1 breakapart probe can also be used to distinguish rare soft tissue sarcoma, a clear cell sarcoma, from malignant myeloma, a distinction that is difficult to make via either histology or immunohistology. The EWS-ATF1 (Activating Transcription Factor 1) translocation, t(12;22) (q13;q12), has been identified in 70-90% of clear cell sarcoma yet has not been observed in malignant myeloma6. This translocation can be detected using the EWSR1 breakapart probe.

Pathology

RefeRenCes 1. 2. 3. 4. 5. 6. 7.

FISH has been shown to be a more sensitive and reliable method than RT-PCR for the diagnosis of EWS in solid tissues7.

11q24.3

FLI1

ETS1 D11S4369 D11S1017

KCNJ1

D11S912 D11S3491 D11S3463 D11S4123 D11S4150

94kb

79kb

100kb

22q12.1-q12.2 EWSR1 EMID1 AP1B1 D22S991E RASL10A D22S448

139kb

100kb

NEFH RFPL1 THOC5

D22S590

NIPSNAP1

151kb

107

Cat. No. LPs 018-s

(5 tests)

Cat. No. LPs 018

(10 tests)

FGFR1 Breakapart/Amplification Fibroblast Growth Factor Receptor 1 (FGFR1), located on chromosome 8, was the first gene to be shown to be amplified in some breast cancers1 and is also translocated in some patients with 8p11 myeloproliferative syndrome2.

Pathology

Amplification of the gene is thought to be the causative factor in around 10% of breast tumours3 and has been shown to provide a poor prognosis to patients as over-expression of the gene product can lead to early relapse4. In common with other genetic defects in lymphoproliferative disorders, like the BCR/ABL translocation in CML, the FGFR1 gene contains sequences that could code for a putative tyrosine kinase protein5,6, which has been implicated in myeloproliferative syndrome (also known as EMS or Stem cell leukaemia/lymphoma syndrome, SCLL), marking out the importance of this gene in both solid tumours and cancers of the blood. There are at least eight partner genes involved with FGFR1 translocations, including ZNF198 (the most common7), FOP, CEP110, BCR, HERV-K, FGFR10P2, TIF1 and MYO18A8. Cytocell has developed a three-colour combined breakapart and amplification FISH probe for FGFR1 that can be used in either bone marrow samples from myeloproliferative syndrome (EMS) patients or tissue sections from patients where gene amplification may be suspected. In EMS, the breakapart strategy will show the split of one of the two fusion signals along with a blue centromere to enumerate chromosome 8. In patients that are being tested for amplifications of FGFR1, the non-translocated FGFR1 FISH probe will appear as a fusion signal and this will appear amplified. The chromosome 8 centromere probe will also act as a control probe in these cases.

D8Z2

8p11.23-p11.22

DDHD2

LETM2 WHSC1L1 FGFR1

PPAPDC1B

D8S135

D8S389

267kb

272kb 100kb

108

D8S2317

RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8.

Theillet et al., Genes Chromosomes Cancer 1993;7:219-26 Macdonald et al., Leukemia 1995;9:1628-30 Courjal F et al., Cancer Res 1997;57(19):4360-7 Turner N et al., Cancer Res 2010;70(5):2085-94 Ruta M et al., Oncogene 1988;3:9-15 Smedley et al., Hum Mol Genet 1998;7(4):637-42 Xiao et al., Nature Genet 1998;18:84-7 Huret JL. FGFR1 (Fibroblast Growth Factor Receptor 1). Atlas Genet Cytogenet Oncol Haematol. December 2008

Cat. No. LPs 001-s

(5 tests)

Cat. No. LPs 001

(10 tests)

HER2 (ERBB2) Amplification The HER2 (ERBB2) Human Epidermal growth factor Receptor 2 gene, located at chromosome band 17q12, is a member of the Epidermal Growth Factor (EGF) receptor family1. It is activated and amplified in 20-30% of breast cancers2 and has been correlated with a poor prognosis for the patient3. Treatment of patients carrying the amplification using the monoclonal antibody RefeRenCes

survival time by specifically targeting cells overexpressing HER24 and

removing them from the system.

2. 3.

Similar results have been obtained for a variety of other malignant

Pathology

Herceptin庐 (Trastuzumab) has been shown to be effective, increasing

Coussens L, Yang-Feng TL et al., Science 1985;230(4730):1132-9 Slamon DJ et al., Science 1987;235(4785):177-82 L贸pez-Guerrero JA et al., Int J Cancer. 2006 Apr 1;118(7):1743-9

neoplasms overexpressing HER2 including ovarian5, stomach6,

salivary gland7 and small cell lung8 cancers.

Slamon DJ et al., Science 1989;244(4905):707-12

Gravalos C, Jimeno A, Ann Oncol 2008;19(9):1523-9

Kauraniemi P et al., Oncogene 2004;23(4):1010-3

Vidal L et al., Head Neck 2009;31(8):1006-12

Ugocsai et al., Anticancer Res. 2005;25(4):3061-6

D17Z1

17q12

PPP1R1B

STARD3 PGAP3

HER2 (ERBB2) GRB7 D17S754 D17S2147

IKZF3 D17S1215

347kb 100kb

109

Cat. No. LPs 017-s

(5 tests)

Cat. No. LPs 017

(10 tests)

MALT1 Breakapart Extranodal marginal zone B-cell lymphoma (MZBCL) of the Mucosa-Associated Lymphoid Tissue (MALT) type is characterised by two main translocations involving MALT1; t(11;18)(q21;q21.32) and t(14;18)(q32;q21.32)1. Other MALT1 associated translocations are rare1.

Pathology

However, there are no MALT1 translocations in nodal or splenic lymphomas1. The t(11;18) BIRC3 (Baculoviral IAP repeat containing 3 protein2,3)/MALT1 translocation is present in 18-33% of cases of MALT lymphoma2 and the resulting fusion protein induces NF-ÎşB (nuclear factor kappa-light-chain-enhancer of activated B-cells), resulting in transcriptional activation3. 18% of MALT lymphomas harbour the t(14;18) MALT1/IGH translocation4. The genetic abnormalities in MALT lymphomas reflect their site of origin. The t(14;18) translocation was most frequently found in MALT1 lymphomas of the parotid gland, liver, skin, and ocular adnexa - sites rare for the t(11;18). However, the pulmonary and gastrointestinal MALT lymphomas show high frequencies of t(11;18) and absence of the t(14;18)1,4.

RefeRenCes 1. 2. 3. 4.

18q21.31-q21.32 MALT1 NEDD4L

ALPK2

D18S881 D18S887 D18S1333

171kb

OACYLP ZNF532 SEC11C GRP

D18S531 D18S1265 D18S1117 D18S1129

228kb

132kb 100kb

110

306kb

Murga PEM et al., Leukemia 2003;17(11):2225-9 Auer IA et al., Ann Oncol 1997;8(10):979-85 Lucas PC et al., J Biol Chem 2001;276(22):19012-9 Streubel B et al., Blood 2003;101(6):2335-9

Cat. No. LPs 016-s

(5 tests)

Cat. No. LPs 016

(10 tests)

MDM2 Amplification The MDM2 gene, located at 12q15, when overexpressed, enhances the tumourigenic potential of cells. The oncogene product forms a tight complex with the p53 tumour suppressor protein and can inhibit p53 mediated transactivation, leading to escape from p53 regulated growth control1. The Murine Double Minute 2 (MDM2) gene has been shown to be amplified in around 7% of human tumours2.

Pathology

Many tumours overexpress MDM2, the most common being soft tissue tumours (20%), osteosarcomas (16%) and oesophageal carcinomas (13%)3. The use of FISH in well differentiated liposarcoma has been a valuable diagnostic tool4,5, whilst small-molecule MDM2 inhibitors that could act as innovative therapeutic tools have also been identified6.

RefeRenCes 1.

Momanad J et al., Cell 1992;69(7):1237-45

Forslund et al., Mol Cancer Res. 2008 Feb;6(2):205-11

Momand J, Nuc Acid Res 1998;26(15):3453-9

Weaver J et al., Modern Path 2008;21(8):943-9

Sirvent N et al., Am J Surg Pathol 2007;31(10):1476-98

Vassilev LT, Trends Mol Med 2007;13(1):23-31

D12Z1

12q15

MDM2 NUP107

CPM D12S1501

146kb 100kb

111

Cat. No. LPs 009-s

(5 tests)

Cat. No. LPs 009

(10 tests)

N-MYC (MYCN) Amplification The proto-oncogene N-MYC (MYCN), located on chromosome 2 at 2p24.3, is a transcription factor that plays a role in regulation of cell growth and proliferation.

Pathology

It is mainly expressed in the developing nervous system and is critical during neural crest embryogenesis. Myelocytomatosis viral homologue (MYCN) becomes rapidly down-regulated as tissues become terminally differentiated and growth-arrested1. Over-expression of MYCN seems to block differentiation and increase cell proliferation. MYCN amplification is the most important unfavourable prognostic factor for neuroblastoma and is amplified in 25% of cases2. Neuroblastoma is a dominating group of neuron tumours and is one of the most common solid tumours in children3.

2p24.3

2q11.2 MYCN LAF4 (AFF3) D2S2719 RH17899

D2S2710

140kb

201kb 100kb

112

RefeRenCes 1.

Thomas WD et al., Int J of Bioch and Cell Biol

2. 3.

2004;36(5):771-5 Look et al., J Clin Oncol. 1991 Apr;9(4):581-91 Heim and Mitelman, Cancer cytogenetics 2nd Ed. 1995

Cat. No. LPs 012-s

(5 tests)

Cat. No. LPs 013-s (5 tests)

Cat. No. LPs 012

(10 tests)

Cat. No. LPs 013

(10 tests)

PAX3 and PAX7 Breakapart Rhabdomyosarcoma (RMS) is the most common soft-tissue sarcoma in children. One of the primary histological subtypes is the alveolar RMS (ARMS)1.

In ARMS cases that are negative for translocations involving FOXO1, there are two other variant PAX3 translocations that could be present - t(X;2)(q13;q36.1) PAX3-FOXO44 and t(2;2)(q36.1;p23) PAX3-NCOA15.

PAX3

PAX7 Breakapart

Pathology

The majority (55%) of ARMS are associated with the t(2;13)(q36.1;q14) translocation, and less commonly (22%) with t(1;13)(p36;q14), leading to the fusion of transcription factor FOXO1 (Forkhead Box protein 1) to the transcription factors PAX3 (Paired Box protein 3) and PAX7, respectively2. The distinction between the t(1;13) and t(2;13) in ARMS is important as patients with the t(2;13) have a more adverse outcome than those with the t(1;13)3.

RefeRenCes 1. 2. 3. 4. 5.

Kodet R et al., Am J Surg Pathol 1993;17(5):443-53 Ahn et al., Oncol Rep. 2013 August; 30(2): 968â&#x20AC;&#x201C;978 Sorensen et al., J Clin Oncol 2002;20:2672-9 Barr et al., Cancer Res 2002;62:4704-10 Wachtel et al., Cancer Res 2004:64(16):5539-45

Cat. No. LPs 012

2q36.1

PAX3

SGPP2 D2S313

D2S102

D2S2300

D2S2599

168kb

124kb 100kb

PAX7

Cat. No. LPs 013

1p36.13 KLHDC7A

PAX7

IGSF21 D1S1345

D1S2598

D1S2644

TAS1R2 D1S3604

D1S1524

D1S1324 109kb

139kb 100kb

113

Cat. No. LPs 011-s

(5 tests)

Cat. No. LPs 011

(10 tests)

RB1 Deletion Retinoblastoma (Rb) is a cancer of immature retina cells that occurs in infants and small children1. The protein encoded by the 180kb Retinoblastoma 1 (RB1) tumour suppressor gene, located on 13q14.2, may form complexes with oncoproteins and block their tumourigenic activity2. Deletion of this gene, particularly homozygous deletion, is therefore a causal event in the development of retinoblastoma.

Pathology

The RB1 gene also plays a role in secondary tumours arising in retinoblastoma patients, such as osteosarcoma and some soft tissue sarcomas3. The RB1 gene may also be deleted as a result of a progressional tumourigenic event in some leukaemias4, as well as in some breast, lung, bladder, oesophagus and prostate cancers5.

RefeRenCes 1. 2. 3. 4.

Heim and Mitelman, Cancer Cytogenetics 2nd Ed. 1995 Whyte et al., Nature 1988;334(6178):124-9 Draper et al., Br J Cancer 1986;53(5):661-71 Juneau et al., Cancer Genet Cytogenet. 1998 Jun;103(2):117-23

Benedict et al., J. clin. Invest., 85, 988â&#x20AC;&#x201C;993 (1990)

13qter

13q14.2

RB1 D13S645

D13S153

D13S1211E

318kb 100kb

114

D13S818

Cat. No. LPs 022-s

(5 tests)

Cat. No. LPs 022

(10 tests)

ROS1 Breakapart The receptor tyrosine kinase c-ros oncogene 1 (ROS1) is an orphan receptor tyrosine kinase of the insulin receptor family and is located at 6q221. ROS1 consists of a large extracellular domain that is composed of six fibronectin repeats, a transmembrane domain, and an intracellular kinase domain. While the function of ROS1 is undefined, it has been shown to play an important role in the differentiation of epididymal epithelium2.

ROS1 rearrangements with the fusion partner GOPC (golgi-associated PDZ and coiled-coil motif containing) have also been implicated in Glioblastoma and Cholangiocarcinoma5,7. ROS1 Fusions activate the pSTAT3, PI3K/AKT/mTOR and the SHP-2 phosphatase pathways8,9.

Pathology

ROS1 rearrangements have been reported to define a molecular subset of Non Small-Cell Lung Cancer (NSCLC)3. Rearrangements of ROS1 with fusion partners SLC34A2 (solute carrier family 34 (sodium phosphate), member 2)4 and CD74 (Cluster of Differentiation 74), have been shown to occur in less than 2% of patients with NSCLC3. Patients harbouring ROS1 rearrangement have been shown to respond to treatment with ALK/MET tyrosine kinase inhibitors, such as Xalkori速 (crizotinib)5,6.

RefeRenCes 1. 2. 3. 4. 5. 6.

Matsushime H et al., Mol Cell Biol 1986;6:3000-4 Yeung CH et al., Biol Reprod 1999;61:1062-9 Bergethon K et al., J Clin Oncol 2012;30(8):863-70 Davies KD et al., Cancer Res 2012;72(8):1538-7445 Matsuura et al., Oncol Rep. 2013 Oct;30(4):1675-80 Ou SH et al., Expert Rev Anticancer Ther 2012;12(4):447-56 7. Yasuda H et al., J Thorac Oncol 2012;7(7):1086-90 8. Birchmeier C et al., Proc Natl Acad Sci 1987;84:9270-9274 9. Gu TL et al., PLoS One 2011;6: e15640 10. Charest A et al., Genes Chromosomes Cancer 2003;37:58-71

6q22.1

FAM162B GPRC6A

ROS1

RFX6

D6S1873

D6S2428

299kb

171kb

D6S1072

DCBLD1 GOPC

NUS1

D6S1073

D6S1954

406kb 100kb

115

Cat. No. LPs 010-s

(5 tests)

Cat. No. LPs 010

(10 tests)

SRD (CHD5) Deletion The 1p36 region is frequently deleted in a broad range of human cancers1.

Pathology

The Chromodomain Helicase DNA binding domain 5 (CHD5) gene acts as a tumour suppressor at 1p36.31 and is frequently deleted in human gliomas1, leukaemias/lymphomas2 and neuroblastomas3. Deletion of the short arm of chromosome 1 is one of the most characteristic genetic changes in neuroblastoma, a tumour of the sympathetic nervous system. This is the most common childhood solid extracranial tumour, accounting for around 8%-10% of childhood cancers and 15% of childhood cancer deaths4. The CHD5 gene has been characterised as the lead tumour suppressor candidate from the 1p36 smallest region of consistent deletion (SRD) region in neuroblastoma5.

RefeRenCes 1. 2. 3. 4.

Bagchi, Mills Canc Res 2008;68(8):2551-6 Maser et al., Nature 2007;447:966-71 Okawa et al., Oncogene 2008;27:803-10 Broudeur and Maris, Neuroblastoma in Principles and Practice of Pediatric Oncology. 5th Ed. Philadelphia, PA: Lippincott: 933-970, 2006 Fujita et al., J Natl Cancer Inst 2008;100:940-9

1qter

1p36.31 KCNAB2

D1S1323

SRD (CHD5)

D1S83

RNF207 RPL22 ICMT GPR153 D1S286E

210kb 100kb

116

D1S2870

D1S2531

ACOT7 D1S1250

Cat. No. LPs 014-s

(5 tests)

Cat. No. LPs 014

(10 tests)

SYT (SS18) Breakapart Synovial sarcomas account for up to 10% of soft-tissue sarcomas, typically arising in the para-articular regions in adolescent and young adults1.

Pathology

A characteristic SYT(SS18)-SSX fusion gene resulting from the chromosomal translocation t(X;18)(p11;q11.2) is detectable in more than 90% of synovial sarcomas2, suggesting this is the primary causal event. The translocation fuses the SYT gene from chromosome 18q11.2 to either of two highly homologous genes at Xp11: SSX1 (Synovial Sarcoma X Breakpoint 1) or SSX2. In less than 1% of cases, SYT will be fused to a third gene, SSX43. SYT-SSX1 and SYT-SSX2 are thought to disrupt transcription and the subsequent expression of specific target genes4,5.

RefeRenCes 1.

Enzinger FM, Weiss SW. Synovial sarcoma. In: Enzinger FM, Weiss SW, eds. Soft tissue tumors, 3rd ed. St. Louis: Mosby-Year Book, 1995:757â&#x20AC;&#x201C;86

Sreekantaiah et al., Am J Pathol 1994;144:1121-34

Ladanyi et al., Canc Res 2002;62:135-40

Ladanyi et al., Diagn Mol Pathol 1995;4:162-73

Sorensen, Triche, Semin Cancer Biol 1996;7:3-14

18q11.2

SYT (SS18) D18S1359

SGC35446

148kb

PSMA8

TAF4 B

PMC303366P3

151kb 100kb

117

Cat. No. LPs 021-s

(5 tests)

Cat. No. LPs 021

(10 tests)

TMPRSS2/ERG Deletion/Breakapart Recent studies suggest that over 50% of prostate tumours may carry a chromosomal rearrangement of chromosome 21q221. The genes involved are the androgen-inducible TMPRSS2 (Transmembrane protease, serine 2 (21q22.3)) and an ETS (E-twenty six) family transcription factor, ERG (v-ets erythroblastosis virus E26 oncogene like (21q22.2))1.

Pathology

An apparent intrachromosomal deletion of 3Mb on chromosome 21 fuses TMPRSS2 to ERG. The rearrangement places ERG under the androgen-regulated transcriptional control of TMPRSS22. This fusion is associated with disease progression and the rearrangement in prostate cancer may account for molecular and clinical heterogeneity3. This represents an important subclassification of prostate cancer from a biological and a clinical standpoint3.

KCNJ6

DSCR8 KCNJ15 DSCR4

D21S1439

RefeRenCes 1. 2. 3.

Saramaki et al., Clin Cancer Res 2008;14(11):3395-3400 Lapointe et al., Modern Pathology 2007;20(4):467-473 Perner et al., Cancer Res 2006;66(17):8337-8341

ETS2

ERG SHGC-11427

100kb 288kb

106kb

215kb

21q22.13-q22.2

21q22.2-q22.3

FAM3B TMPRSS2 MX2 MX1 BACE2 D21S1906

PRDM15 ZBTB21 C2CD2 RIPK4 UMODL1 ABCG1

D21S1863

D21S1260

235kb

149kb

143kb

91kb

191kb 100kb

118

D21S1838

152kb

161kb

Cat. No. LPs 002-s

(5 tests)

Cat. No. LPs 002

(10 tests)

TOP2A Amplification/Deletion The Topoisomerase 2A encoding (TOP2A) gene is located on chromosome band 17q21.2, near to the HER2 (ERBB2) oncogene. The TOP2A encoded protein has a function in DNA replication and the transcription of mRNA1,2. Amplification of the TOP2A gene is frequent in breast cancer and is often accompanied by HER2 amplification3. Pathology

TOP2A gene alterations are associated with an increased response to therapy using the anti-cancer drug anthracycline4, while patients with tumours that show normal levels of TOP2A and HER2 do not appear to gain any additional benefit from this drug4.

