Tecan Journal Edition 01/2014

Tecan Journal Life Sciences and Partnering Business

Edition 1/2014

Monitoring the quality of beer – a unique collaboration

pages 8 - 9

Speed and reliability for drug titrations pages 14 - 15

Sample preparation: the heart of NGS pages 18 - 19

Building a case of precision pipetting pages 28 - 29

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CEO WELCOME TECAN JOURNAL 1/2014

Welcome

Welcome to 2014 and the new issue of the Tecan Journal Once again, the SLAS conference and exhibition will provide a snapshot of what Tecan has to offer in 2014, with the launch of several new products. We will be showcasing a number of application-oriented solutions at the exhibition, held in San Diego this year, including the new TouchTools™ PCR Wizard for user-friendly reaction set-up, and the recently launched AC Extraction Plate™.

This ‘smart’ consumable device is designed to simplify sample preparation for mass spectrometry, and reflects the growing demand for application-specific products within the life sciences market, as discussed

by Klaus Lun – Head of Corporate Development – in the latest Leading the debate column (page 31). Tecan is well placed to deliver further innovations in this area, bringing together our liquid handling expertise and in-depth understanding of our customers’ workflows to provide genuine time-saving alternatives for common laboratory tasks. Combined with our global

support and training – including the web-based Tecan Academy training tool – this ensures we can support our customers’ application needs, both now and in the future.

No Tecan Journal would be complete without stories of how you, our customers, are using Tecan instruments, and this edition offers articles on a wide range of applications, from cystic fibrosis biochip development in Russia to DNA profiling for forensics in the USA. This issue also highlights the degree to which assay miniaturization is now commonplace across many sectors, with a number of articles highlighting the various low volume pipetting options available for use with the Freedom EVO® workstation.

I hope you enjoy the Tecan Journal and have a prosperous 2014, David Martyr, CEO

CONTENTS TECAN JOURNAL 1/2014

pages 8-9

“The wonderful thing about having this opportunity to work with Tecan and Stiegl is that the students gain experience of science in the context of work.” pages 14-15

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CEO Welcome

4 New TouchTools PCR Wizard aids automated PCR set-up 4 Nested disposable tips now available for Liquid Handling Arms 5 Software updates enhance flexibility of HP D300 5 Tecan Academy to be available worldwide 6 AC Extraction Plate – a unique sample preparation tool for LC-MS 7 Extended flexibility of Cavro® Omni Robot 8 - 9 Monitoring the quality of beer – a unique collaboration 10 - 11 Automation paves the way for faster vaccine development 12 - 13 Faster and more reliable screening for cystic fibrosis mutations

pages 30-31

Novartis has a long history of working with Tecan’s Partnering Business for the development of automated workstations for blood banking applications.

Contents

pages 28-29

14 - 15 Speed and reliability for drug titrations 16 - 17 Customizing automated colony picking 18 - 19 Sample preparation: the heart of NGS 20 - 21 Integrated nanoliter dispensing aids drug discovery 22 - 23 Bespoke forensics 24 - 25

Deciphering the epigenetic code

26 - 27 High throughput nanoliter pipetting with the MCA 384 28 - 29 Building a case of precision pipetting 30 - 31 Pooling resources 31

Leading the debate

32 Events

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PRODUCT NEWS TECAN JOURNAL 1/2014

PRODUCT NEWS TECAN JOURNAL 1/2014

New TouchTools™ PCR Wizard aids automated PCR set-up

Software updates enhance flexibility of HP D300

Tecan has launched the TouchTools PCR Wizard, an easy-to-use Freedom EVOware® add-on offering straightforward automation of PCR reaction set-up on Freedom EVO® platforms. This new tool simplifies the set-up of applications – including end-point, real-time and multiplex PCR, sequencing, genotyping and gene expression, as well as pathogen and mutagenesis detection – helping to reduce training time and costs.

The latest software updates for the HP D300 Digital Dispenser ensure even greater versatility for drug discovery applications. The recently released version 2.2 software includes a number of updates to improve day-to-day operation of the HP D300 for new and existing customers, making it even faster to set up and run your experiments.

The PCR Wizard’s effortless touchscreen operation and step-by-step instructions guide users through the set-up process, allowing sample information to be entered manually, imported from a file or identified by barcode scanning. Users can quickly and easily optimize 96- and 384-well PCR plate layouts to meet specific workflow needs, using up to 96 master mixes and defining their own controls and dilution curves. Seamless data transfer to Bio-Rad and Life Technologies real-time cyclers avoids transcription errors,

and optional integrated sample tracking further increases process security. With just a single set-up required for multiple PCR plates per run, efficiency is considerably enhanced and, for maximum flexibility, the PCR Wizard can be used in conjunction with the Freedom EVOware Normalization Wizard.

To find out more on Tecan’s TouchTools PCR Wizard, visit www.tecan.com/pcrwizard

The PCR Wizard offers easy automation of PCR reaction set-up

Nested disposable tips now available for Liquid Handling Arms The demand for ever-increasing throughput means that many laboratories are looking for solutions to increase the throughput of their automated systems. Tecan has created Nested LiHa Disposable Tips specifically to meet this need, allowing up to five trays of the new 350 μl tips to be stacked on a single SLAS-format carrier, with fully automated tip and rack handling through Freedom EVOware.