RefeRenCes 1.

Chen AY, Liu LF, Ann Rev Pharmacol Toxicol

1994;34:191-218 Tsai-Pflugfelder M et al., Proc Nat Acad Sci

1988;85:7177-81 Bofin AM et al., Cytopath 2003;14(6):314-9

O'Malley et al., J Natl Cancer Inst 2009;101(9):644-650

D17Z1

17q21.2

TOP2A D17S1335

IGFBP4

TNS4

D17S1230

164kb 100kb

119

Cat. No. LPs 005-s

(5 tests)

Cat. No. LPs 005

(10 tests)

ZNF217 Amplification The Zinc Finger protein 217 gene (ZNF217), which functions as a transcription repressor for a variety of genes1, is a strong oncogene candidate mapped within the 260kb minimum common amplicon at 20q13.22. ZNF217 is amplified in breast cancer2,3, ovarian cancer and other tumours3,4,5 and is associated with aggressive tumour behaviour6. It has been shown that the silencing of ZNF217 inhibits ovarian cancer cell growth and their invasive ability in cancer cell lines7.

Pathology

RefeRenCes 1.

20pter

20q13.2

ZNF217 D20S183

D20S840 D20S211

245kb 100kb

120

Quinlan KG et al., Mol Cell Biol 2006;26:8159-72

Collins C et al., Proc Natl Acad Sci 1998;95:8703-8

Yang SH et al., Clin Cancer Res 2005;11:612-20

Iwabuchi H et al., Cancer Res 1995;55:6172-80

Bar-Shira A et al., Cancer Res 2002;62:6803-7

Tanner MM et al., Clin Canc Res 1995;1:1455-61

Sun G et al., Int J Oncol 2008;32:1065-71

Prenatal Prenatal

Contents 123

Aquarius速 FAST FISH Prenatal Enumeration Kits

124

Prenatal

Aquarius速 Prenatal Enumeration Kits

Cytocell's prenatal Fluorescence In Situ Hybridisation (FISH) assays are designed for the rapid and accurate detection of the most common foetal chromosomal disorders. Trisomy of chromosome 21, resulting in Down syndrome1, is one of the most common chromosome abnormalities in humans and the risk of having an affected child is known to increase with maternal age2. The syndrome represents a particular combination of phenotypic findings, including characteristic facial appearance, a single palmar crease and mental retardation, and may also present with hearing and heart defects. Affected individuals show a highly increased incidence of leukaemia, particularly acute megakaryocytic leukaemia3.

Prenatal

Trisomy of chromosome 18, resulting in Edwards syndrome, occurs in around 1 in 6000-8000 live births with a female sex bias4. The clinical findings are variable, though many exhibit growth delay, heart defects and craniofacial anomalies, as well as possible limb and kidney abnormalities5. The rarest trisomy, trisomy 13, responsible for Patau syndrome occurs in approximately 1 in 16,000 newborns6. Individuals with Patau syndrome present abnormalities affecting many parts of the body, including the heart, spinal cord, eyes, limbs, face/skull and muscles6. Aberrant copy numbers of the X and Y chromosomes can lead to various sex chromosome disorders, such as Klinefelter (47,XXY), Turner (45,X) and other syndromes caused by variations in copy number of X and/or Y. These syndromes have variable incidences and clinical findings7. Cytocell Prenatal kits contain fluorescent probes for easy identification of trisomies 21, 18 and 13 present in Down, Edwards and Patau syndrome, respectively, as well as multiple sex chromosome aneuploidies.

RefeRenCes 1. 2. 3. 4. 5. 6. 7.

122

Lejeune et al., C. R. Acad. Sci. 1959; 248: 1721-1722 Penrose et al., J. Genet. 1933; 27: 219-224 http://www.omim.org/entry/190685 http://www.ojrd.com/content/7/1/81/abstract Cereda and Carey. Orphanet J Rare Dis 2012; 7:81 http://ghr.nlm.nih.gov/condition/trisomy-13 Visootsak and Graham. Orphanet Journal of Rare Diseases 2006, 1:42

Cat. No. LPf 001-s

(5 tests)

Cat. No. LPf 002-s (5 tests)

Cat. No. LPf 001

(10 tests)

Cat. No. LPf 002

(10 tests)

Cat. No. LPf 001-30 (30 tests)

Cat. No. LPf 003-s (5 tests)

Cat. No. LPf 001-50 (50 tests)

Cat. No. LPf 003

(10 tests)

Aquarius® FAST FISH Prenatal Kits The Aquarius® FAST FISH Prenatal kit allows detection of trisomies 13, 18 and 21 (Down syndrome) and sex chromosome aneuploidies utilising a 2 hour hybridisation protocol. Aquarius® FAST FISH Prenatal kits provide the benefits of: • 2 hour hybridisation protocol demonstrating high intensity signals and minimal background. • Economical kit formats: 5, 10, 30** or 50** tests. • Liquid stable reagents premixed in hybridisation solution and provided with DAPI counterstain. Each kit contains the variable probe sets, details of which are listed below. **Not available for LPF002 and LPF003.

Cat. No. LPf 001

Probe set 1:

DXZ1

Prenatal

X centromere Xp11.1-q11.1 (DXZ1) Green Y centromere Yp11.1-q11.1 (DYZ3) Orange 18 centromere 18p11.1-q11.1 (D18Z1) Blue DYZ3

Probe set 2: 13 unique sequence (13q14.2) Green 21 unique sequence (21q22.13) Orange

D18Z1 Cat. No. LPf 002

X centromere Xp11.1-q11.1 (DXZ1) Green Y centromere Yp11.1-q11.1 (DYZ3) Orange 18 centromere 18p11.1-q11.1 (D18Z1) Blue 13q14.2

ITM2B

D13S1195

Cat. No. LPf 003

RB1

D13S1155

D13S917

D13S915

D13S153

124kb

13 unique sequence (13q14.2) Green

RCBTB2

D13S1218

416kb 100kb

21 unique sequence (21q22.13) Orange

21q22.13

DYRK1A D21S270

KCNJ6 D21S1867 D21S1972

D21S337 D21S1439 D21S1440

DSCR4 D21S1425 D21S1917 D21S1444 D21S1238

288kb

348kb

DSCR8 D21S341 D21S1883 106kb

100kb

123

Cat. No. LPA 001-s

(5 tests)

Cat. No. LPA 002 (10 tests)*

Cat. No. LPA 001

(10 tests)

Cat. No. LPA 003 (10 tests)*

Cat. No. LPA 001-30 (30 tests)

Cat. No. LPA 004 (10 tests)*

Cat. No. LPA 001-50 (50 tests)

Cat. No. LPA 005 (10 tests)*

* also available as 5 tests

Aquarius® Prenatal Enumeration Kits The Aquarius® Prenatal Enumeration range allows detection of trisomies 13, 18 and 21 (Down syndrome) and sex chromosome aneuploidies utilising an overnight hybridisation protocol. Aquarius® Prenatal kits provide the benefits of: • Overnight hybridisation protocol demonstrating high intensity signals and minimal background. • Economical kit formats: 5, 10, 30** or 50** tests. • Liquid stable reagents premixed in hybridisation solution and provided with DAPI counterstain. Each kit contains the following probe sets. **Not available for LPA002, 003, 004 or 005.

Cat. No. LPA 001

Probe set 1:

DXZ1

X centromere Xp11.1-q11.1 (DXZ1) Green Prenatal

Y centromere Yp11.1-q11.1 (DYZ3) Orange 18 centromere 18p11.1-q11.1 (D18Z1) Blue Probe set 2:

DYZ3

13 unique sequence (13q14.2) Green 21 unique sequence (21q22.13) Orange

Cat. No. LPA 002

D18Z1

X centromere Xp11.1-q11.1 (DXZ1) Green Y centromere Yp11.1-q11.1 (DYZ3) Orange 18 centromere 18p11.1-q11.1 (D18Z1) Blue Cat. No. LPA 003

13q14.2

ITM2B

13 unique sequence (13q14.2) Green 21 unique sequence (21q22.13) Orange

D13S1195

RB1

D13S1155

D13S917

D13S153

124kb

Cat. No. LPA 004

RCBTB2 D13S915 D13S1218

416kb 100kb

18 centromere 18p11.1-q11.1 (D18Z1) Blue Cat. No. LPA 005

13 unique sequence (13q14.2) Green 18 centromere 18p11.1-q11.1 (D18Z1) Blue 21 unique sequence (21q22.13) Orange

21q22.13

DYRK1A D21S270

KCNJ6 D21S1867 D21S1972

D21S337 D21S1439 D21S1440

DSCR4 D21S1425 D21S1917 D21S1444 D21S1238

288kb

348kb 100kb

124

DSCR8 D21S341 D21S1883 106kb

Microdeletion

Contents 127

Alagille (JAG1)

128

Angelman (UBE3A/D15S10)

129

CHARGE

130

Cri-Du-Chat and SOTOS Probe Combination

131

DiGeorge II (10p14)

132

DiGeorge and 22q13.3 Deletion Syndrome Probe Combinations

134

Kallmann (KAL1) and Steroid Sulphatase Deficiency (STS) Probe Combination

135

Langer-Giedion

136

Monosomy 1p36

137

Neurofibromatosis Type 1

138

Prader-Willi/Angelman (SNRPN)

139

Rubinstein-Taybi

140

Saethre-Chotzen/Williams-Beuren Combination

141

SHOX

142

Smith-Magenis (RAI1 and FLII)/ Miller-Dieker Probe Combinations

144

SRY

145

Williams-Beuren

146

Wolf-Hirschhorn

147

XIST

126

Microdeletion Microdeletion syndromes are a heterogeneous group of disorders brought about by the deletion of specific regions of chromosomal DNA, causing haploinsufficiencies of important genes. These deletions are difficult to visualise using standard cytogenetic techniques, but Fluorescence In Situ Hybridisation (FISH) can resolve these submicroscopic deletions and has therefore become the method of choice for the diagnosis of these disorders. Cytocellâ&#x20AC;&#x2122;s comprehensive range of Microdeletion probes features products for some of the rarest human genetic syndromes. With this in mind, we offer all Microdeletion probes in economical five, or standard ten, test kits.

Cat. No. LPU 012-s

(5 tests)

Cat. No. LPU 012

(10 tests)

Alagille (JAG1) Alagille syndrome (AGS) is an autosomal dominant disorder (with reduced penetrance) characterised by abnormalities of the liver, heart, skeleton, eye and face1,2. Mutations in the 36kb long human gene Jagged1 (JAG1), located on chromosome 20p12, have been identified as causal for the abnormalities found in patients with AGS3. This gene encodes a ligand for the Notch 1 transmembrane receptor, which plays a key role in cell fate determination and differentiation3,4. The syndrome has also been noted in a patient with a deletion larger than 3Mb, including JAG1, associated with a translocation t(3;20)(q13.3;p12.2)4.

RefeRenCes 1. 2. 3. 4.

Alagille D et al., J Pediatr 1987;110:195-200 OMIM entryâ&#x2122;Ż 118450: http://www.omim.org/entry/118450 Oda T et al., Nature Genet 1997;16:235-42 Oda T et al., Human Mutat 2000;16:92

20qter Microdeletion

20p12.2 JAG1 D20S507 D20S160

100kb

D20S1091

D20S894

124kb

127

Cat. No. LPU 006-s

(5 tests)

Cat. No. LPU 006

(10 tests)

Angelman (UBE3A/D15S10) In 70% of patients with Angelman syndrome (AS), a large de novo maternal deletion of 3-4Mb at 15q11.2-q13 is observed1,2,3. The remaining 30% of cases have underlying causes such as paternal uniparental disomy of the same region (~2%), imprinting defects (~2-3%) and mutations of the UBE3A gene1. The UBE3A gene lies within the minimum AS critical region4 approximately 400kb telomeric to the SNRPN gene. It shows preferential expression of the maternal allele in the brain5 and is mutated in 20-30% of AS patients with normal methylation and biparental contribution of 15q11-13. It is considered to be one of the causative AS genes4,5.

RefeRenCes 1. 2. 3. 4. 5. 6.

Microdeletion

The Angelman region probe covers approximately 108kb of genomic DNA, targets most of the UBE3A gene and includes the D15S10 locus. This probe may be used to identify deletions of the AS region, though it will not detect small intragenic deletions or mutations of UBE3A. The probe may also be used to help determine the nature of a Prader-Willi syndrome deletion detected with the SNRPN/Imprinting Centre probe (see LPU005). Large, 3-4Mb deletions of 15q11-13 will cause the deletion of both probe regions (SNRPN/IC and UBE3A/D15S10). Smaller deletions incorporating the IC and SNRPN, will not cause deletion of the UBE3A/D15S10 probe. These deletions may indicate a much higher risk of recurrence (possibly via grandmatrilineal inheritance) and carriers, and their families, may require further investigation6.

OMIM entry â&#x2122;Ż105830 http://www.omim.org/entry/105830 Butler MG, Am J Med Genet 1990;35:319-32 Clayton-Smith J, Pembrey M, E J Med Genet 1992;29:412-5 Sutcliffe JS et al., Genome Res 1997;7:368-77 Rougeulle C, Lalande M, Neurogenetics 1998;1:229-37 Ming et al., Am. J. Med. Genet. 92: 19-24, 2000

15qter

15q11.2-q12

Angelman Syndrome Region

SNRPN PWAR5

IPW PWAR1

D15S63

GABRB3

D15S10

100kb

128

UBE3A

108kb

Cat. No. LPU 021-s

(5 tests)

Cat. No. LPU 021

(10 tests)

CHARGE CHARGE syndrome is an autosomal dominant disorder that occurs in approximately 1 in 12,000 births1. The acronym CHARGE summarises six main clinical features: ocular Coloboma, Heart defects of any type, Atresia of the choaneae, Retardation, Genital and Ear anomalies2. Errors in the chromodomain 7 (CHD7) gene were identified as being causative for the syndrome in around 60% of patients with a clinical diagnosis of CHARGE3. CHD7 is located in 8q12.1-q12.2 and is 189kb in size. The CHD7 protein plays a role in chromatin organisation and is a member of the chromodomain helicase DNA-binding (CHD) proteins. CHD7 has an important function in early embryonic development and is ubiquitously expressed in several foetal and adult tissues, including those affected in CHARGE syndrome3. Most CHD7 mutations are

RefeRenCes 1.

Kallen et al., Teratology 1999: 60: 334-343

Pagon RA et al., J Pediat 1981;99:223-7

Vissers LE et al., Nat Genet 2004;36:955-7

Jongmans MC et al., J Med Genet 2005;43:306-14

Bergman et al., Eur J Med Genet. 2008; 51(5):417-25

truncating, leading to haploinsufficiency, and are generally de novo3,4. Microdeletions (or microduplications) have been proposed to account for up to 10% of CHARGE patients5.

Microdeletion

D8Z2

8q12.1-q12.2

CHD7

RAB2A D8S1929

100kb

D8S2048

D8S1986

D8S260

310kb

129

Cat. No. LPU 013-s

(5 tests)

Cat. No. LPU 013

(10 tests)

Cri-Du-Chat and SOTOS Probe Combination Cri-Du-Chat syndrome consists of multiple congenital anomalies, mental retardation, microcephaly, abnormal face and a mewing cry in infants. Cri-Du-Chat Syndrome is associated with deletions, which vary in size, of part of the short arm of chromosome 51. The estimated prevalence varies between 1 in 20,000 to 1 in 50,000 births2, making it one of the more common deletion syndromes.

RefeRenCes

A critical chromosomal region involved in the high-pitched cry has

Lejeune J et al., C R Hebd Seances Acad Sci

1963;257:3098-102 Niebuhr E et al., Hum Genet 1978;44:227-75

been mapped to the proximal part of chromosome band 5p15.3 . 3

The region involved in the remaining features of the syndrome has been mapped to 5p15.2

3,4,5

SOTOS syndrome is a neurological disorder characterised by a distinctive facial appearance, overgrowth in childhood and developmental delay6. Malignant tumour formation has also been reportedly associated with SOTOS syndrome7.

Mainardi PC et al., J Med Genet 2001;38:151-8

Overhauser J et al., Hum Mol Genet 1994;3:247-52

Wu Q et al., Eur J Hum Genet 2005;13:475-85

Cole TR and Hughes HE, J Med Genet 1994;31(1):20-32

Maldonado V et al., Am J Dis Child 1984;138:486-8

Tatton-Brown K and Rahman N, Eur J Hum Genet

2007;15:264-71 Kurotaki N et al., Nat Genet 2002;30:365-6

NSD1, a gene encoding a histone methyltransferase, and implicated in chromatin regulation8, was identified as the gene disrupted by the Microdeletion

5q35 breakpoint in a patient carrying a chromosomal translocation9. Haploinsufficiency of the NSD1 gene appears to be the major cause of SOTOS syndrome.

5p15.31

5p15.2

5q35

UBE2QL1

FGFR4 NSUN2 D5S2703 D5S2630

D5S1637E D5S2678

NSD1

D5S2281E D5S2260E D5S2221E

167kb

193kb

CTNND2

D5S2883 159kb

130

RGS14

100kb

Cat. No. LPU 015-s

(5 tests)

Cat. No. LPU 015

(10 tests)

DiGeorge II (10p14) DiGeorge syndrome1, and a variety of congenital malformation syndromes including Velocardiofacial syndrome (VCFS)2, share the deletion of chromosome 22 at 22q11.22,3,4,5. These chromosome 22 deletions are collectively coined CATCH22, a mnemonic that covers the clinical findings of Cardiac abnormality, Abnormal facies, Thymic aplasia, Cleft palate and Hypocalaemia/Hyperthyroidism due to a chromosome 22 deletion. In DiGeorge syndrome, however, cases have also been found in which patients have a deletion on chromosome 10p13.4 (DGS2) instead of chromosome 226,7,8. The deletion of the DGS2 locus on 10p may be 50 times less frequent than that of the DGS1 locus on 22q and has been estimated to occur in 1 in 200,000 live births9. A gene called BRUNOL3 (now named CELF2) has been identified within the 300kb minimally deleted region of DGS2 and is postulated to be involved in the DGS2 deletion10. BRUNOL3 is a candidate gene for the heart defect and thymus

RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.

DiGeorge AM, J Pediatr 1965;67:907 Shprintzen RJ et al., Cleft Palate J 1978;15:56-62 Wilson DI et al., J Med Genet 1993;30:852-6 Driscoll DA et al., J Med Genet 1992;50:924-33 Burn J et al., J Med Genet 1993;30:822-4 Schuffenhauer S et al., Ann Genet 1995;38(3):162-7 Daw SC et al., Nat Genet 1996;13:458-60 Dasouki M et al., Am J Med Genet 1997;73(1):72-5 Berend SA et al., Am J Med Genet 2000;91(4):313-7 Lichtner P et al., J Mol Med 2002;80:431-42 Yatsenko SA et al., Clin Genet 2004;66:128-36

hypoplasia/aplasia associated with partial monosomy 10p10 and may be involved in atrial septal defects (ASDs), a common cardiac anomaly associated with DGS211. Microdeletion

D10Z1

10p14

CELF2 D10S2235

D10S2196

D10S1632

D10S1364E D10S2420 100kb

144kb

131

Cat. No. LPU 004-s

(5 tests)

Cat. No. LPU 004

(10 tests)

DiGeorge and 22q13.3 Deletion Syndrome Probe Combinations DiGeorge Syndrome DiGeorge syndrome1, and a variety of congenital malformation syndromes including Velocardiofacial syndrome (VCFS)2, share the deletion of chromosome 22 at 22q11.22,3,4,5. These chromosome 22 deletions are collectively coined CATCH22, a mnemonic that covers the clinical findings of Cardiac abnormality, Abnormal facies, Thymic aplasia, Cleft palate and Hypocalaemia/Hyperthyroidism due to a chromosome 22 deletion. In addition, around 29% of nonsyndromic patients with isolated conotruncal defects have been shown to have a 22q11.2 microdeletion6. The incidence of these anomalies is estimated to be 1:4000 to 1:9700 live births7 and the deletion of 22q11.2 therefore represents one of the most common genetic defects.

Microdeletion

A region of approximately 2Mb, referred to as the DiGeorge Critical Region (DGCR), is the most commonly deleted region and occurs in up to 90% of patients5,8,9. Within the DGCR, a minimal critical region of 300-480kb has been described10,11, containing several genes, including TUPLE1 (HIRA), TBX1, SLC25A1 (CTP) and CLTD.

RefeRenCes 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19.

Pinsky L, DiGeorge AM, J Pediatr 1965;66:1049-54 Shprintzen RJ et al., Cleft Palate J 1978;15:56-62 Burn J et al., J Med Genet 1993;30:822-4 Wilson DI et al., J Med Genet 1993;30:852-6 Driscoll DA et al., J Am Hum Genet 1992;50:924-33 Goldmuntz E et al., J Med Genet 1993;30:807-12 Tezenas Du Montcel S et al., J Med Genet 1996;33:719 Driscoll DA et al., Am J Med Genet 1992;44(2):261-8 Scambler PJ et al., Genomics 1991;10:201-6 Halford S et al., Hum Mol Genet 1993;2(12):2099-107 Carlson C et al., Am J Hum Genet 1997;61:620-9 Phelan MC et al., Am J Med Genet 2001;101(2):91-9 Phelan MC. Orphanet Journal of Rare Diseases 2008, 3:14 Prasad C et al., Clin Genet 2000;57(2):103-9 Beeckers TM et al., J Neurochem 2002;81(5):903-10 Bonaglia MC et al., Am J Hum Genet 2001;69(2):261-8 Anderlid BM et al., Hum Genet 2002;110(5):439-43 Wilson HL et al., J Med Genet 2003;40(8):575-84 Dupont C et al., French Speaking Cytogeneticists Association Congress 2003 20. Luciani J et al., J Med Genet 2003;40(9):690-6 21. Chen CP et al., Prenat Diagn 2003;23(6):504-8

22q13.3 Deletion Syndrome The 22q13.3 deletion syndrome presents a recognisable phenotype characterised by hypotonia, delay or absence of expressive speech, global developmental delay, normal to accelerated growth and mild dysmorphic features12,13. Some deletions of the terminal region of chromosome 22q are cytogenetically visible. However, a few cases of cryptic deletions have been reported12,14, suggesting that the actual incidence of 22q telomere deletion may be higher than previously thought. Several observations of patients with 22q13.3 deletion showed that the SHANK3 (ProSAP2)20 gene, encoding a structural protein of the postsynaptic density of excitation synapses and expressed in the cortex and cerebellum of the brain15, was disrupted15,16,17 or deleted18, making it a candidate causative gene for this syndrome. The deletion varies dramatically in size from 130kb to 9Mb18,19,20. The use of 22q subtelomeric probes, distal to the ARSA gene, have therefore been recommended for examining all 22q13.3 deletions20,21.

132

Cat. No. LPU 010-s (5 tests)

Cat. No. LPU 014-s (5 tests)

Cat. No. LPU 010

Cat. No. LPU 014

VCFS TUPLE 1

(10 tests)

Cat. No. LPU 004

22q13.33

22q11.21

HIRA (TUPLE1)

DGCR14

SHANK3 ACR CDC45 Telomere

DGCR6 DGCR2

CLTCL1 D22S75

UFD1L

D22S1095E

D22S451

D22S944

100kb

113kb

VCFS N25

RABL2B

ARSA

44kb

Cat. No. LPU 010

22q11.21

22q13.33 Microdeletion

HIRA (TUPLE1)

DGCR14

SHANK3 ACR CDC45 Telomere

DGCR6 DGCR2

CLTCL1 D22S75

UFD1L

D22S1095E

D22S451

D22S944

ARSA

RABL2B

N25 63kb

TBX1

44kb

100kb

Cat. No. LPU 014

22q11.21

HIRA (TUPLE1)

TBX1

CDC45 SEPT5

22q13.33

DGCR8

SHANK3 ACR

GNB1L Telomere

UFD1L

D22S1637 D22S1627

D22S1662

211kb

ARSA 100kb

RABL2B

44kb

133

Cat. No. LPU 016-s

(5 tests)

Cat. No. LPU 016

(10 tests)

Kallmann (KAL1) and Steroid Sulphatase Deficiency (STS) Probe Combination Kallmann syndrome (KS) is a developmental disease characterised by olfactory deficiency3 and hypogonadotrophic hypogonadism (HH), which is responsible for the absence of spontaneous puberty1.

RefeRenCes 1. 2. 3. 4. 5.

Kallmann syndrome is a heterogeneous developmental genetic disorder affecting approximately 1 in 8,000 males and 1 in 40,000 females2. Reports indicate three modes of inheritance: X-linked, autosomal dominant and autosomal recessive1,4. It has been shown that mutations in the KAL1 gene on Xp22.3 result in the X-linked form of KS5. KAL1 consists of 14 exons and extends over 200kb and abnormalities of KAL1 reported in patients with KS include missense and nonsense mutations, splice site mutations, intragenic deletions and submicroscopic chromosomal deletions involving the entire KAL1 gene7.

Kallmann FJ et al., Am J Ment Defic 1944;48:203-36 Hu Y et al., Int J Biochem Cell Biol 2003;35:1157-62 Hockaday TD, Postgrad Med J 1966;42:572-4 White BJ, Am J Med Genet 1983;15:417-35 Hardelin JP et al., Human Mol Genet 1993;2:373-7

Del Castillo I et al., Nat Genet 1992;2:305-10

Izumi Y et al., Endocr J 2001;48:143-9

Wells RS et al., Arch Dermatol 1965;92(1):1-6

Valdes-Flores M et al., J Invest Dermatol.

2001;116(3):456-8 10. Hernandez-Martin A et al., Br J Dermatol 1999;141(4):617-27 11. Hazan C et al., Dermatology Online 2005;11(4):12 12. Paige DG et al., Br J Dermatol 1994;131(5):622-9

Microdeletion

Steroid Sulphatase Deficiency (STS) (also known as X-linked Ichthyosis)8 is the second most common type of ichthyosis and one of the most frequent human enzyme deficiency disorders. Deficiency of the STS enzyme is known to be responsible for dark, adhesive and regular scaling of the skin9. The gene encoding this protein maps to the distal short arm of chromosome X, which escapes X-chromosome inactivation and has the highest ratio of chromosomal deletions among all genetic disorders10. Complete deletions of the STS gene have been found in more than 90% of patients11. The deletions can extend to involve neighbouring genes, causing contiguous gene defects. Therefore, STS may be associated with KS12.

DXZ1

Xp22.31

KAL1

STS

HDHD1

DXS7500 DXS7731 DXS7965 DXS6767 282kb

134

DXS7470 DXS278

100kb

FAM9A

DXS7053 DXS7714

334kb

Cat. No. LPU 022-s

(5 tests)

Cat. No. LPU 022

(10 tests)

Langer-Giedion Langer-Giedion syndrome (LGS; tricho-rhino-phalangeal syndrome type II) is an autosomal dominant contiguous gene deletion syndrome involving chromosome bands 8q23.3 and 8q24.11. LGS is characterised by cranio-facial and skeletal abnormalities including multiple cartilaginous exostoses and cone-shaped epiphyses. Mental retardation is also a common finding. LGS combines the clinical features of two autosomal dominant diseases: tricho-rhino-phalangeal syndrome type 1 and multiple cartilaginous exostoses (caused by defects in the TRPS1 and EXT1 genes respectively). Both genes involved in these conditions are within the Langer-Giedion deletion region, though TRPS1 maps more than 1Mb proximal to EXT12,3.

RefeRenCes 1. 2. 3.

Buhler, Malik, Am J Med Genet 1984;19:113-9 Ludecke HJ et al., Hum Mol Genet 1995;4:31-6 Hou et al., Genomics 1995;29(1):87-97

8q24.11

8q23.3

TRPS1

EXT1

D8S565 D8S98 D8S547 115kb

D8S1009 D8S1020

131kb

Microdeletion

D8Z2

100kb

165kb

D8S527

D8S43

206kb

135

Cat. No. LPU 020-s

(5 tests)

Cat. No. LPU 020

(10 tests)

Monosomy 1p36 Monosomy 1p36 (1p36 deletion syndrome) is one of the most common terminal deletion syndromes, occurring in an estimated 1 in 10,000 births1. It is characterised by developmental delay, growth abnormalities and craniofacial dysmorphism. Minor cardiac malformations, sensorineural hearing loss and opthalmological anomalies have also been observed2. Deletions are extremely variable and range from 1.5 to 10.5Mb3.

Microdeletion

The SKI gene, located at 1p36.33, was deleted in all individuals tested with 1p36 deletion syndrome4. This gene is involved in neural tube development and muscle differentiation5 and deletions in mice produce phenotypes with some similarities to those seen in individuals with 1p36 deletion syndrome6.

RefeRenCes 1. 2. 3. 4. 5. 6.

Shaffer, Lupski et al., Annu Rev Genet 2000;34:297-329 Slavotinek A et al., J Med Genet 1999;36:657-663 Heilstedt HA et al., Am J Hum Genet 2003;72:1200-12 Colmenares C, Nat Genet 2002;30:106-9 Kaufman CD et al., Mech Dev 2000;95:147-62 Berk M et al., Genes Dev 1997;11:2029-39

1qter

1p36.33 GABRD

SKI

PRKCZ D1S1328

D1S243

100kb

136

MORN1 D1S2515

115kb

Cat. No. LPU 017-s

(5 tests)

Cat. No. LPU 017

(10 tests)

Neurofibromatosis Type 1 Neurofibromatosis type 1 (NF1) is a relatively common autosomal dominant disorder, occurring in 1 in 3,000-4,000 people1. It is a characterised by neurofibromas, cafĂŠ-au-lait spots, freckles, Lisch nodules, bone deformities, learning disabilities, macrocephaly, short stature and predisposition to developing tumours such as myeloid malignancies, gliomas and pheochromocytomas2,3,4. NF1 is caused by mutations of the tumour suppressor gene, Neurofibromin 1 (NF1), which spans approximately 280kb and is located at 17q11.245. Mutations encompass both single nucleotide substitutions and large genomic deletions. Patients with deletions of the entire gene typically have a more severe presentation than those with intragenic mutations6. Approximately 5-20% of patients with NF1 carry a heterozygous deletion and thus lack one copy of the NF1 gene and further 11 or more contiguous genes7. There are two common sized recurrent deletions, both mediated by non-allelic homologous recombination between regions of high sequence homology: Type 1, spanning 1.4Mb between segmental duplicons and Type 2, with breakpoints in the SUZ12 gene and its pseudogene 1.2Mb away8. Atypical deletions have also been noted with non-recurrent breakpoints8.

RefeRenCes 1.

Laycock-van Spyk S et al., Human Genomics

2011; 5:623-690 Bader JL et al., Ann N J Acad Sci 1986;486:57-65

Huson SM and Hughes RAC, The Neurofibromatoses:

Hall, London. 1994 Trovo-Marqui AB, Tajara EH et al., Clin Genet

2006;70:1-13 Cichowski K, Jacks T et al., Cell 2001;104(4):593-604

A Pathogenic and Clinical Overview. Chapman and

Pasmant E et al., Hum Mutat. 2010 Jun;31(6):E1506-18

Jeong SY et al., J Korean Med Sci. 2010

May;25(5):804-8 Steinmann et al., Eur J Hum Genet 2008;16:572-580

Microdeletion

17pter

17q11.2 RNF135

NF1 D17S1307

RAB11FIP4 D17S2162

D17S1972

D17S1681 100kb

143kb

137

Cat. No. LPU 005-s

(5 tests)

Cat. No. LPU 005

(10 tests)

Prader-Willi/Angelman (SNRPN) Prader-Willi Syndrome (PWS) and Angelman Syndrome (AS) are distinct neurogenetic disorders caused by the loss of function of genes on chromosome 15 (bands 15q11-13), on either the paternally or maternally inherited chromosome, respectively1. In 70% of patients, a large interstitial deletion of 3-4Mb is observed1,2. In around 3% of patients, an imprinting defect is observed, caused by either an epimutation or a microdeletion of the Imprinting Centre (IC)1,3. Uniparental disomy, in which both chromosome 15s are inherited from the same parent, accounts for most of the remaining patients with PWS/AS1. The SNRPN gene is one of four imprinted loci that are expressed from the paternal chromosome 15 region (15q11-13) and maps to the

RefeRenCes 1. 2. 3. 4. 5.

Butler MG. Curr Genomics. 2011 May; 12(3): 204â&#x20AC;&#x201C;215 Clayton-Smith J and Pembrey M. J Med Genet 1992;29:412-5 Buiting K et al., Am J Hum Genet 1998;63(1):170-80 Glenn C et al., Am J Hum Genet 1996;58:335-46 Buiting K et al., Nat Genet 1995;9:395-400

Dittrich B et al., Nat Genet 1996;14:163-70

minimally deleted region (MDR) involved in PWS5. Its chromosomal location and imprinting status suggest it plays a possible role in the aetiology of PWS4. The imprinting centre (IC) maps to a 100kb region proximal to SNRPN. Parental deletions or mutations in the IC impair the imprinting process Microdeletion

in 15q11-13 and cause one of two distinct diseases in their offspring5,6. Most of the PWS imprinting deletions involve SNRPN and are approximately 200kb in size. The AS imprinting deletions are small (approximately 40kb), involve the BD3 region, and do not include SNRPN.

15qter

15q11.2 Imprinting Centre

SNRPN

IPW PAR1 PWAR5

D15S63

D15S10

170kb

138

UBE3A

100kb

Cat. No. LPU 023-s

(5 tests)

Cat. No. LPU 023

(10 tests)

Rubinstein-Taybi Rubinstein-Taybi is a well-defined syndrome characterised by short stature, mental retardation, facial abnormalities, and broad thumbs and first toes1. This condition was described in 19572 but a larger series of cases described in 1963 by Rubinstein and Taybi1 led to the current syndrome name. It is an autosomal-dominant disorder with a frequency of 1 in 100,000 newborns3. The Rubinstein-Taybi syndrome (RTS) locus resides in chromosome band 16p13.3 and includes a gene encoding a cAMP response element binding protein (CREBBP)4. This gene spans approximately 150kb4 and dosage abnormalities are the common cause of RTS5, with microdeletions of this region accounting for 10-15% of cases5. Disruptions of CREBBP, by either gross chromosomal rearrangements or point mutations, have also been shown to be responsible for Rubinstein-Taybi syndrome4,6.

RefeRenCes 1.

Rubinstein JH, Taybi H, Am J Dis Child 1963;105:588-608

Matsoukas and Theodorou Chir Orthop Reparatrice Apar

Mot 1957;43:142-6 Jacobs et al., Clin Ophthalmol. 2012; 6: 1369â&#x20AC;&#x201C;1371

Petrij F et al., J Med Genet 2000;37(3):168-76

Stef M et al., Eur J Hum Genet 2007;15(8):843-7

Bartsch O et al., Eur J Hum Genet 1999;7(7):748-56

Microdeletion

D16Z2

16p13.3 DNASE1 TRAP1

D16S3382

D16S2906 146kb

CREBBP

D16S3386

153kb

100kb

139

Cat. No. LPU 024-s

(5 tests)

Cat. No. LPU 024

(10 tests)

Saethre-Chotzen/Williams -Beuren Combination Saethre-Chotzen syndrome is a rare, congenital, autosomal dominant disorder characterised by craniofacial and limb abnormalities1. The incidence of this syndrome is estimated to be 1 in 25,000-50,000 live births, though due to the phenotype often being very mild, it is possible that the syndrome is under diagnosed1. The identification of TWIST1 (a basic helix-loop-helix transcription factor on chromosome band 7p21.1) as a causative gene2,3 has proved invaluable for the diagnosis of this phenotypically variable disorder1.

Williams-Beuren Syndrome (WBS) is a rare neurodevelopmental disorder caused by a deletion (approx. 1.5-1.8Mb in size, containing around 28 genes6) within chromosome band 7q11.234. The incidence of this syndrome is estimated at 1 in 7,500 to 20,000 live births5,6.

Microdeletion

Patients display a distinctive ‘elfin’ facial appearance, connective tissue problems, SupravalVular Aortic Stenosis (SVAS), growth retardation, renal anomalies, transient hypercalcaemia, hyperacusis and mental retardation7. Haploinsufficiency or hemizygosity of the elastin (ELN) gene has been identified as being responsible for the SVAS8,9 but none of the other clinical features of the syndrome have been unequivocally attributed to specific genes within the WBS deleted region. These genotype-phenotype correlations are made more difficult in WBS patients as the deletion has also been shown to have an effect on normal copy number genes that neighbour the deletion breakpoints10. The Saethre-Chotzen/Williams-Beuren Combination contains a red probe that covers the TWIST1 gene for Saethre-Chotzen syndrome and a green probe covering the area around the ELN gene in the Williams-Beuren syndrome deleted region.

TWIST1

HDAC9

FERD3L

D7S1459 D7S2495 D7S1683 D7S1400

100Kb

179kb

7p21.1

7q11.23 WBSCR22

CLDN4 WBSCR28

ELN

EIF4H

FZD9 BAZ1B

140

GTF2I NCF1

LIMK1 WBSCR27 D7S2476

148kb

GTF2IRD1 CLIP2

TBL2 RFC2 D7S613 144kb

204kb

100kb

RefeRenCes Orphanet ♯ ORPHA794: www.orpha.net Howard TD et al., Nat Genet 1997;15:36-41 El Ghouzzi V et al., Nat Genet 1997;15:42-6 Francke U et al., Hum Mol Genet 1999;8:1947-54 Stromme et al., J. Child. Neurol 2002;17:269-71 OMIM ♯194050. www.omim.org/194050 Pober BR and Dykens EM. Child Adolesc Psychiatr Clin North Am 1996;5:929-43 8. Li DY et al., Hum Mol Genet 1997;6:1021-8 9. Tassabehji M et al., Hum Mol Genet 1997;6:1029-36 10. Merla et al., Am J Hum Genet 2006; 79:332-341 1. 2. 3. 4. 5. 6. 7.

Cat. No. LPU 025-s

(5 tests)

Cat. No. LPU 025

(10 tests)

SHOX The SHOX (Short stature Homeobox-containing gene) is located in the pseudoautosomal region (PAR1) of chromosomes X and Y, in bands Xp22.33 and Yp11.321. The gene encodes a transcription factor of 292 and 225 amino acids (SHOXa and SHOXb respectively), whose translated proteins differ in the C-terminal regions. SHOX is a cell-specific homeodomain protein involved in cell cycle and growth regulation and activates transcription in osteogenic cells2. SHOX haploinsufficiency is involved in the aetiology of idiopathic short stature and the short stature observed in Turner syndrome3. Homozygous loss of the SHOX gene has been correlated with Langer type mesomelic dysplasia. Subsequently, heterozygous SHOX mutations were also shown to cause Leri-Weill dyschondrosteosis4. The incidence of SHOX deficiency is between 1 in 2000 and 1 in 5000 in the general population and between 1 in 40 and 1 in 150 in short people5,6.

RefeRenCes 1. 2. 3. 4.

Rao E et al., Nat Genet 1997;16:54-63 Rao E et al., Hum Mol Genet 2001;10:3083-91 Clement-Jones M et al., Hum Mol Genet. 2000 Mar 22;9(5):695-702 Robertson S et al., J Med Genet. 2000 Dec;37(12):959-64

5. 6.

Leka SK et al., Hormones 2006;5:107-18 Jorge AL et al., Clin Endocri 2007;66:130-5

Microdeletion

DXZ1

DYZ1 Yp11.32 Xp22.33

SHOX

DXYS153

DYS290 DXYS28 137kb

DXYS86

DXYS15

100kb

141

Cat. No. LPU 007-s

(5 tests)

Cat. No. LPU 019-s

(5 tests)

Cat. No. LPU 007

(10 tests)

Cat. No. LPU 019

(10 tests)

Smith-Magenis (RAI1 and FLII)/Miller-Dieker Probe Combinations Smith-Magenis syndrome (SMS) is a multiple congenital anomaly syndrome characterised by mental retardation, neurobehavorial abnormalities, sleep disturbances, short stature, minor craniofacial and skeletal anomalies, congenital heart defects and renal anomalies1,2. It is one of the most frequently observed human microdeletion syndromes and is associated with an interstitial deletion of the chromosome band 17p11.22. Molecular studies in SMS patients suggest a minimally deleted region (MDR) spanning approximately 700kb3,5, though the common deletion is around 4Mb in size4. The proximal boundary of the MDR is within a region of overlap between the FLII and LLGL1 genes, and the distal boundary within the PEMT gene3. Deletions or mutations in RAI1 (Retinoic Acid Induced 1) gene, which lies within the MDR, are associated with the syndrome3,5,6,7. RAI1 was shown to be the primary gene responsible for most features of SMS8,9. Microdeletion

Whilst deletion of the 17p11.2 region results in SMS, duplication of the same region results in a similar, yet distinct, disorder known as Potocki-Lupski syndrome10. Phenotypically this shares many similarities to SMS, though it is generally milder, but does have some unique clinical findings10. The common duplication involves the same 4Mb region as the SMS deletion as both syndromes are mediated by non-allelic homologous recombination between flanking low copy repeat regions4. Miller-Dieker syndrome (MDS) is a multiple malformation characterised by classical lissencephaly, a characteristic facial appearance and sometimes other birth defects11. It is associated with visible or submicroscopic rearrangements within chromosome band 17p13.3 in almost all cases12. Isolated lissencephaly sequence (ILS) consists of classical lissencephaly with no other major anomalies13. Submicroscopic deletions of chromosome 17p13.3 have been detected in almost 40% of these patients12. MDS is considered a contiguous gene deletion syndrome where deletion of physically contiguous genes leads to the complex phenotypic abnormalities observed. The PAFAH1B1 (LIS1) gene is located at 17p13.3 and is recognised as the causative gene for the lissencephaly phenotype in both MDS and ILS14,15. Deletions in MDS patients always include the PAFAH1B1 gene, together with other telomeric loci to a distance in excess of 250kb14.

142

RefeRenCes 1.

Smith ACM et al., Am J Hum Genet 1986;24:393-414

Stratton RF et al., Am J Med Genet 1986;24:421-32

Vlangos CN et al., Am J Med Genet 2005;132A(3):278-82

Lupski. Nature Genetics 2007; 39:S43 - S47

Girirajan S et al., J Med Genet 2005;42:820-8

6. 7. 8. 9. 10. 11. 12. 13. 14. 15.

Bi W et al., Am J Med Genet 2006;140(22):2454-63 Slager RE et al., Nat Genet 2003;33:466-8 Schoumans J et al., Eur J Med Genet 2005;48(3):290-300 Girirajan S et al., Genet Med 2006;8(7):417-27 Potocki et al., Am J Hum Genet 2007; 80 (4): 633â&#x20AC;&#x201C;649 Dobyns WB et al., Am J Hum Genet 1991;48:584-94 Dobyns WB et al., J Am Med Assoc 1993;270:2838-42 Dobyns WB et al., Neurology 1992;42:1375-88 Chong SS et al., Hum Mol Genet 1997;6(2):147-55 Lo Nigro C et al., Hum Mol Genet 1997;6(2):157-64

FLII

Cat. No. LPU 007

17p13.3

17p11.2

Common Deletion Region

RAI1

PAFAH1B1 CLUH D17S379

D17S2111 D17S2027 D17S1566

117kb

AF021115/ AF021118 D17S258

37kb 38kb

100kb

Cat. No. LPU 019

17p11.2

17p13.3

LRRC48 MYO15A DRG2 SMCR7 TOM1L2 FLII

PAFAH1B1

RAI1SREBF1

CLUH D17S379

D17S2021

D17S620

Microdeletion

RAI1

LRRC48 MYO15A SREBF1 DRG2 SMCR7 TOM1L2 FLII TOP3A

D17S2027 D17S2111

117kb

D17S1566

D17S620

AF021115/ AF021118 D17S258

100kb

D17S2021

158kb

143

Cat. No. LPU 026-s

(5 tests)

Cat. No. LPU 026

(10 tests)

SRY SRY (sex-determining region Y), located in band Yp11.31, is the genetic master switch of mammalian sex determination1. It encodes a transcription factor that is a member of the high mobility group (HMG) -box family of DNA binding proteins2. In mammals, it triggers the development of undifferentiated gonads into testes3. Human zygotes with mutations in SRY develop into XY females, while XX zygotes in the presence of SRY develop a male phenotype with occasional ambiguous genitalia4,5. Translocations of X and Y are rarely reported but often lead to sex reversal6. RefeRences 1. 2. 3. 4. 5. 6.

DXZ1

DYZ1

Microdeletion

Kashimada et al., Development 2010 ;137:3921-3930 Sinclair AH et al., Nature 1990;346:240-4 Koopman P et al., Nature 1991;351:117-21 Iida T et al., Hum Mol Genet 1994;3:1437-8 Kusz K et al., J Med Gene 1999;36:452-6 Ellaithi M et al., BMC Ped 2006;6:11

Yp11.31 CD99

PAR

SRY

RPS4Y1

ZFY

RH38681 DYS242

DYS234

DYS376 30kb

144

50kb

100kb

Cat. No. LPU 011-s

(5 tests)

Cat. No. LPU 011

(10 tests)

Williams-Beuren Williams-Beuren Syndrome (WBS) is a rare neurodevelopmental disorder caused by a deletion (approximately 1.5-1.8Mb in size, containing around 28 genes) within chromosome band 7q11.231. The incidence of this syndrome is estimated at 1 in 7,500 to 20,000 live births2,3,4. Patients display a distinctive ‘elfin’ facial appearance, connective tissue problems, supravalvular aortic stenosis (SVAS), growth retardation, renal anomalies, transient hypercalcaemia, hyperacusis and mental retardation5. Haploinsufficiency of the elastin (ELN) gene has been

RefeRenCes

identified as being responsible for the SVAS6,7 but none of the other

1. 2. 3. 4. 5.

clinical features of the syndrome have been unequivocally attributed to specific

genes

within

the

WBS

deleted

region.

These genotype-phenpotype correlations are made more difficult in WBS patients as the deletion has also been shown to have an effect on

6. 7. 8.

normal copy number genes that neighbour the deletion breakpoints . 8

Francke U et al., Hum Mol Genet 1999;8:1947-54 Stromme et al., J. Child. Neurol 2002;17:269-71 OMIM ♯194050. www.omim.org/194050 Schubert C. Cell Mol Life Sci 2009; 66(7):1178-97 Pober BR, Dykens EM, Child Adolesc Psychiatr Clin North Am 1996;5:929-43 Ewart et al., Nat Genet 1993; 5(1):11-16 Tassabehji M et al., Hum Mol Genet 1997;6:1029-36 Merla et al., Am J Hum Genet 2006; 79:332-341

Microdeletion

D7Z1

7q11.23 WBSCR22

CLDN4 WBSCR28

ELN

EIF4H

TBL2 FZD9 BAZ1B

GTF2IRD1

GTF2I NCF1

CLIP2 LIMK1 WBSCR27

D7S2476

RFC2 D7S613

148kb

144kb

204kb

100kb

145

Cat. No. LPU 009-s

(5 tests)

Cat. No. LPU 009

(10 tests)

Wolf-Hirschhorn Wolf-Hirschhorn syndrome is a multiple malformation syndrome characterised by severe growth deficiency, severe to profound mental retardation with the onset of convulsions in early infancy, microcephaly, sacral dimples and a characteristic face ('Greek helmet appearance')1,2. The phenotype results from the partial deletion of the short arm of chromosome 4 (4p16.3). Molecular analyses of patients with small terminal and interstitial deletions have allowed the definition of the Wolf-Hirschhorn Critical Region, which is 165kb in size and lies between D4S166 and D4S33273.

Microdeletion

4qter!

4p16.3! FGFR3

D4S168

LETM1

NELFA (WHSC2) MMSET (WHSC1)

D4S166

100kb 223kb

146

D4S43

RefeRenCes 1.

Wilson MG et al., Hum Genet 1981;59:297-307

Kohlschmidt et al., Prenat Diagn 2000;20(2):152-5

Wright TJ et al., Hum Mol Genet 1997;6(2):317-24

Cat. No. LPU 018-s

(5 tests)

Cat. No. LPU 018

(10 tests)

XIST In humans, one X chromosome is inactivated (Xi) in every female cell in order to achieve transcriptional balance. An X-linked inactivation centre (XIC) is responsible for the initiation of X inactivation. The exact size of the XIC is unclear but it includes the X-inactive specific transcript (XIST) gene at Xq13.2. This encodes a large non-coding RNA that is initially expressed on both X chromosomes before ceasing expression on the active X and becoming upregulated on the X that is to become inactivated1. The XIST RNA product coats the future Xi chromosome, spreading out from the XIC. Very small ring r(X) chromosomes that do not include the XIST gene have been associated with a more severe phenotype in syndromes such as Turner Syndrome2,3.

RefeRenCes 1. 2. 3.

Boumil RM, Lee JT et al., Hum Mol Genet 2001;10(20):2225-32 Le Caignec C et al., Prenat Diagn 2003;23(2):143-5 Bouayed Abdelmoula N, Ann Genet 2004;47(3):305-13

Microdeletion

DXZ1

Xq13.2

CHIC1

XIST DXS8235 DXS9758 DXS7717

100kb

DXS8079

189kb

147

148

Microdeletion

Paints

Paints/Satellites/ Subtelomeres

Contents 150

Painting Probes

151

Summary of Painting Probes

152

Chromoprobe Multiprobe® OctoChrome™

Painting Probes Cytocell’s Whole Chromosome Painting Probes consist of libraries of DNA sequences derived from flow-sorted chromosomes. These libraries contain sequences stretching over the entire length of the chromosome and provide superior coverage of each human

chromosome.

Applications

include

analysis

chromosome partners involved in translocations; identification of the chromosome of origin of marker chromosomes; confirmation of results obtained from M-FISH and SKY testing and may be of particular interest to those studying mutagenesis of human chromosomes as a result of exposure to genotoxic agents. Cytocell offers chromosome painting probes in the Aquarius® liquid format (summarised on page 149) and on a Chromoprobe Multiprobe®

device

where

FISH

probes

covering

chromosomes are reversibly bound to one 8 square device,

Paints

illustrated opposite.

150

Summary of Painting Probes Cytocell offers a comprehensive range of Whole Chromosome Painting probes, available in the Aquarius速 liquid format. The probes are available in either a red or a green fluorophore (Texas Red速 or FITC spectra respectively) and are supplied, ready-to-use, in hybridisation solution. The kits are available in an economical 5 test format and are supplied with DAPI counterstain.

Green Whole Chromosome Paints

Red Whole Chromosome Paints Cat. No. LPP 01R

Cat. No. LPP 02G

Cat. No. LPP 02R

Cat. No. LPP 03G

Cat. No. LPP 03R

Cat. No. LPP 04G

Cat. No. LPP 04R

Cat. No. LPP 05G

Cat. No. LPP 05R

Cat. No. LPP 06G

Cat. No. LPP 06R

Cat. No. LPP 07G

Cat. No. LPP 07R

Cat. No. LPP 08G

Cat. No. LPP 08R

Cat. No. LPP 09G

Cat. No. LPP 09R

Cat. No. LPP 10G

Cat. No. LPP 10R

Cat. No. LPP 11G

Cat. No. LPP 11R

Cat. No. LPP 12G

Cat. No. LPP 12R

Cat. No. LPP 13G

Cat. No. LPP 13R

Cat. No. LPP 14G

Cat. No. LPP 14R

Cat. No. LPP 15G

Cat. No. LPP 15R

Cat. No. LPP 16G

Cat. No. LPP 16R

Cat. No. LPP 17G

Cat. No. LPP 17R

Cat. No. LPP 18G

Cat. No. LPP 18R

Cat. No. LPP 19G

Cat. No. LPP 19R

Cat. No. LPP 20G

Cat. No. LPP 20R

Cat. No. LPP 21G

Cat. No. LPP 21R

Cat. No. LPP 22G

Cat. No. LPP 22R

Cat. No. LPP 0XG

Cat. No. LPP 0XR

Cat. No. LPP 0YG

Cat. No. LPP 0YR

Paints

Cat. No. LPP 01G

151

Cat. No. PMP 802

(2 devices)

Cat. No. PMP 804

(5 devices)

Cat. No. PMP 803

(10 devices)

Chromoprobe Multiprobe® OctoChrome™ Cytocell's Chromoprobe Multiprobe® OctoChrome™ combines the utility of an 8 square Multiprobe device and our Whole Chromosome Painting probes (labelled in 3 different colours), to allow all 24 chromosomes to be identified on a single slide. The OctoChrome™ device therefore allows simultaneous analysis of the whole genome on one slide, in one hybridisation. Each square of the device carries whole chromosome painting probes for three different chromosomes labelled in three different colour fluorophores: red, green and blue (Texas Red®, FITC and Aqua spectra, respectively). These are visible simultaneously with a DAPI/FITC/Texas Red® triple filter or individually through specific single filters. The arrangement of chromosome combinations on the Octochrome™ device has been specifically designed to facilitate the identification of non-random chromosome rearrangements that are found in the most common leukaemias.

Paints

Chromoprobe Multiprobe® OctoChrome™ Device Layout

152

Satellites

Satellite Enumeration Probes Contents 154

Satellite Enumeration Probes

155

Dual Labelled Satellite Probe Sets

155

Acro-P-Arm Probe

Cytocell’s Satellite Enumeration probes are chromosome specific sequences generated from highly repeated human satellite DNA located in the centromeric, pericentromeric or heterochromatic regions of each chromosome. These probes allow rapid identification and enumeration of human chromosomes in interphase and metaphase cells of postnatal samples. Cytocell offers a complete range of satellite probes available in the Aquarius® liquid format. The probes are available independently and directly labelled in either red or green. They are produced in a concentrated form to allow the mixing, if required, of up to 3 satellite probes in the same hybridisation. The kits are supplied in an economical 5 test format and come complete with hybridisation solution and DAPI counterstain.

Satellites

Green Satellite Enumeration Probes

154

Red Satellite Enumeration Probes

Cat. No. LPe 001G

Cat. No. LPe 001R

Cat. No. LPe 002G

Cat. No. LPe 002R

Cat. No. LPe 003G

Cat. No. LPe 003R

Cat. No. LPe 004G

Cat. No. LPe 004R

Cat. No. LPe 005G (Chromosome 1,5,19)

Cat. No. LPe 005R (Chromosome 1,5,19)

Cat. No. LPe 006G

Cat. No. LPe 006R

Cat. No. LPe 007G

Cat. No. LPe 007R

Cat. No. LPe 008G

Cat. No. LPe 008R

Cat. No. LPe 009G

Cat. No. LPe 009R

Cat. No. LPe 010G

Cat. No. LPe 010R

Cat. No. LPe 011G

Cat. No. LPe 011R

Cat. No. LPe 012G

Cat. No. LPe 012R

Cat. No. LPe 013G (Chromosome 13,21)

Cat. No. LPe 013R (Chromosome 13,21)

Cat. No. LPe 014G (Chromosome 14,22)

Cat. No. LPe 014R (Chromosome 14,22)

Cat. No. LPe 015G

Cat. No. LPe 015R

Cat. No. LPe 016G

Cat. No. LPe 016R

Cat. No. LPe 017G

Cat. No. LPe 017R

Cat. No. LPe 018G

Cat. No. LPe 018R

Cat. No. LPe 020G

Cat. No. LPe 020R

Cat. No. LPe 0XG

Cat. No. LPe 0XR

Cat. No. LPe 0YcG

Cat. No. LPe 0YcR

Cat. No. LPe 0YqG

Cat. No. LPe 0YqR

Cat. No. LPe 0XYc Cat. No. LPe 0XYq

Dual Labelled Satellite Probe Sets We also offer two dual labelled X and Y probe sets, available in the Aquarius速 liquid range in a 10 test format. These may be used to identify human X and Y chromosomes in both interphase and metaphase cells. XYc: Xp11.1-q11.1 directly labelled with a green fluorophore and

XYq probe (patient after sex-mismatched bone marrow transplant)

Yp11.1-q11.1 with a red fluorophore. XYq: Xp11.1-q11.1 directly labelled with a green fluorophore and Yq12 with a red fluorophore. These probes are designed for use on cultured peripheral blood and bone marrow cells.

Cat. No. LPe nOR

Acro-P-Arm Probe The Nucleolar Organiser Regions (NOR) contain clusters of genes which code for the three largest structural rRNA molecules (5.8S, 18S and 28S). Satellites

These rRNA genes are critically important for the viability of the cell and represent around 0.5% of the human diploid genome. They are found in the short arm of the acrocentric chromosomes and are the region around which the nucleoli develop at the end of mitosis1. A NOR can translocate to a terminal region of another chromosome. In rare instances this can be pathogenic, particularly when the

RefeRenCes 1. 2.

translocation has led to a deletion at the tip of the recipient chromosome2. It has been suggested that the restructuring of the rRNA genes is the most common chromosomal alteration in adult solid

3. 4.

McClintock B, Z Zellforsch Mikrosk Anat 1934;21:294-328 Gardner RJM, Grant R Sutherland, Chromosome abnormalities and genetic counseling, Oxford University Press p240 2004 Stults DM et al., Cancer Res 2009;69(23):9096-104 Goodpasture C, Bloom SE, Chromosoma 1975;53:37-50

tumours3. In routine cytogenetic analysis, NOR can be used to delineate marker chromosomes through a process of silver staining the NOR (known as AgNOR staining4). However, the technique relies on translation of protein and if this is not present, conventional silver staining will not stain the NOR. Cytocell's FISH probe has been developed to overcome this problem so that presence of the acrocentric chromosomes in the marker can be detected.

155

156

Satellites

Subtelomeres

Contents 158

Subtelomere Specific Probes

159

Aquarius速 Subtelomere Specific Probes

160

Chromoprobe Multiprobe速-T Applications

161

Chromoprobe Multiprobe速 -T Device

Subtelomere Specific Probes Chromosomal rearrangements involving the ends of chromosomes have emerged as an important cause of genetic disease given the gene-rich nature of the regions adjacent to the telomeres1. The importance of such subtelomeric chromosome rearrangements has been clearly shown by their observed association with unexplained mental retardation and congenital abnormalities2. Individual subtelomere specific probes have been used to focus on particular subtelomeric regions and have resulted in the establishment of syndromes such as the chromosome 1p36 deletion syndrome3,10 and the 22q13.3 deletion syndrome4. The probes are also finding applications in the investigation of autistic disorders5, recurrent miscarriages6 and haematological malignancies7. Cytocell's subtelomere specific probes are located in the most distal region of chromosome specific DNA on each chromosome. Beyond this unique sequence material is the 100 to 300kb region of telomere associated repeat followed by the cap of between 3 to 20kb of tandemly repeated (TTAGGG)n sequence8.

Subtelomeres

The probes have been chosen from the most distal unique sequence to provide the best possible specificity, whilst also being applicable for routine use for the examination of subtelomeric enumeration and integrity. The original second-generation set of probes is derived from PAC clones9 and was established in conjunction with the Institute of Molecular Medicine, part of Oxford University, in the UK11. Continuing product improvements have led to some substitutions with alternative cosmid (35-40kb) or BAC (150kb) clones to give improved signal strength or chromosome specificity.

For references, see Chromoprobe Multiprobe速- T Applicaitions page 160.

158

Aquarius® Subtelomere Specific Probes Cytocell also offers a complete set of subtelomere specific probes available in the Aquarius® liquid format. The set identifies 41 of the 46 human subtelomeres with the exclusion of the p-arm telomeres of the acrocentric chromosomes. The probes are available independently and directly labelled in either a red or a green fluorophore (Texas Red® or FITC spectra respectively). The probes are supplied in an economical 5 test format and are concentrated to allow the mixing, if required, of up to 3 Aquarius® subtelomere specific probes in the same hybridisation. The kits come complete with hybridisation solution, DAPI counterstain and full instructions for use. For probe specifications, please refer to the Aquarius® Subtelomere Specific Probe Range Summary chart in the Index section.

p-arm Subtelomere Specific Probes

q-arm Subtelomere Specific Probes

LPT 01PR/G

LPT 01QR/G

LPT 02PR/G

LPT 02QR/G

LPT 03PR/G

2q NP LPT 02QnPR/G

LPT 04PR/G

LPT 03QR/G

LPT 05PR/G

LPT 04QR/G

LPT 06PR/G

LPT 05QR/G

LPT 07PR/G

LPT 06QR/G

LPT 08PR/G

LPT 07QR/G

LPT 09PR/G

LPT 08QR/G

10p LPT 10PR/G

LPT 09QR/G

11p LPT 11PR/G

10q

LPT 10QR/G

12p LPT 12PR/G

11q

LPT 11QR/G

12q

LPT 12QR/G

13q

LPT 13QR/G

14q

LPT 14QR/G

15q

LPT 15QR/G

16p LPT 16PR/G

16q

LPT 16QR/G

17p LPT 17PR/G

17q

LPT 17QR/G

18p LPT 18PR/G

18q

LPT 18QR/G

19p LPT 19PR/G

19q

LPT 19QR/G

20p LPT 20PR/G

20q

LPT 20QR/G

21q

LPT 21QR/G

22q

LPT 22QR/G

XpYp LPT XYPR/G

Subtelomeres

XqYq LPT XYQR/G

159

Chromoprobe Multiprobe® -T Applications Subtelomeric rearrangements in idiopathic mental retardation and/or in malformation syndromes Over the past 20 years, there have been numerous large and small scale studies that have shown the importance of subtelomeric chromosome rearrangements as a major cause of mental retardation and/or malformation syndromes. The largest study, involving screening of 11,688 cases, reported clinically significant subtelomeric abnormalities in around 2.5% of cases, with an additional 0.5% detection rate of familial variants12. Previous studies showed abnormality rates to be between 2 and 29%, with the large variance in figures most likely being due to sampling biases, with estimates being higher in patients with moderate to severe metal retardation than those with a mild version12,13,14. The Chromoprobe Multiprobe®-T assay allows, in one single experiment, the identification of subtle chromosome rearrangements in patients suspected of carrying a chromosome anomaly, but who have an apparently normal karyotype.

Characterisation of known abnormalities Subtelomeric chromosome rearrangement screening has been clearly associated with the establishment of new syndromes such as the chromosome 1p36 deletion syndrome10 and the 22q13.3 deletion syndrome11. RefeRenCes

Subtelomeres

Autistic disorders Several reports have associated subtelomeric chromosomal rearrangements with autistic disorders5.

Recurrent miscarriages Subtelomeric rearrangements are also being investigated in recurrent miscarriages6.

Haematological cancers Other clinical applications include the characterisation of haematological abnormalities7 initially detected by standard cytogenetic studies but where further submicroscopic rearrangements cannot be ruled out by the limited resolution of standard karyotyping. Therefore, telomere screening provides confirmation and further characterisation of these cases.

160

1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14.

Saccone et al., Proc Natl Acad Sci USA 1992;89(11):4913-7 Flint et al., Nat Genet 1997;15(3):252-7 Heilstedt et al., Clin Genet 2003;64(4):310-6 Luciani et al., J Med Genet 2003;40(9):690-6 Wolff et al., Genet in Med 2002;4(1):10-4 Yakut et al., Clin Genet 2002;61(1):26-31 Tosi et al., Genes Chrom Cancer 1999;25(4):384-92 Moyzis et al., Proc Natl Acad Sci USA 1988;85:6622-6 Knight et al., Am J Hum Genet 2000;67:320–32 Institute of Molecular Medicine and National Institute of Health Collaboration, Nat Genet 1997;14:86-9 Knight et al., Eur J Hum Genet 1997;5:1-6 Ravnan et al., J Med Genet 2006;43:478–489 Biesecker LG. Am J Med Genet 2002;107:263–6 Knight et al., Lancet 1999;354(9191):1676–81

Cat. No. PMP 009

(2 devices)

Cat. No. PMP 008

(5 devices)

Cat. No. PMP 007

(10 devices)

Chromoprobe Multiprobe速 -T Device The Chromoprobe Multiprobe速-T device is divided into 24 squares. Each square carries subtelomere specific probes for both the p-arm and the q-arm of one of the 23 chromosomes (except for the acrocentric chromosomes). The p-arm and the q-arm probes for each chromosome are labelled in different colours with two spectrally independent fluorophores (green and red respectively). These are located together in the corresponding Multiprobe square. This format provides each other with an internal hybridisation control and effective chromosome identification.

2p 3p

10p

11p

12p

10q

11q

12q

13q

14q

16p 16q

15q

2QNP

XpYp 17p 2111b1 17q

18p 18q

20p 20q

21q

22q

XqYq

2q NP

Subtelomeres

19p 19q

161

162

Subtelomeres

ZOO FISH

ZOO FISH For information regarding products soon to be available in the Cytocell ZOO FISH probe range, or to discuss your requirements for a custom ZOO FISH probe, please contact Cytocell.

Aquarius® ZOO FISH Range To further complement our Aquarius® Murine Whole Chromosome Painting probe range Cytocell has also developed liquid FISH probes for the following species: • Pig - Whole Chromosome Painting Probes

Pig Chromosome 1,X,Y on a Pig metaphase

- Subtelomere Probes • Chicken - Whole Chromosome Painting Probes - Subtelomere Probes

Chromoprobe Multiprobe® Macroarray Cytocell’s Chromoprobe Multiprobe® Murine Octochrome combines the utility of an 8 square device and whole chromosome painting probes (labelled in 3 different colours), to allow all 21 mouse chromosomes to be identified. ZOO FISH

Using our unique Chromoprobe process, multiple mouse probes are reversibly bound to a single glass slide providing a convenient screening tool for assessment of chromosome numbers, breakages or rearrangements.

Chromoprobe Multiprobe® Murine Octochrome

Custom ZOO Probes Cytocell offers a custom design and build service to produce unique FISH probes using our BAC-2-FISHTM process. This exciting service enables the creation of personalised probes that meet your specific needs.

164

Murine Painting Probes* Cytocell offers a comprehensive range of Murine Whole Chromosome Painting probes for the assessment of chromosome number, breakage or rearrangement. Our Whole Chromosome Paints were initially developed from flow sorted Mus musculus chromosomes in the laboratory of Prof. Malcolm Ferguson-Smith, Cambridge University Department of Veterinary Medicine, UK. With current advances in murine research, Cytocell has optimised each of the Murine Painting probes for use on Formalin Fixed Paraffin Embedded (FFPE) tissue and fixed cell suspensions. Having reviewed current laboratory practices, we are the only manufacturer to offer optional hyb. times – 4 hours or overnight. The probes are available in either a red or a green fluorophore (Texas Red® or FITC spectra respectively) to enable multiple paints to be combined in a single reaction. They are provided ready-to-use in hybridisation solution and supplied with DAPI counterstain. The kits are available in an economical 5 or 10 test format. Aquarius® Murine Whole Chromosome Painting probes provide you with the advantage of: • FAST hyb. time – 4 hours or overnight

• Multiple sample types

• Ability to mix multiple paints

• Ready-to-use reagents

• Simple FISH protocol

• Specific high intensity signals

• Minimal background

• Economical kit format

Cat. No. AMP 01R

Cat. No. AMP 02G

Cat. No. AMP 02R

Cat. No. AMP 03G

Cat. No. AMP 03R

Cat. No. AMP 04G

Cat. No. AMP 04R

Cat. No. AMP 05G

Cat. No. AMP 05R

Cat. No. AMP 06G

Cat. No. AMP 06R

Cat. No. AMP 07G

Cat. No. AMP 07R

Cat. No. AMP 08G

Cat. No. AMP 08R

Cat. No. AMP 09G

Cat. No. AMP 09R

Cat. No. AMP 10G

Cat. No. AMP 10R

Cat. No. AMP 11G

Cat. No. AMP 11R

Cat. No. AMP 12G

Cat. No. AMP 12R

Cat. No. AMP 13G

Cat. No. AMP 13R

Cat. No. AMP 14G

Cat. No. AMP 14R

Cat. No. AMP 15G

Cat. No. AMP 15R

Cat. No. AMP 16G

Cat. No. AMP 16R

Cat. No. AMP 17G

Cat. No. AMP 17R

Cat. No. AMP 18G

Cat. No. AMP 18R

Cat. No. AMP 19G

Cat. No. AMP 19R

Cat. No. AMP 0XG

Cat. No. AMP 0XR

Cat. No. AMP 0YG

Cat. No. AMP 0YR

ZOO FISH

Cat. No. AMP 01G

*These products are for research use only, not for use in diagnostic procedures.

165

166

ZOO FISH

Accessories

Accessories Accessories Cat. no.

Description

PCN004

Hybridisation Chamber

Unit size

PCN007

24 Square Template Slides

100

PCN008

8 Square Template Slides

100

PCN002

Cytocell Slide Surface Thermometer

Ancillary Reagents Cat. no.

Description

PCA005

Rubber Solution Glue

Unit size

PCN003

Mounting Medium

10ml

DES500L

0.125µg/ml DAPI

500μl

DES1000L

0.125μg/ml DAPI

1000µl

DFS500L

1.0µg/ml DAPI

500μl

DSS500L

0.0625μg/ml DAPI

500µl

HA500L

Hybridisation Solution A

500μl

HA1000L

Hybridisation Solution A

1000μl

HB500L

Hybridisation Solution B

500μl

HB1000L

Hybridisation Solution B

1000μl

PCA003

20x SSC

100ml

15g

Microscope filters* Cat. no.

Description

Unit size

N/A

FITC Filter

N/A

DAPI Filter

N/A

Texas Red Filter

N/A

DEAC Filter

N/A

FITC/Texas Red Dual Filter

N/A

FITC/DAPI/Texas Red Triple Filter

Accessories

* Filter cubes are available upon request, please specify the name of the microscope manufacturer and model name/number.

168

Indices

Aquarius® Haematology Probe Range summary Probe name

Chromosome Region

Probe Type

13q14.3

13q14.2-q14.3

Deletion

13qter

5 or 10

LPH 006

Alpha Satellite 12 Plus for CLL

12p11.1-q11.1

Enumeration

−

5 or 10

LPH 069

AML1 (RUNX1)

21q22.12

Breakapart

−

5 or 10

LPH 027

AML1/ETO (RUNX1/RUNX1T1) Dual Fusion

21q22.12/8q21.3

Translocation

−

5 or 10

LPH 026

ATM

11q22.3

Deletion

BCL6

3q27.3

Breakapart

5 or 10

LPH 011

−

5 or 10

LPH 035

22q11.22-q11.23/9q34.11-q34.12 Translocation

−

5 or 10

LPH 007

BCR/ABL(ABL1) Plus Dual Fusion

22q11.22-q11.23/9q34.11-q34.12 Translocation

−

5 or 10

LPH 038

CBFβ/MYH11 Dual Fusion

16p13.11/16q22.1

Translocation

−

5 or 10

LPH 022

CKS1B/CDKN2C(P18)

1p32.3/1q21.3

Amplification/Deletion

−

5 or 10

LPH 039

cMYC (MYC)

8q24.21

Breakapart

−

5 or 10

LPH 010

CRLF2

Xp22.33/Yp11.32

Breakapart

D13S319 Plus

13q14.2

Deletion

13qter

5 or 10

D13S319/13qter/12cen

13q14.2/12cen

Deletion/Enumeration

13qter

5 or 10

LPH 066

D13S25

13q14.3

Deletion

13qter

5 or 10

LPH 043

Del(5q)

5p15.31-5q13.2

Deletion

5p15.31

5 or 10

LPH 024

Del(7q)

7q22.1-q22.2/7q31.2

Deletion

−

5 or 10

LPH 025

Del(20q)

20q12/20q13.12

Deletion

−

5 or 10

LPH 020

E2A (TCF3)

19p13.3

Breakapart

−

5 or 10

LPH 019

E2A/PBX1 Dual Fusion

19p13.3/1q23.3

Translocation

−

5 or 10

LPH 079

E2A/PBX1/HLF Dual Fusion

19p13.3/1q23.3/17q22

Translocation

−

5 or 10

LPH 080

EVI1 (MECOM)

3q26.2

Breakapart

−

5 or 10

LPH 036

−

50µl or 100µl RU-LPH 085** LPH 068

FIP1L1/CHIC2/PDGFRA

4q12

Deletion/Fusion

−

5 or 10

LPH 032

IGH Plus

14q32.33

Breakapart

−

5 or 10

LPH 070

IGH/BCL2 Plus Dual Fusion

14q32.33/18q21.33

Translocation

−

5 or 10

LPH 071

IGH/CCND1 Plus Dual Fusion

14q32.33/11q13.3

Translocation

−

5 or 10

LPH 072

IGH/CCND3 Plus Dual Fusion

14q32.33/6p21

Translocation

−

5 or 10

LPH 075

IGH/cMYC(MYC) Plus Dual Fusion

14q32.33/8q24.21

Translocation

−

5 or 10

LPH 076

IGH/FGFR3 Plus Dual Fusion

14q32.33/4p16.3

Translocation

−

5 or 10

LPH 074

IGH/MAF Plus Dual Fusion

14q32.33/16q23.1-q23.2

Translocation

−

5 or 10

LPH 073

IGH/MAFB Plus Dual Fusion

14q32.33/20q12

Translocation

−

5 or 10

LPH 077

IGH/MYEOV Plus Dual Fusion

14q32.33/11q13.3

Translocation

−

5 or 10

LPH 078

IGK

2p11.2

Breakapart

−

5 or 10

LPH 034

IGL

22q11.21-q11.23

Breakapart

−

5 or 10

LPH 033

MLL (KMT2A)

11q23.3

Breakapart

−

5 or 10

LPH 013

MLL/AFF1 Dual Fusion

11q23.3/4q21.3-q22.1

Translocation

−

5 or 10

LPH 081

MLL/MLLT1 Dual Fusion

11q23.3/19p13.3

Translocation

−

50µl or 100µl RU-LPH 082**

MLL/MLLT3 Dual Fusion

11q23.3/9p21.3

Translocation

−

50µl or 100µl RU-LPH 083**

MLL/MLLT4 Dual Fusion

11q23.3/6q27

Translocation

−

50µl or 100µl RU-LPH 084**

MYB

6q23.3

Deletion

D6Z1

5 or 10

LPH 016

P16 (CDKN2A)

9p21.3

Deletion

D9Z3

5 or 10

LPH 009

P2RY8

Xp22.33/Yp11.32

Deletion

−

P53 (TP53)

17p13.1

Deletion

D17Z1

5 or 10

LPH 017

P53(TP53)/ATM Probe Combination

17p13.1/11q22.3

Deletion

−

5 or 10

LPH 052

PDGFRB

5q32

Breakapart

−

5 or 10

LPH 031

FAST PML/RARα(RARA) Dual Fusion 15q24.1/17q21.1-q21.2

Translocation

−

5 or 10

LPH 064

PML/RARα(RARA) Dual Fusion

Translocation

−

5 or 10

LPH 023

15q24.1/17q21.1-q21.2

50µl or 100µl RU-LPH 086**

RARα (RARA)

17q21.1-q21.2

Breakapart

−

5 or 10

LPH 065

TCL1

14q32.13-q32.2

Breakapart

−

5 or 10

LPH 046

TCRAD

14q11.2

Breakapart

−

5 or 10

LPH 047

TCRB (TRB)

7q34

Breakapart

−

5 or 10

LPH 048

TEL/AML1 (ETV6/RUNX1) Dual Fusion 12p13.2/21q22.12

Translocation

−

5 or 10

LPH 012

TLX1

10q24.31

Breakapart

−

5 or 10

LPH 049

TLX3

5q35.1

Breakapart

−

5 or 10

LPH 050

** for research use only, not for use in diagnostic procedures.

Indices

D11Z1

BCR/ABL(ABL1) Dual Fusion

* for 5 test kit add -S to catalogue number, e.g: LPH ###-S

170

Control Probe no. Tests Cat. no.*

CLL PROfILeR Kit, LPH 067 or LPH 067-s Product Description

Chromosome Region

Probe Type

P53(TP53)/ATM

17p13.1/11q22.3

Deletion

D13S319/13qter/12cen

13q14.2/12cen

Deletion/Enumeration

Control Probe

no. Tests

−

5 or 10

13qter

5 or 10

Control Probe

no. Tests

* for 5 test kit add -S to catalogue number, e.g: LPH ###-S

CLL Plus screening Panel, LPH 087 or LPH 087-s Product Description

Chromosome Region

Probe Type

P53 (TP53)

17p13

Deletion

D17Z1

5 or 10

ATM

11q22.3

Deletion

D11Z1

5 or 10

MYB

6q23

Deletion

D6Z1

5 or 10

13q14.3

Deletion

13qter

5 or 10

Alpha Satellite 12 Plus for CLL

12p11.1-q11.1

Enumeration

−

5 or 10

* for 5 test kit add -S to catalogue number, e.g: LPH ###-S

Chromoprobe Multiprobe® - ALL v2 system Range summary Probe name

no. of Devices

Cat. no.

Chromoprobe Multiprobe® - ALL System

PMP 030

Chromoprobe Multiprobe® - ALL System

PMP 031

Chromoprobe Multiprobe® - ALL System

PMP 032

Chromoprobe Multiprobe® - ALL System

PMP 033*

* supplied as 4 x 5 Multiprobe devices

Chromoprobe Multiprobe® - CLL system Range summary Probe name

no. of Devices

Cat. no.

Chromoprobe Multiprobe® - CLL System

PMP 018

Chromoprobe Multiprobe® - CLL System

PMP 017

Chromoprobe Multiprobe® - CLL System

PMP 016

Chromoprobe Multiprobe® - CLL System

PMP 020*

* supplied as 4 x 5 Multiprobe devices

Chromoprobe Multiprobe® - AML/MDs system Range summary Probe name

no. of Devices

Cat. no.

Chromoprobe Multiprobe® - AML System

PMP 025

Chromoprobe Multiprobe® - AML System

PMP 026

Chromoprobe Multiprobe® - AML System

PMP 027

Chromoprobe Multiprobe® - AML System

PMP 028*

* supplied as 4 x 5 Multiprobe devices

Indices

171

Aquarius® Tissue Pretreatment Kit summary Product Description

Kit format

Cat. no.

Aquarius® Tissue Pretreatment Kit*

Reagent 1 (1x1L), Reagent 2 (1x10mL)

LPS 100

* This product is provided under an agreement between Life Technologies Corporation and Cytocell Ltd and is available for human diagnostic or life science use only.

Aquarius® Haematopathology Probe Range summary Probe name

Chromosome Region

Probe Type

Control Probe

no. Tests

Cat. no.*

BCL2

18q21.33-q22.1

Breakapart

−

5 or 10

LPS 028

BCL6

3q27.3-q28

Breakapart

−

5 or 10

LPS 029

CCND1

11q13.3

Breakapart

−

5 or 10

LPS 030

IGH

14q32.33

Breakapart

−

5 or 10

LPS 032

IGH/BCL2 Dual Fusion

14q32.33/18q21.33

Translocation

−

5 or 10

LPS 033

IGH/CCND1 Dual Fusion

14q32.33/11q13.3

Translocation

−

5 or 10

LPS 031

IGH/MALT1 Dual Fusion

14q32.33/18q21.31-q21.32

Translocation

−

5 or 10

LPS 034

IGH/MYC Dual Fusion

14q32.33/8q24.21

Translocation

−

5 or 10

LPS 035

IGK

2p11.2

Breakapart

−

5 or 10

LPS 038

IGL

22q11.21-q11.23

Breakapart

−

5 or 10

LPS 039

MYC

8q24.21

Breakapart

−

5 or 10

LPS 027

P16 (CDKN2A)

9p21.3

Deletion

D9Z3

5 or 10

LPS 036

P53 (TP53)

17p13.1

Deletion

D17Z1

5 or 10

LPS 037

* for 5 test kit add -S to catalogue number, e.g: LPS ###-S

Aquarius® Pathology Probe Range summary Probe name

Chromosome Region

Probe Type

ALK

2p23.2-p23.1

Breakapart

CHOP (DDIT3)

12q13.3

Breakapart

C-MET (MET)

7q31.2

Amplification

EGFR

7p11.2

Amplification

EML4

2p21

EWSR1

22q12.1-q12.2

EWSR1/ERG Dual Fusion

21q22.13-q22.2/22q12.1-q12.2 Translocation

FGFR1

8p11.23-p11.22

Breakapart/Amplification

FLI1/EWSR1 Dual Fusion

11q24.3/22q12.1-q12.2

HER2 (ERBB2) MALT1

Indices

Cat. no.*

−

5 or 10

LPS 019

−

5 or 10

LPS 015

D7Z1

5 or 10

LPS 004

D7Z1

5 or 10

LPS 003

Breakapart

−

5 or 10

LPS 020

Breakapart

−

5 or 10

LPS 006 LPS 008

−

5 or 10

D8Z2

5 or 10

LPS 018

Translocation

−

5 or 10

LPS 007

17q12

Amplification

D17Z1

5 or 10

LPS 001

18q21.31-q21.32

Breakapart

−

5 or 10

LPS 017

MDM2

12q15

Amplification

D12Z1

5 or 10

LPS 016

N-MYC (MYCN)

2p24.3/2q11.2

Amplification

AFF3 (2q11.2)

5 or 10

LPS 009

PAX3

2p36.1

Breakapart

−

5 or 10

LPS 012

PAX7

1p36.13

Breakapart

LPS 013

RB1

13q14.2

Deletion

ROS1

6q22.1

Breakapart

SRD (CHD5)

1p36.31

Deletion

SYT (SS18)

18q11.2

Breakapart

TMPRSS2/ERG

21q22.2-q22.3/21q22.13-q22.2 Deletion/Breakapart

TOP2A

17q21.2

Amplification/Deletion

ZNF217

20q13.2

Amplification

* for 5 test kit add -S to catalogue number, e.g: LPS ###-S

172

Control Probe no. Tests

−

5 or 10

13qter

5 or 10

LPS 011

−

5 or 10

LPS 022

1qter

5 or 10

LPS 010

−

5 or 10

LPS 014

ERG (21q22.2)

5 or 10

LPS 021

D17Z1

5 or 10

LPS 002

20pter

5 or 10

LPS 005

Aquarius速 FAST fIsH Prenatal Probe Range summary Product Description

Locus

Chromosome Region

X centromere

DXZ1

Xp11.1-q11.1

Y centromere

DYZ3

Yp11.1-q11.1

18 centromere

D18Z1

18p11.1-q11.1

13 unique sequence

N/A

13q14.2

21 unique sequence

N/A

21q22.13

X centromere

DXZ1

Xp11.1-q11.1

Y centromere

DYZ3

Yp11.1-q11.1

18 centromere

D18Z1

18p11.1-q11.1

13 unique sequence

N/A

13q14.2

21 unique sequence

N/A

21q22.13

Probe set 1 and 2

Probe set 1

Probe set 2

no. Tests

Cat. no.*

5, 10, 30 or 50

LPF 001

5 or 10

LPF 002

5 or 10

LPF 003

* for 5, 30 or 50 test kit add -S, -30 or -50 to the catalogue number respectively, e.g: LPF### -S, LPF### -30 or LPF### -50

Aquarius速 Prenatal Probe Range summary Product Description

Locus

Chromosome Region

X centromere

DXZ1

Xp11.1-q11.1

Y centromere

DYZ3

Yp11.1-q11.1

18 centromere

D18Z1

18p11.1-q11.1

13 unique sequence

N/A

13q14.2

21 unique sequence

N/A

21q22.13

X centromere

DXZ1

Xp11.1-q11.1

Y centromere

DYZ3

Yp11.1-q11.1

18 centromere

D18Z1

18p11.1-q11.1

13 unique sequence

N/A

13q14.2

21 unique sequence

N/A

21q22.13

N/A

13q14.2

Probe set 1 and 2

Probe set 1

Probe set 2

Probe set 3 13 unique sequence 18 centromere

D18Z1

18p11.1-q11.1

21 unique sequence

N/A

21q22.13

18 centromere blue

D18Z1

18p11.1-q11.1

no. Tests

Cat. no.*

5, 10, 30 or 50

LPA 001

5 or 10

LPA 002

5 or 10

LPA 003

5 or 10

LPA 005

5 or 10

LPA 004

* for 5, 30 or 50 test kit add -S, -30 or -50 to the catalogue number respectively, e.g: LPA### -S, LPA### -30 or LPA### -50

Indices

173

Aquarius® Microdeletion Probe Range summary Probe name

Chromosome Region

Probe Loci

Alagille (JAG1)

20p12.2

JAG1

20qter

5 or 10

LPU 012

Angelman (UBE3A/D15S10)

15q11.13

UBE3A/D15S10

15qter

5 or 10

LPU 006

D8Z1

5 or 10

LPU 021

−

5 or 10

LPU 013

CHARGE

8q12.1-q12.2

CHD7

Cri-Du-Chat and SOTOS Probe Combination

5p15.31/5p15.2/5q35

UBE2QL1, CTNND2, NSD1

DiGeorge II (10p14)

10p14

CELF2

D10Z1

5 or 10

LPU 015

DiGeorge TBX1 and 22q13.3 Probe Combination

22q11.21/22q13.33

TBX1, SHANK3

−

5 or 10

LPU 014

DiGeorge/VCFS N25 and 22q13.3 Probe Combination

22q11.21/22q13.33

N25/D22S75, SHANK3

−

5 or 10

LPU 010

DiGeorge/VCFS TUPLE1 and 22q13.3 Probe Combination

22q11.21/22q13.33

TUPLE1, SHANK3

−

5 or 10

LPU 004

KAL1, STS

DXZ1

5 or 10

LPU 016

Kallmann (KAL1) and Steroid Xp22.31 Sulphatase Deficiency (STS) Probe Combination Langer-Giedion

8q23.3/8q24.11

TRPS1, EXT1

D8Z2

5 or 10

LPU 022

Monosomy 1p36

1p36.33

SKI

1qter

5 or 10

LPU 020

Neurofibromatosis Type 1

17q11.2

NF1

17pter

5 or 10

LPU 017

Prader-Willi/Angelman (SNRPN)

15q11.2

SNRPN

15qter

5 or 10

LPU 005

Rubinstein-Taybi

16p13.3

CREBBP

D16Z2

5 or 10

LPU 023

Saethre-Chotzen/Williams-Beuren Probe Combination

7p21.1/7q11.23

TWIST1, WBSCR/ELN

−

5 or 10

LPU 024

SHOX

Xp22.33/Yp11.32

SHOX

DXZ1, DYZ1

5 or 10

LPU 025

Smith-Magenis (RAI1)/ Miller-Dieker Probe Combination

17p11.2/17p13.3

RAI1, PAFAH1B1

−

5 or 10

LPU 019

Smith-Magenis (FLII)/ Miller-Dieker Probe Combination

17p11.2/17p13.3

FLII, PAFAH1B1

−

5 or 10

LPU 007

SRY

Yp11.31

SRY

Williams-Beuren

7q11.23

WBSCR/ELN

Indices

DXZ1, DYZ1

5 or 10

LPU 026

D7Z1

5 or 10

LPU 011

Wolf-Hirschhorn

4p16.3

MMSET, NEFLA

4qter

5 or 10

LPU 009

XIST

Xq13.2

XIST

DXZ1

5 or 10

LPU 018

* for 5 test kit add -S to catalogue number, e.g: LPU ###-S

174

Control Probe no. Tests Cat. no.*

Aquarius® Whole Chromosome Painting Probe Range summary Chromosome

fluorescent Label

Red or Green

no. Tests 5

Cat. no.* LPP 01R/G

Red or Green

LPP 02R/G

Red or Green

LPP 03R/G

Red or Green

LPP 04R/G

Red or Green

LPP 05R/G

Red or Green

LPP 06R/G

Red or Green

LPP 07R/G

Red or Green

LPP 08R/G

Red or Green

LPP 09R/G

Red or Green

LPP 10R/G

Red or Green

LPP 11R/G

Red or Green

LPP 12R/G

Red or Green

LPP 13R/G

Red or Green

LPP 14R/G

Red or Green

LPP 15R/G

Red or Green

LPP 16R/G

Red or Green

LPP 17R/G

Red or Green

LPP 18R/G

Red or Green

LPP 19R/G

Red or Green

LPP 20R/G

Red or Green

LPP 21R/G

Red or Green

LPP 22R/G

Red or Green

LPP 0XR/G

Red or Green

LPP 0YR/G

* R specifies a red label, G specifies a green label

Whole Chromosome Paint Combinations Chromosome

Description

1/2/4

Whole chromosome paint combination 1,2,4 (3 colour, 3 probe combination) directly labelled

no. Tests

Cat. no.*

LPP 124

* Minimum order of ten units (100 tests). Orders are subject to 4-6 weeks lead time

Chromoprobe Multiprobe®-OctoChrome™ Paint system Range summary Probe name

no. of Devices

Cat. no.

Chromoprobe Multiprobe® - OctoChrome™ System

PMP 802

Chromoprobe Multiprobe® - OctoChrome™ System

PMP 804

Chromoprobe Multiprobe® - OctoChrome™ System

PMP 803

Indices

175

Aquarius® satellite enumeration Probe Range summary Chromosome

Locus

Chromosome Region

DnA Class

D1Z1

1q12

satellite III

LPE 001R/G

D2Z2

2p11.1-q11.1

LPE 002R/G

D3Z1

3p11.1-q11.1

LPE 003R/G

D4Z1

4p11.1-q11.1

α-satellite

LPE 004R/G

1/5/19

D1Z7

1p11.1-q11.1

LPE 005R/G

D5Z2

5p11.1-q11.1

α-satellite

D19Z3

19p11.1-q11.1

D6Z1

6p11.1-q11.1 7p11.1-q11.1

LPE 007R/G

D8Z2

8p11.1-q11.1

α-satellite

LPE 006R/G

D7Z1

α-satellite

LPE 008R/G

D9Z3

9q12

satellite III

LPE 009R/G

D10Z1

10p11.1-q11.1

LPE 010R/G

D11Z1

11p11.1-q11.1

LPE 011R/G

D12Z3

12p11.1-q11.1

α-satellite

LPE 012R/G

13/21

D13Z1

13p11.1-q11.1

LPE 013R/G

D21Z1

21p11.1-q11.1

α-satellite

14/22

D14Z1

14p11.1-q11.1

LPE 014R/G

D22Z1

22p11.1-q11.1

D15Z4

15p11.1-q11.1

LPE 015R/G

D16Z2

16p11.1-q11.1

LPE 016R/G

D17Z1

17p11.1-q11.1

LPE 017R/G

D18Z1

18p11.1-q11.1

LPE 018R/G

D20Z1

20p11.1-q11.1

LPE 020R/G

DXZ1

Xp11.1-q11.1

LPE 0XR/G

DYZ3

Yp11.1-q11.1

LPE 0YcR/G

DYZ1

Yq12

α-satellite

satellite III

LPE 0YqR/G

XYc Dual Labelled

DXZ1

Xp11.1-q11.1

LPE 0XYc

DYZ3

Yp11.1-q11.1

LPE 0XYq

no. Tests

Cat. no.

LPE NOR

XYq Dual Labelled

DXZ1

Xp11.1-q11.1

DYZ1

Yq12

α-satellite

no. Tests

Cat. no.*

satellite III

* R specifies a red label and G specifies a green label.

Indices

Acro-P-Arm Probe

176

Chromosome

Colour

13, 14, 15, 21, 22

Red

Aquarius® subtelomere specific Probe Range summary Probe specificity

Clone name

Marker (sTs)

Max. physical distance from Telomere (kb)

Cat. no.*

CEB108

RH120573

987

LPT 01PR/G

160H23

GDB:315525

LPT 01QR/G

dJ892G20

D2S2983

LPT 02PR/G

dJ1011O17

D2S2986

277

LPT 02QR/G

2q NP

172I13

D2S447

311

LPT 02QNPR/G

dJ1186B18

D3S4559

213

LPT 03PR/G

196F4

D3S1272

959

LPT 03QR/G

36P21

D4S3360

LPT 04PR/G

dJ963K6

D4S139

372

LPT 04QR/G

189N21

RH120167

2254

LPT 05PR/G

240G13

D5S2907

222

LPT 05QR/G

62I11

STS-H99640

147

LPT 06PR/G

57H24

D6S2522

230

LPT 06QR/G

109a6

RH104000

118

LPT 07PR/G

2000a5

RH48601

138

LPT 07QR/G

dJ580L5

RH40619

150

LPT 08PR/G

489D14

D8S595

202

LPT 08QR/G

43N6

RH65569

226

LPT 09PR/G

112N13

D9S2168

167

LPT 09QR/G

10p

306F7

STS-N35887

271

LPT 10PR/G

10q

137E24

RH44494

138

LPT 10QR/G

11p

dJ908H22

D11S2071

189

LPT 11PR/G

11q

dJ770G7

D11S4974

3447

LPT 11QR/G

12p

496A11

D12S200

771

LPT 12PR/G

12q

221K18

RH81094

LPT 12QR/G

13q

163C9

D13S1825

LPT 13QR/G

14q

dJ820M16

D14S1420

143

LPT 14QR/G

15q

154P1

D15S936

328

LPT 15QR/G

16p

121I4

SHGC-16929

147

LPT 16PR/G

16q

240G10

RH80305

331

LPT 16QR/G

17p

2111b1

D17S2199

143

LPT 17PR/G

17q

362K4

−

LPT 17QR/G

18p

74G18

D18S552

141

LPT 18PR/G

18q

dJ964M9

D18S1390

155

LPT 18QR/G

19p

dJ546C11

D19S676E

260

LPT 19PR/G

19q

F21283

RH102404

LPT 19QR/G

20p

dJ106L1

D20S210

165

LPT 20PR/G

20q

81F12

RH10656

103

LPT 20QR/G

21q

63H24

D21S1446

LPT 21QR/G

22q

99K24

D22S1726

101

LPT 22QR/G

XpYp**

839D20

DXYS129

344

LPT XYPR/G

225F6

DXYS154

LPT XYQR/G

C8.2/1

SYBL1

131

LPT XYQR/G

XqYq***

* ** *** NP

R specifies a red label, G specifies a green label This probe is specific for the p-arms of both X and Y This probe is specific for the q-arms of both X and Y Non Polymorphic

Chromoprobe Multiprobe®-T subtelomere system Range summary Probe name

no. of Devices

Cat. no.

Chromoprobe Multiprobe® - T System

PMP 009

Chromoprobe Multiprobe® - T System

PMP 008

Chromoprobe Multiprobe® - T System

PMP 007

Indices

177

Aquarius速 Murine Painting Probe Range summary Chromosome

fluorescent Label

Red or Green

5 or 10

AMP 01R/G

Red or Green

5 or 10

AMP 02R/G

Red or Green

5 or 10

AMP 03R/G

Red or Green

5 or 10

AMP 04R/G

Red or Green

5 or 10

AMP 05R/G

Red or Green

5 or 10

AMP 06R/G

Red or Green

5 or 10

AMP 07R/G

Red or Green

5 or 10

AMP 08R/G

Red or Green

5 or 10

AMP 09R/G

Red or Green

5 or 10

AMP 10R/G

Red or Green

5 or 10

AMP 11R/G

Red or Green

5 or 10

AMP 12R/G

Red or Green

5 or 10

AMP 13R/G

Red or Green

5 or 10

AMP 14R/G

Red or Green

5 or 10

AMP 15R/G

Red or Green

5 or 10

AMP 16R/G

Red or Green

5 or 10

AMP 17R/G

Red or Green

5 or 10

AMP 18R/G

Red or Green

5 or 10

AMP 19R/G

Red or Green

5 or 10

AMP 0XR/G

Red or Green

5 or 10

AMP 0YR/G

* R specifies a red label and G specifies a green label.

Indices

* for 5 test kit add -S to catalogue number, e.g: AMP ###-S

178

no. Tests

Cat. no.*

Accessories Cat. no.

Description

Unit size

PCN004

Hybridisation Chamber

PCN007

24 Square Template Slides

100

PCN008

8 Square Template Slides

100

PCN002

Cytocell Slide Surface Thermometer

Ancillary Reagents Cat. no.

Description

Unit size

PCA005

Rubber Solution Glue

15g

PCN003

Mounting Medium

10ml

DES500L

0.125µg/ml DAPI

500μl

DES1000L

0.125μg/ml DAPI

1000µl

DFS500L

1.0µg/ml DAPI

500μl

DSS500L

0.0625μg/ml DAPI

500µl

HA500L

Hybridisation Solution A

500μl

HA1000L

Hybridisation Solution A

1000μl

HB500L

Hybridisation Solution B

500μl

HB1000L

Hybridisation Solution B

1000μl

PCA003

20x SSC

100ml

Microscope filters* Cat. no.

Description

N/A

FITC Filter

Unit size 1

N/A

DAPI Filter

N/A

Texas Red Filter

N/A

DEAC Filter

N/A

FITC/Texas Red Dual Filter

N/A

FITC/DAPI/Texas Red Triple Filter

* Filter cubes are available upon request, please specify the name of the microscope manufacturer and model name/number.

Indices

179

Indices

Index by Chromosome

180

Chromosome Region

Probe Name

1-22 X, Y 1-22 X, Y 1-22, X, Y 1-22, X, Y 1-22 X, Y 1p36.33 1p36.31 1p36.13 1p32.3/1q21.3 1q21.3/1p32.3 1q23.3/19p13.3 1q23.3/17q22/19p13.3 2p24.3/2q11.2 2p23.2-p23.1 2p21 2p11.2 2p11.2 2q36.1 3q26.2 3q27.3 3q27.3-q28 4p16.3 4p16.3/14q32.33 4q12 4q21.3-q22.1/11q23.3 5p15.31/5q31.2 5p15.31/5p15.2/5q35 5p15.2/5p15.31/5q35 5q31.2/5p15.31 5q32 5q35/5p15.31/5p15.2 5q35.1 6p21/14q32.33 6q22.1 6q23.3 6q27/11q23.3 7p21.1/7q11.23 7p11.2 7q11.23 7q11.23/7p21.1 7q22.1-q22.2/7q31.2 7q31.2/7q22.1-q22.2 7q31.2 7q34 8p11.23-p11.22 8q12.1-q12.2 8q21.3/21q22.12 8q23.3/8q24.11 8q24.11/8q23.3 8q24.21 8q24.21 8q24.21/14q32.33 8q24.21/14q32.33 9p21.3/11q23.3 9p21.3 9p21.3 9q34.11-q34.12/22q11.22-q11.23 9q34.11-q34.12/22q11.22-q11.23 10p14 10q24.31 11q13.3 11q13.3/14q32.33 11q13.3/14q32.33

Painting Probes-Aquarius® Painting Probes-Chromoprobe Multiprobe® OctoChrome Satellite Enumeration Probes-Aquarius® Subtelomere Specific Probes-Aquarius® Subtelomere Specific Probes-Chromoprobe Multiprobe®-T Monosomy 1p36 SRD (CHD5) Deletion PAX7 Breakapart CKS1B/CDKN2C(P18) Amplification/Deletion CKS1B/CDKN2C(P18) Amplification/Deletion E2A/PBX1 Translocation, Dual Fusion E2A/PBX1/HLF Translocation, Dual Fusion N-MYC (MYCN) Amplification ALK Breakapart EML4 Breakapart IGK Breakapart IGK Breakapart (Haematopathology) PAX3 Breakapart EVI1 (MECOM) Breakapart BCL6 Breakapart BCL6 Breakapart (Haematopathology) Wolf-Hirschhorn IGH/FGFR3 Plus Translocation, Dual Fusion FIP1L1/CHIC2/PDGFRA Deletion/Fusion MLL/AFF1 Translocation, Dual Fusion Del(5q) Deletion Cri-Du-Chat & SOTOS Probe Combination Cri-Du-Chat & SOTOS Probe Combination Del(5q) Deletion PDGFRB Breakapart Cri-Du-Chat & SOTOS Probe Combination TLX3 Breakapart IGH/CCND3 Plus Translocation, Dual Fusion ROS1 Breakapart MYB Deletion MLL/MLLT1 Translocation, Dual Fusion Saethre-Chotzen/Williams-Beuren Combination EGFR Amplification Williams-Beuren Saethre-Chotzen/Williams-Beuren Combination Del(7q) Deletion Del(7q) Deletion C-MET (MET) Amplification TCRB (TRB) Breakapart FGFR1 Breakapart/Amplification CHARGE AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion Langer-Giedion Langer-Giedion cMYC (MYC) Breakapart MYC Breakapart (Haematopathology) IGH/cMYC(MYC) Plus Translocation, Dual Fusion IGH/MYC Translocation, Dual Fusion (Haematopathology) MLL/MLLT3 Translocation, Dual Fusion P16 (CDKN2A) Deletion P16 (CDKN2A) Deletion (Haematopathology) BCR/ABL(ABL1) Translocation, Dual Fusion BCR/ABL(ABL1) Plus Translocation, Dual Fusion DiGeorge II (10p14) TLX1 Breakapart CCND1 Breakapart (Haematopathology) IGH/CCND1 Plus Translocation, Dual Fusion IGH/CCND1 Translocation, Dual Fusion (Haematopathology)

Control Region Cat. No. − − − − − 1qter 1qter − − − − − AFF3 (2q11.2) − − − − − − − − 4qter − − − 5p15.31 − − 5p15.31 − − − − − D6Z1 − − D7Z1 D7Z1 − − − D7Z1 − D8Z2 D8Z1 − D8Z2 D8Z2 − − − − − D9Z3 D9Z3 − − D10Z1 − − − −

Page No.

LPP xxR/G PMP 80x LPE xxxR/G LPT xxxP/Q, R/G PMP 00x LPU 020 LPS 010 LPS 013 LPH 039 LPH 039 LPH 079 LPH 080 LPS 009 LPS 019 LPS 020 LPH 034 LPS 038 LPS 012 LPH 036 LPH 035 LPS 029 LPU 009 LPH 074 LPH 032 LPH 081 LPH 024 LPU 013 LPU 013 LPH 024 LPH 031 LPU 013 LPH 050 LPH 075 LPS 022 LPH 016 RU-LPH 082 LPU 024 LPS 003 LPU 011 LPU 024 LPH 025 LPH 025 LPS 004 LPH 048 LPS 018 LPU 021 LPH 026 LPU 022 LPU 022 LPH 010 LPS 027 LPH 076 LPS 035 RU-LPH 083 LPH 009 LPS 036 LPH 007 LPH 038 LPU 015 LPH 049 LPS 030 LPH 072 LPS 031

150 152 154 158 160 136 116 113 25 25 37 38 112 100 104 50 91 113 39 23 84 146 46 40 53 33 130 130 33 60 130 69 44 115 56 54 140 103 145 140 34 34 102 66 108 129 19 135 135 28 93 45 90 54 57 94 21 22 131 68 85 43 88

Chromosome

Probe Name

11q13.3/14q32.33 11q22.3 11q22.3/17p13.1 11q23.3 11q23.3/4q21.3-q22.1 11q23.3/6q27 11q23.3/9p21.3 11q23.3/19p13.3 11q24.3/22q12.1-q12.2 12p13.2/21q22.12 12p11.1-q11.1 12q13.3 12q15 13q14.2-q14.3 13q14.2 13q14.2/12cen 13q14.2 13q14.3 14q11.2 14q32.13-q32.2 14q32.33 14q32.33 14q32.33/11q13.3 14q32.33/11q13.3 14q32.33/11q13.3 14q32.33/16q23.1-q23.2 14q32.33/18q21.31-q21.32 14q32.33/18q21.33 14q32.33/18q21.33-q22.1 14q32.33/20q12 14q32.33/4p16.3 14q32.33/6p21 14q32.33/8q24.21 14q32.33/8q24.21 15q11.2 15q11.2-q12 15q24.1/17q21.1-q21.2 15q24.1/17q21.1-q21.2 16p13.3 16p13.11/16q22.1 16q22.1/16p13.11 16q23.1-q23.2/14q32.33 17p13.3/17p11.2 17p13.3/17p11.2 17p13.1 17p13.1 17p13.1/11q22.3 17p11.2/17p13.3 17p11.2/17p13.3 17q11.2 17q12 17q21.1-q21.2 17q21.1-q21.2/15q24.1 17q21.1-q21.2/15q24.1 17q21.2 17q22/1q23.3/19p13.3 18q11.2 18q21.31-q21.32 18q21.31-q21.32/14q32.33 18q21.33-q22.1 18q21.33/14q32.33 18q21.33-q22.1/14q32.33 19p13.3/11q23.3

IGH/MYEOV Plus Translocation, Dual Fusion ATM Deletion P53(TP53)/ATM Probe Combination MLL (KMT2A) Breakapart MLL/AFF1 Translocation, Dual Fusion MLL/MLLT4 Translocation, Dual Fusion MLL/MLLT3 Translocation, Dual Fusion MLL/MLLT1 Translocation, Dual Fusion FLI1/EWSR1 Translocation, Dual Fusion TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion Alpha Satellite 12 Plus for CLL CHOP (DDIT3) Breakapart MDM2 Amplification 13q14.3 Deletion D13S319 Plus Deletion D13S319/13qter/12cen Deletion/Enumeration RB1 Deletion D13S25 Deletion TCRAD Breakapart TCL1 Breakapart IGH Plus Breakapart IGH Breakapart (Haematopathology) IGH/CCND1 Plus Translocation, Dual Fusion IGH/CCND1 Translocation, Dual Fusion (Haematopathology) IGH/MYEOV Plus Translocation, Dual Fusion IGH/MAF Plus Translocation, Dual Fusion IGH/MALT1 Translocation, Dual Fusion (Haematopathology) IGH/BCL2 Plus Translocation, Dual Fusion IGH/BCL2 Translocation, Dual Fusion (Haematopathology) IGH/MAFB Plus Translocation, Dual Fusion IGH/FGFR3 Plus Translocation, Dual Fusion IGH/CCND3 Plus Translocation, Dual Fusion IGH/cMYC(MYC) Plus Translocation, Dual Fusion IGH/MYC Translocation, Dual Fusion (Haematopathology) Prader-Willi/Angelman (SNRPN) Angelman (UBE3A/D15S10) FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion Rubinstein-Taybi CBFβ/MYH11 Translocation, Dual Fusion CBFβ/MYH11 Translocation, Dual Fusion IGH/MAF Plus Translocation, Dual Fusion Smith-Magenis(FLII)/Miller-Dieker Probe Combination Smith-Magenis(RAI1)/Miller-Dieker Probe Combination P53 (TP53) Deletion P53 (TP53) Deletion (Haematopathology) P53(TP53)/ATM Probe Combination Smith-Magenis(FLII)/Miller-Dieker Probe Combination Smith-Magenis(RAI1)/Miller-Dieker Probe Combination Neurofibromatosis Type 1 HER2 (ERBB2) Amplification RARα (RARA) Breakapart FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion TOP2A Amplification/Deletion E2A/PBX1/HLF Translocation, Dual Fusion SYT (SS18) Breakapart MALT1 Breakapart IGH/MALT1 Translocation, Dual Fusion (Haematopathology) BCL2 Breakapart (Haematopathology) IGH/BCL2 Plus Translocation, Dual Fusion IGH/BCL2 Translocation, Dual Fusion (Haematopathology) MLL/MLLT1 Translocation, Dual Fusion

Control Region Cat. No. − D11Z1 − − − − − − − − − − D12Z1 13qter 13qter 13qter 13qter 13qter − − − − − − − − − − − − − − − − 15qter 15qter − − D16Z2 − − − − − D17Z1 D17Z1 − − − 17pter D17Z1 − − − D17Z1 − − − − − − − −

LPH 078 LPH 011 LPH 052 LPH 013 LPH 081 RU-LPH 084 RU-LPH 083 RU-LPH 082 LPS 007 LPH 012 LPH 069 LPS 015 LPS 016 LPH 006 LPH 068 LPH 066 LPS 011 LPH 043 LPH 047 LPH 046 LPH 070 LPS 032 LPH 072 LPS 031 LPH 078 LPH 073 LPS 034 LPH 071 LPS 033 LPH 077 LPH 074 LPH 075 LPH 076 LPS 035 LPU 005 LPU 006 LPH 064 LPH 023 LPU 023 LPH 022 LPH 022 LPH 073 LPU 007 LPU 019 LPH 017 LPS 037 LPH 052 LPU 007 LPU 019 LPU 017 LPS 001 LPH 065 LPH 064 LPH 023 LPS 002 LPH 080 LPS 014 LPS 017 LPS 034 LPS 028 LPH 071 LPS 033 RU-LPH 082

Page No. 49 20 59 52 53 54 54 54 107 67 101 111 30 30 32 114 30 65 64 41 86 43 88 49 47 89 42 82 48 46 44 45 90 138 128 61 62 139 24 24 47 142 142 58 95 59 142 142 137 109 63 61 62 119 38 117 110 89 83 42 87 54

Indices

181

Chromosome

Probe name

19p13.3 19p13.3/1q23.3 19p13.3/1q23.3/17q22 20p12.2 20q12.2/14q32.33 20q12/20q13.12 20q13.12/20q12 20q13.2 21q22.12 21q22.12/12p13.2 21q22.12/8q21.3 21q22.13-q22.2/21q22.2-q22.3 21q22.13-q22.2/22q12.1-q12.2 21q22.2-q22.3/21q22.13-q22.2 22q11.21-q11.23 22q11.21-q11.23

E2A (TCF3) Breakapart − E2A/PBX1 Translocation, Dual Fusion − E2A/PBX1/HLF Translocation, Dual Fusion − Alagille (JAG1) 20qter IGH/MAFB Plus Translocation, Dual Fusion − Del(20q) Deletion − Del(20q) Deletion − ZNF217 Amplification 20pter AML1 (RUNX1) Breakapart − TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion − AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion − TMPRSS2/ERG Deletion/Breakapart ERG (21q22.2) EWSR1/ERG Translocation, Dual Fusion − TMPRSS2/ERG Deletion/Breakapart ERG (21q22.2) IGL Breakapart − IGL Breakapart (Haematopathology) −

LPH 019 LPH 079 LPH 080 LPH 012 LPH 077 LPH 020 LPH 020 LPS 005 LPH 027 LPH 012 LPH 026 LPS 021 LPS 008 LPS 021 LPH 033 LPS 039

36 37 38 127 48 35 35 120 18 67 19 118 106 118 51 92

22q11.21/22q13.33

DiGeorge TBX1 & 22q13.3 Deletion Syndrome Probe Combination

−

LPU 014

132

22q11.21/22q13.33

DiGeorge/VCFS N25 & 22q13.3 Deletion Syndrome Probe Combination

−

LPU 010

132

−

LPU 004

132

− − − − −

LPH 007 LPH 038 LPS 006 LPS 007 LPS 008

21 22 105 107 106

LPU 014

132

DiGeorge/VCFS TUPLE1 & 22q13.3 Deletion Syndrome Probe Combination 22q11.22-q11.23/9q34.11-q34.12 BCR/ABL(ABL1) Translocation, Dual Fusion 22q11.22-q11.23/9q34.11-q34.12 BCR/ABL(ABL1) Plus Translocation, Dual Fusion 22q12.1-q12.2 EWSR1 Breakapart 22q12.1-q12.2/11q24.3 FLI1/EWSR1 Translocation, Dual Fusion 22q12.1-q12.2/21q22.13-q22.2 EWSR1/ERG Translocation, Dual Fusion

22q11.21/22q13.33

DiGeorge TBX1 & 22q13.3 Deletion Syndrome Probe Combination

−

22q13.33/22q11.21

DiGeorge/VCFS N25 & 22q13.3 Deletion Syndrome Probe Combination

−

LPU 010

132

22q13.33/22q11.21

DiGeorge/VCFS TUPLE1 & 22q13.3 Deletion Syndrome Probe Combination CRLF2 Breakapart SHOX P2RY8 Deletion

−

LPU 004

132

RU-LPH 085 LPU 025 RU-LPH 086

29 141 29

LPU 016

134

Xp22.31 Xp11.1-q11.1/Yp11.1-q11.1 Xp11.1-q11.1/Yq12 Xq13.2 Yp11.32/Xp22.33 Yp11.32/Xp22.33 Yp11.32/Xp22.33 Yp11.31 Yp11.1-q11.1/Xp11.1-q11.1 Xp11.1-q11.1/Yq12 Various Various Various Various Various Various Various Various

Indices

Page no.

22q13.33/22q11.21

Xp22.33/Yp11.32 Xp22.33/Yp11.32 Xp22.33/Yp11.32

182

Control Region Cat. no.

Kallmann (KAL1) & Steroid Sulphatase Deficiency (STS) Probe Combination Dual labelled Satellite Probe Set XYc Dual labelled Satellite Probe Set XYq XIST CRLF2 Breakapart SHOX P2RY8 Deletion SRY Dual labelled Satellite Probe Set XYc Dual labelled Satellite Probe Set XYq Acro-P-Arm Probe ALL-Chromoprobe Multiprobe® AML/MDS-Chromoprobe Multiprobe® CLL PROFILER Kit CLL Plus Screening Panel CLL-Chromoprobe Multiprobe® FAST FISH Prenatal Enumeration Probes Prenatal Enumeration Probes

− DXZ1, DYZ1 − DXZ1 − − DXZ1 − DXZ1, DYZ1 − DXZ1, DYZ1 − − − − − − − − − −

LPE 0XYc LPE 0XYq LPU 018 RU-LPH 085 LPU 025 RU-LPH 086 LPU 026 LPE 0XYc LPE 0XYq LPE NOR PMP 03x PMP 02x LPH 067 LPH 087 PMP 01x LPF 00x LPA 00x

147 29 141 29 144

155 74 78 26 27 76 123 124

Index by Gene Name Chromosome Region

Product Name

Cat. No.

ABL (ABL1)

9q34.12

AFF1 ALK AML1

4q21.3-q22.1 2p23.2-p23.1 21q22.12

ATM

11q22.3

BCL2

18q21.33

BCL6

3q27.3

BCR

22q11.23

BRUNOL3 CBFB

10p14 16q22.1

CCND1

11q13.3

CCND3 CDKN2A

6p21.1 9p21.3

CDKN2C CELF2 CHD5 CHD7 CHIC2 CHOP CKS1B c-MET cMYC

1p32.3 10p14 1p36.31 8q12.1-q12.2 4q12 12q13.3 1q21.3 7q31.2 8q24.21

CREBBP CRLF2 D13S319

16p13.3 Yp11.32/Xp22.33 13q14.2

D13S25 DDIT3 E2A

13q14.3 12q13.3 19p13.3

EGFR ELN

7p11.2 7q11.23 7q11.23 17q12 21q22.2

BCR/ABL(ABL1) Translocation Dual Fusion BCR/ABL(ABL1) Plus Translocation Dual Fusion ALL-Chromoprobe Multiprobe® MLL/AFF1 Translocation, Dual Fusion ALK Breakapart AML1 (RUNX1) Breakapart AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® AML/MDS-Chromoprobe Multiprobe® ATM Deletion P53(TP53)/ATM Probe Combination CLL PROFILER Kit CLL-Chromoprobe Multiprobe® BCL2 Breakapart (Haematopathology) IGH/BCL2 Plus Translocation, Dual Fusion IGH/BCL2 Translocation, Dual Fusion (Haematopathology) CLL-Chromoprobe Multiprobe® BCL6 Breakapart BCL6 Breakapart (Haematopathology) BCR/ABL(ABL1) Translocation Dual Fusion BCR/ABL(ABL1) Plus Translocation Dual Fusion ALL-Chromoprobe Multiprobe® DiGeorge II (10p14) CBFβ/MYH11 Translocation, Dual Fusion AML/MDS-Chromoprobe Multiprobe® CCND1 Breakapart (Haematopathology) IGH/CCND1 Plus Translocation, Dual Fusion IGH/CCND1 Translocation, Dual Fusion (Haematopathology) CLL-Chromoprobe Multiprobe® IGH/CCND3 Plus Translocation, Dual Fusion P16 (CDKN2A) Deletion P16 (CDKN2A) Deletion (Haematopathology) ALL-Chromoprobe Multiprobe® CKS1B/CDKN2C(P18) Amplification/Deletion DiGeorge II (10p14) SRD (CHD5) Deletion CHARGE FIP1L1/CHIC2/PDGFRA Deletion/Fusion CHOP (DDIT3) Breakapart CKS1B/CDKN2C(P18) Amplification/Deletion C-MET (MET) Amplification cMYC (MYC) Breakapart MYC Breakapart (Haematopathology) IGH/cMYC(MYC) Plus Translocation, Dual Fusion IGH/MYC Translocation, Dual Fusion (Haematopathology) ALL-Chromoprobe Multiprobe® Rubinstein-Taybi CRLF2 Breakapart D13S319 Plus Deletion D13S319/13qter/12cen Deletion/Enumeration CLL PROFILER Kit D13S25 Deletion CHOP (DDIT3) Breakapart E2A (TCF3) Breakapart E2A/PBX1 Translocation, Dual Fusion E2A/PBX1/HLF Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® EGFR Amplification Williams-Beuren Saethre-Chotzen/Williams-Beuren Combination HER2 (ERBB2) Amplification TMPRSS2/ERG Deletion/Breakapart EWSR1/ERG Translocation, Dual Fusion

LPH 007 LPH 038 PMP 03x LPH 081 LPS 019 LPH 027 LPH 026 LPH 012 PMP 03x PMP 02x LPH 011 LPH 052 LPH 067 PMP 01x LPS 028 LPH 071 LPS 033 PMP 01x LPH 035 LPS 029 LPH 007 LPH 038 PMP 03x LPU 015 LPH 022 PMP 02x LPS 030 LPH 072 LPS 031 PMP 01x LPH 075 LPH 009 LPS 036 PMP 03x LPH 039 LPU 015 LPS 010 LPU 021 LPH 032 LPS 015 LPH 039 LPS 004 LPH 010 LPS 027 LPH 076 LPS 035 PMP 03x LPU 023 RU-LPH 085 LPH 068 LPH 066 LPH 067 LPH 043 LPS 015 LPH 019 LPH 079 LPH 080 PMP 03x LPS 003 LPU 011 LPU 024 LPS 001 LPS 021 LPS 008

ERBB2 ERG

Page No. 21 22 74 53 100 18 19 67 74 78 20 59 26 76 83 42 87 76 23 84 21 22 74 131 24 78 85 43 88 76 44 57 94 74 25 131 116 129 40 101 25 102 28 93 45 90 74 139 29 30 32 26 30 101 36 37 38 74 103 145 140 109 118 106

Indices

Gene

183

Indices

184

Gene

Chromosome Region

Product name

Cat. no.

Page no.

ETO

8q21.3

ETV6

12p13.2

EVI1 EWSR1

3q26.2 22q12.2

EXT1 FGFR1 FGFR3 FIP1L1 FLI1 FLII HER2

8q24.11 8p11.23-p11.22 4p16.3 4q12 11q24.3 17p11.2 17q12

AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion AML/MDS-Chromoprobe Multiprobe® TEL/AML1 (EVT6/RUNX1) Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® EVI1 (MECOM) Breakapart EWSR1 Breakapart FLI1/EWSR1 Translocation, Dual Fusion EWSR1/ERG Translocation, Dual Fusion Langer-Giedion FGFR1 Breakapart/Amplification IGH/FGFR3 Plus Translocation, Dual Fusion FIP1L1/CHIC2/PDGFRA Deletion/Fusion FLI1/EWSR1 Translocation, Dual Fusion Smith-Magenis(FLII)/Miller-Dieker Probe Combination HER2 (ERBB2) Amplification

LPH 026 PMP 02x LPH 012 PMP 03x LPH 036 LPS 006 LPS 007 LPS 008 LPU 022 LPS018 LPH 074 LPH 032 LPS 007 LPU 007 LPS 001

19 78 67 74 39 105 107 106 135 108 46 40 107 142 109

HIRA

22q11.21

LPU004

132

HLF IGH

17q22 14q32.33

IGK

2p11.2

IGL JAG1

22q11.21-q11.23 22q11.21-q11.23 20p12.2

DiGeorge/VCFS TUPLE1 & 22q13.3 Deletion Syndrome Probe Combination E2A/PBX1/HLF Translocation, Dual Fusion IGH Plus Breakapart IGH Breakapart (Haematopathology) IGH/BCL2 Plus Translocation, Dual Fusion IGH/BCL2 Translocation, Dual Fusion (Haematopathology) IGH/CCND1 Plus Translocation, Dual Fusion IGH/CCND1 Translocation, Dual Fusion (Haematopathology) IGH/CCND3 Plus Translocation, Dual Fusion IGH/cMYC(MYC) Plus Translocation, Dual Fusion IGH/FGFR3 Plus Translocation, Dual Fusion IGH/MAF Plus Translocation, Dual Fusion IGH/MAFB Plus Translocation, Dual Fusion IGH/MALT1 Translocation, Dual Fusion (Haematopathology) IGH/MYC Translocation, Dual Fusion (Haematopathology) IGH/MYEOV Plus Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® CLL-Chromoprobe Multiprobe® IGK Breakapart IGK Breakapart (Haematopathology) IGL Breakapart IGL Breakapart (Haematopathology) Alagille (JAG1)

LPH 080 LPH 070 LPS 032 LPH 071 LPS 033 LPH 072 LPS 031 LPH 075 LPH 076 LPH 074 LPH 073 LPH 077 LPS 034 LPS 035 LPH 078 PMP 03x PMP 01x LPH 034 LPS 038 LPH 033 LPS 039 LPU 012

38 41 86 42 87 43 88 44 45 46 47 48 89 90 49 74 76 50 91 51 92 127

KAL1

Xp22.31

LPU016

134

KMT2A

11q23.3

MAF MAFB MALT1

16q23.2 20q12 18q21.32

MDM2 MECOM MET MLL

12q15 3q26.2 7q31.2 11q23.3

MLLT1 MLLT3 MLLT4 MYB

19p13.3 9p21.3 6q27 6q23.3

LPH 013 LPH 081 RU-LPH 082 RU-LPH 083 RU-LPH 084 PMP 03x PMP 02x LPH 073 LPH 077 LPS 017 LPS 034 LPS 016 LPH 036 LPS 004 LPH 013 LPH 081 RU-LPH 082 RU-LPH 083 RU-LPH 084 PMP 03x PMP 02x RU-LPH 082 RU-LPH 083 RU-LPH 084 LPH 016

52 53 54 54 54 74 78 47 48 110 89 111 39 102 52 53 54 54 54 74 78 54 54 54 56

Kallmann (KAL1) & Steroid Sulphatase Deficiency (STS) Probe Combination MLL (KMT2A) Breakapart MLL/AFF1 Translocation, Dual Fusion MLL/MLLT1 Translocation, Dual Fusion MLL/MLLT3 Translocation, Dual Fusion MLL/MLLT4 Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® AML/MDS-Chromoprobe Multiprobe IGH/MAF Plus Translocation, Dual Fusion IGH/MAFB Plus Translocation, Dual Fusion MALT1 Breakapart IGH/MALT1 Translocation, Dual Fusion (Haematopathology) MDM2 Amplification EVI1 (MECOM) Breakapart C-MET (MET) Amplification MLL (KMT2A) Breakapart MLL/AFF1 Translocation, Dual Fusion MLL/MLLT1 Translocation, Dual Fusion MLL/MLLT3 Translocation, Dual Fusion MLL/MLLT4 Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® AML/MDS-Chromoprobe Multiprobe® MLL/MLLT1 Translocation, Dual Fusion MLL/MLLT3 Translocation, Dual Fusion MLL/MLLT4 Translocation, Dual Fusion MYB Deletion

Gene

Chromosome Region

MYC

8q24.21

MYCN MYEOV MYH11

2p24.3 11q13.3 16p13.11

NF1 N-MYC NSD1 P16

17q11.2 2p24.3 5q35.2-q35.3 9p21.3

P2RY8 P53

Yp11.32/Xp22.33 17p13.1

PAX3 PAX7 PBX1

2q36.1 1p36.13 1q23.3

PDGFRA PDGFRB PML

4q12 5q32 15q24.1

RAI1 17p11.2 RARα (RARA) 17q21.2

RB1 ROS1 RUNX1

13q14.2 6q22.1 21q22.12

RUNX1T1

8q21.3

SHOX SNRPN SRD SRY SS18

Xp22.33/Yp11.32 15q11.2 1p36.31 Yp11.31 18q11.2

STS

Xp22.31

SYT TBX1 TCF3

18q11.2 22q11.21 19p13.3

TCL1 A/B TCRA TCRB TCRD TEL

14q32.13-q32.2 14q11.2 7q34 14q11.2 12p13.2

Product name

Cat. no.

Page no.

CLL PROFILER Kit CLL-Chromoprobe Multiprobe® cMYC (MYC) Breakapart MYC Breakapart (Haematopathology) IGH/cMYC(MYC) Plus Translocation, Dual Fusion IGH/MYC Translocation, Dual Fusion (Haematopathology) ALL-Chromoprobe Multiprobe® N-MYC (MYCN) Amplification IGH/MYEOV Plus Translocation, Dual Fusion CBFβ/MYH11 Translocation, Dual Fusion AML/MDS-Chromoprobe Multiprobe® Neurofibromatosis Type 1 N-MYC (MYCN) Amplification Cri-Du-Chat & SOTOS Probe Combination P16 (CDKN2A) Deletion P16 (CDKN2A) Deletion (Haematopathology) ALL-Chromoprobe Multiprobe® P2RY8 Deletion P53 (TP53) Deletion P53 (TP53) Deletion (Haematopathology) P53(TP53)/ATM Probe Combination CLL PROFILER Kit AML/MDS-Chromoprobe Multiprobe® CLL-Chromoprobe Multiprobe® PAX3 Breakapart PAX7 Breakapart E2A/PBX1 Translocation, Dual Fusion E2A/PBX1/HLF Translocation, Dual Fusion FIP1L1/CHIC2/PDGFRA Deletion/Fusion PDGFRB Breakapart FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion AML/MDS-Chromoprobe Multiprobe® Smith-Magenis(RAI1)/Miller-Dieker Probe Combination FAST PML/RARα(RARA) Translocation, Dual Fusion PML/RARα(RARA) Translocation, Dual Fusion RARα (RARA) Breakapart AML/MDS-Chromoprobe Multiprobe® RB1 Deletion ROS1 Breakapart AML1 (RUNX1) Breakapart AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® AML/MDS-Chromoprobe Multiprobe® AML1/ETO (RUNX1/RUNX1T1) Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® SHOX Prader-Willi/Angelman (SNRPN) SRD (CHD5) Deletion SRY SYT (SS18) Breakapart

LPH 067 PMP 01x LPH 010 LPS 027 LPH 076 LPS 035 PMP 03x LPS 009 LPH 078 LPH 022 PMP 02x LPU 017 LPS 009 LPU 013 LPH 009 LPS 036 PMP 03x RU-LPH 060 LPH 017 LPS 037 LPH 052 LPH 067 PMP 02x PMP 01x LPS 012 LPS 013 LPH 079 LPH 080 LPH 032 LPH 031 LPH 064 LPH 023 PMP 02x LPU 019 LPH 064 LPH 023 LPH 065 PMP 02x LPS 011 LPS 022 LPH 027 LPH 026 LPH 012 PMP 03x PMP 02x LPH 026 PMP 02x LPU 025 LPU 005 LPS 010 LPU 026 LPS 014

26 76 28 93 45 90 74 112 49 24 78 137 112 130 57 94 74 29 58 95 59 26 78 76 113 113 37 38 40 60 61 62 78 142 61 62 63 78 114 115 18 19 67 74 78 19 74 141 138 116 144 117

Kallmann (KAL1) & Steroid Sulphatase Deficiency (STS) Probe Combination SYT (SS18) Breakapart DiGeorge TBX1 & 22q13.3 Deletion Syndrome Probe Combination E2A (TCF3) Breakapart E2A/PBX1 Translocation, Dual Fusion E2A/PBX1/HLF Translocation, Dual Fusion ALL-Chromoprobe Multiprobe® TCL1 Breakapart TCRAD Breakapart TCRB (TRB) Breakapart TCRAD Breakapart TEL/AML1 (ETV6/RUNX1) Translocation, Dual Fusion ALL-Chromoprobe Multiprobe®

LPU016

134

LPS 014 LPU 014 LPH 019 LPH 079 LPH 080 PMP 03x LPH 046 LPH 047 LPH 048 LPH 047 LPH 012 PMP 03x

117 132 36 37 38 74 64 65 66 65 67 74

Indices

185

Indices

186

Gene

Chromosome Region

Product name

Cat. no.

Page no.

TLX1 TLX3 TMPRSS2 TOP2A TP53

10q24.31 5q35.1 21q22.3 17q21.2 17p13.1

TRA TRB TRD TRPS1

14q11.2 7q34 14q11.2 8q23.3

TLX1 Breakapart TLX3 Breakapart TMPRSS2/ERG Deletion/Breakapart TOP2A Amplification/Deletion P53 (TP53) Deletion P53 (TP53) Deletion (Haematopathology) P53(TP53)/ATM Probe Combination CLL PROFILER Kit AML/MDS-Chromoprobe Multiprobe速 CLL-Chromoprobe Multiprobe速 TCRAD Breakapart TCRB (TRB) Breakapart TCRAD Breakapart Langer-Giedion

LPH 049 LPH 050 LPS 021 LPS 002 LPH 017 LPS 037 LPH 052 LPH 067 PMP 02x PMP 01x LPH 047 LPH 048 LPH 047 LPU 022

68 69 118 119 58 95 59 26 78 76 65 66 65 135

TUPLE1

22q11.21

LPU 004

132

TWIST1 UBE3A XIST ZNF217

7p21.1 15q11.2 Xq13.2 20q13.2

DiGeorge/VCFS TUPLE1 & 22q13.3 Deletion Syndrome Probe Combination Saethre-Chotzen/Williams-Beuren Combination Angelman (UBE3A/D15S10) XIST ZNF217 Amplification

LPU 024 LPU 006 LPU 018 LPS 005

140 128 147 120

Pathology Products by Disease State Chromosome Region

Cytocell Products

Cat. no.

Breast

7q31.2 7p11.2 8p11.23-p11.22 17q12 17q21.2 20q13.2

C-MET (MET) Amplification EGFR Amplification FGFR1 Breakapart/Amplification HER2 (ERBB2) Amplification TOP2A Amplification/Deletion ZNF217 Amplification

LPS LPS LPS LPS LPS LPS

004 003 018 001 002 005

102 103 108 109 119 120

Cholangiocarcinoma (Bile duct)

6q22.1

ROS1 Breakapart

LPS 022

115

Colon

7q31.2

C-MET (MET) Amplification

LPS 004

102

Glioma

1p36.31 6q22.1

SRD (CHD5) Deletion ROS1 Breakapart

LPS 010 LPS 022

116 115

2p23.2-p23.1

ALK Breakapart

LPS 019

100

Lung

7q31.2 17q12 2p23.2-p23.1 2p21 6q22.1 7p11.2

C-MET (MET) Amplification HER2 (ERBB2) Amplification ALK Breakapart EML4 Breakapart ROS1 Breakapart EGFR Amplification

LPS LPS LPS LPS LPS LPS

004 001 019 020 022 003

102 109 100 104 115 103

Lymphoma

18q21.31-q21.32 1p36.31 2p23.2-p23.1 18q21.33-q22.1 3q27.3-q28 11q13.3 14q32.33 14q32.33/18q21.33 14q32.33/11q13.3 14q32.33/18q21.31-q21.32 14q32.33/8q24.21 2p11.2 22q11.21-q11.23 8q24.21 9p21.3 17p13.1

MALT1 Breakapart SRD (CHD5) Deletion ALK Breakapart BCL2 Breakapart BCL6 Breakapart CCND1 Breakapart IGH Breakapart IGH/BCL2 Translocation IGH/CCND1 Translocation IGH/MALT1 Translocation IGH/MYC Translocation IGK Breakapart IGL Breakapart MYC Breakapart P16 (CDKN2A) Deletion P53 (TP53) Deletion

LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS LPS

017 010 019 028 029 030 032 033 031 034 035 038 039 027 036 037

110 116 100 83 86 85 86 87 88 89 90 91 92 93 94 95

neuroblastoma

2p24.3 1p36.31 2p23.2-p23.1

N-MYC (MYCN) Amplification SRD (CHD5) Deletion ALK Breakapart

LPS 009 LPS 010 LPS 019

112 116 100

Oesophageal

12q15

MDM2 Amplification

LPS 016

111

Ovarian

7q31.2 17q12 20q13.2

C-MET (MET) Amplification HER2 (ERBB2) Amplification ZNF217 Amplification

LPS 004 LPS 001 LPS 005

102 109 120

Pancreatic

7q31.2

C-MET (MET) Amplification

LPS 004

102

Prostate

21q22.2-q22.3/21q22.13-q22.2

TMPRSS2/ERG Deletion/Breakapart

LPS 021

118

20q13.2

ZNF217 Amplification

LPS 005

120

Retinoblastoma

13q14.2

RB1 Deletion

LPS 011

114

salivary Gland

17q12

HER2 (ERBB2) Amplification

LPS 001

109

sarcoma

12q13.3 22q12.1-q12.2 11q24.3/22q12.1-q12.2 22q12.1-q12.2/21q22.13-q22.2 12q15 2q36.1 1p36.13 18q11.2

CHOP (DDIT3) Breakapart EWSR1 Breakapart FLI1/EWSR1 Translocation EWSR1/ERG Translocation MDM2 Amplification PAX3 Breakapart PAX7 Breakapart SYT (SS18) Breakapart

LPS LPS LPS LPS LPS LPS LPS LPS

015 006 007 008 016 012 013 014

101 105 107 106 111 113 113 117

stomach

7q31.2 17q12 20q13.2

C-MET (MET) Amplification HER2 (ERBB2) Amplification ZNF217 Amplification

LPS 004 LPS 001 LPS 005

102 109 120

Thyroid

7q31.2

C-MET (MET) Amplification

LPS 004

102

Inflammatory Myofibroblastic Tumours

Page no.

Indices

Malignancy

187

Haematology Products by Disease State Haematological Malignancy Chromosome Region

ALL

Acute Lymphoblastic Leukaemia (ALL)

AML

Acute Myeloid Leukaemia (AML)

APL

Acute Promyelocytic Leukaemia (APL)

CEL

Chronic Eosinophilic Leukaemia (CEL)

CLL

Chronic Lymphocytic Leukaemia (CLL)

Indices

CML

188

Chronic Myeloid Leukaemia (CML)

Cytocell Products

Cat. No.

Page No.

21q22.12 22q11.22-q11.23/9q34.11-q34.12 22q11.22-q11.23/9q34.11-q34.12 8q24.21 19p13.3 19p13.3/1q23.3 19p13.3/1q23.3/17q22 14q32.33 14q32.33/8q24.21 11q23.3 11q23.3/4q21.3-q22.1 11q23.3/19p13.3 11q23.3/9p21.3 11q23.3/6q27 6q23.3 9p21.3 14q32.13-q32.2 14q11.2 7q34 12p13.2/21q22.12 10q24.31 5q35.1 Xp22.33/Yp11.32 Xp22.33/Yp11.32

AML1 (RUNX1) Breakapart BCR/ABL(ABL1) Translocation BCR/ABL(ABL1) Plus Translocation cMYC (MYC) Breakapart E2A (TCF3) Breakapart E2A/PBX1 Translocation E2A/PBX1/HLF Translocation IGH Plus Breakapart IGH/cMYC(MYC) Plus Translocation MLL (KMT2A) Breakapart MLL/AFF1 Translocation MLL/MLLT1 Translocation MLL/MLLT3 Translocation MLL/MLLT4 Translocation MYB Deletion P16 (CDKN2A) Deletion TCL1 Breakapart TCRAD Breakapart TCRB (TRB) Breakapart TEL/AML1 (ETV6/RUNX1) Translocation TLX1 Breakapart TLX3 Breakapart CRLF2 Breakapart P2RY8 Deletion

LPH 027 LPH 007 LPH 038 LPH 010 LPH 019 LPH 079 LPH 080 LPH 070 LPH 076 LPH 013 LPH 081 RU-LPH 082 RU-LPH 083 RU-LPH 084 LPH 016 LPH 009 LPH 046 LPH 047 LPH 048 LPH 012 LPH 049 LPH 050 RU-LPH 085 RU-LPH 086

18 21 22 28 36 37 38 41 45 52 53 54 54 54 56 57 64 65 66 67 68 69 29 29

21q22.12 21q22.12/8q21.3 22q11.22-q11.23/9q34.11-q34.12 22q11.22-q11.23/9q34.11-q34.12 16q22.1/16p13.11 5p15.31/5q31.2 7q22.1-q22.2/7q31.2 20q12/20q13.12 3q26.2 11q23.3 11q23.3/19p13.3 11q23.3/9p21.3 11q23.3/6q27 17p13.1 15q24.1/17q21.1-q21.2 15q24.1/17q21.1-q21.2 17q21.1-q21.2

AML1 (RUNX1) Breakapart AML1/ETO (RUNX1/RUNX1T1) Translocation BCR/ABL(ABL1) Translocation BCR/ABL(ABL1) Plus Translocation CBFβ/MYH11 Translocation Del(5q) Deletion Del(7q) Deletion Del(20q) Deletion EVI1 (MECOM) Breakapart MLL (KMT2A) Breakapart MLL/MLLT1 Translocation MLL/MLLT3 Translocation MLL/MLLT4 Translocation P53 (TP53) Deletion FAST PML/RARα(RARA) Translocation PML/RARα(RARA) Translocation RARα (RARA) Breakapart

LPH 027 LPH 026 LPH 007 LPH 038 LPH 022 LPH 024 LPH 025 LPH 020 LPH 036 LPH 013 RU-LPH 082 RU-LPH 083 RU-LPH 084 LPH 017 LPH 064 LPH 023 LPH 065

18 19 21 22 24 33 34 35 39 52 54 54 54 58 61 62 63

15q24.1/17q21.1-q21.2 15q24.1/17q21.1-q21.2 17q21.1-q21.2

FAST PML/RARα(RARA) Translocation PML/RARα(RARA) Translocation RARα (RARA) Breakapart

LPH 064 LPH 023 LPH 065

61 62 63

4q12

FIP1L1/CHIC2/PDGFRA Deletion/Fusion

LPH 032

13q14.2-q14.3 12p11.1-q11.1 11q22.3 13q14.3 13q14.2 13q14.2/12cen 14q32.33 14q32.33/18q21.33 14q32.33/11q13.3 14q32.33/6p21 6q23.3 17p13.1 17p13.1/11q22.3 Various Various

13q14.3 Deletion Alpha Satellite 12 Plus for CLL ATM Deletion D13S25 Deletion D13S319 Plus Deletion D13S319/13qter/12cen Deletion/Enumeration IGH Plus Breakapart IGH/BCL2 Plus Translocation IGH/CCND1 Plus Translocation IGH/CCND3 Plus Translocation MYB Deletion P53 (TP53) Deletion P53(TP53)/ATM Probe Combination CLL PROFILER Kit CLL Plus Screening Panel

LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH

006 069 011 043 068 066 070 071 072 075 016 017 052 067 087

30 20 30 30 32 41 42 43 44 56 58 59 26 27

22q11.22-q11.23/9q34.11-q34.12 22q11.22-q11.23/9q34.11-q34.12 5q32

BCR/ABL(ABL1) Translocation BCR/ABL(ABL1) Plus Translocation PDGFRB Breakapart

LPH 007 LPH 038 LPH 031

21 22 60

HES L

Haematological Malignancy Chromosome Region

Cytocell Products

Hypereosinophilic syndrome (Hes)

Cat. no.

Page no.

4q12

FIP1L1/CHIC2/PDGFRA Deletion/Fusion

LPH 032

Lymphoma (L)

3q27.3 8q24.21 14q32.33 14q32.33/18q21.33 14q32.33/11q13.3 14q32.33/8q24.21 2p11.2 22q11.21-q11.23 17p13.1

BCL6 Breakapart cMYC (MYC) Breakapart IGH Plus Breakapart IGH/BCL2 Plus Translocation IGH/CCND1 Plus Translocation IGH/cMYC(MYC) Plus Translocation IGK Breakapart IGL Breakapart P53 (TP53) Deletion

LPH LPH LPH LPH LPH LPH LPH LPH LPH

035 010 070 071 072 076 034 033 017

23 28 41 42 43 45 50 51 5

Multiple Myeloma (MM)

13q14.2-q14.3 1q21.3/1p32.3 13q14.3 13q14.2 13q14.2/12cen 14q32.33 14q32.33/11q13.3 14q32.33/6p21 14q32.33/4p16.3 14q32.33/16q23.1-q23.2 14q32.33/20q12 14q32.33/11q13.3 17p13.1

13q14.3 Deletion CKS1B/CDKN2C(P18) Amplification/Deletion D13S25 Deletion D13S319 Plus Deletion D13S319/13qter/12cen Deletion/Enumeration IGH Plus Breakapart IGH/CCND1 Plus Translocation IGH/CCND3 Plus Translocation IGH/FGFR3 Plus Translocation IGH/MAF Plus Translocation IGH/MAFB Plus Translocation IGH/MYEOV Plus Translocation P53 (TP53) Deletion

LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH LPH

006 039 043 068 066 070 072 075 074 073 077 078 017

30 25 30 30 32 41 43 44 46 47 48 49 56

Indices

189

Indices

Notes

190

neW