This cost-effective, space-saving solution increases labware capacity and allows optimized use of deck space, minimizing the need for manual intervention and increasing walkaway time for Freedom EVO liquid handling workstations. The nested

The nested format allows up to five trays of tips to be stacked on each SLAS-format carrier

350 ul tip is available in both Tecan Sterile and Tecan Pure options for standard applications, with a Te-Stack version available soon in Tecan Standard purity for higher throughput applications.

To find out more on Tecan’s Nested LiHa Disposable Tips, go to www.tecan.com/consumables

between multiple compounds of interest.

Ideal for cutting-edge research, the new Synergy Wizard allows the user to quickly and easily set up synergy studies for three or more drugs, developing complex experiments with ease. Alongside a host of minor updates to simplify instrument use, these

Format flexibility has been increased with the addition of 1,536-well microplate compatibility, complementing the instrument’s existing 12- to 384-well plate direct dispensing capabilities. This high density format is particularly suited to assay development applications, providing better integration with downstream activities by allowing experiments to be designed and optimized in the same labware type used throughout the workflow. The instrument’s Synergy Wizard has also been improved, allowing straightforward investigation of drug-drug interactions

software upgrades are designed to accelerate experimental set-up for a wide range of drug discovery activities.

To find out more about the HP D300 Digital Dispenser, visit www.tecan.com/digitaltitration

The new Synergy Wizard allows easy set-up of studies using three or more drugs

Tecan Academy to be available worldwide Tecan’s online training tool, the Tecan Academy, will be launched globally in 2014, offering basic training and certification for new operators. The Academy’s library of online content is continuously updated with new material, with recent additions including a new certification course for Freedom EVO 75 operators and a ‘How to’ guide on using the Infinite® series of multimode readers for fluorescence measurements. Each distinct learning module is designed to enhance user understanding for reduced operational errors and higher productivity, all without having to leave your desk!

Many users throughout Europe and the US are already enjoying the benefits of the greater instrument knowledge offered by the Tecan Academy. Ben Davis, a Tecan

Academy user and Scientist in the Technical Development department at LGC Genomics, commented: “The Tecan Academy was recommended to us as a user-friendly way of improving day-to-day operation of our Tecan multimode reader for QC testing. It is very easy to use and navigate, with a clean design and concise graphical representations of the technical aspects of the instrument. Using the Academy has certainly provided a useful refresher on how to apply theoretical understanding to practical investigations, and it was very convenient to use, allowing me to log in and out as required.”

To find out more on the Tecan Academy, visit www.tecan.com/academy

The Tecan Academy offers convenient, web-based training

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product News TECAN JOURNAL 1/2014

Software updates enhance flexibility of HP D300 The latest software updates for the HP D300 Digital Dispenser ensure even greater versatility for drug discovery applications. The recently released version 2.2 software includes a number of updates to improve day-to-day operation of the HP D300 for new and existing customers, making it even faster to set up and run your experiments.

between multiple compounds of interest.

Ideal for cutting-edge research, the new Synergy Wizard allows the user to quickly and easily set up synergy studies for three or more drugs, developing complex experiments with ease. Alongside a host of minor updates to simplify instrument use, these

Format flexibility has been increased with the addition of 1,536-well microplate compatibility, complementing the instrument’s existing 12- to 384-well plate direct dispensing capabilities. This high density format is particularly suited to assay development applications, providing better integration with downstream activities by allowing experiments to be designed and optimized in the same labware type used throughout the workflow. The instrument’s Synergy Wizard has also been improved, allowing straightforward investigation of drug-drug interactions

software upgrades are designed to accelerate experimental set-up for a wide range of drug discovery activities.

To find out more about the HP D300 Digital Dispenser, visit www.tecan.com/digitaltitration

The new Synergy Wizard allows easy set-up of studies using three or more drugs

Tecan Academy to be available worldwide Tecan’s online training tool, the Tecan Academy, will be launched globally in 2014, offering basic training and certification for new operators. The Academy’s library of online content is continuously updated with new material, with recent additions including a new certification course for Freedom EVO 75 operators and a ‘How to’ guide on using the Infinite® series of multimode readers for fluorescence measurements. Each distinct learning module is designed to enhance user understanding for reduced operational errors and higher productivity, all without having to leave your desk!

Many users throughout Europe and the US are already enjoying the benefits of the greater instrument knowledge offered by the Tecan Academy. Ben Davis, a Tecan

Academy user and Scientist in the Technical Development department at LGC Genomics, commented: “The Tecan Academy was recommended to us as a user-friendly way of improving day-to-day operation of our Tecan multimode reader for QC testing. It is very easy to use and navigate, with a clean design and concise graphical representations of the technical aspects of the instrument. Using the Academy has certainly provided a useful refresher on how to apply theoretical understanding to practical investigations, and it was very convenient to use, allowing me to log in and out as required.”

To find out more on the Tecan Academy, visit www.tecan.com/academy

The Tecan Academy offers convenient, web-based training

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product news TECAN JOURNAL 1/2014

AC Extraction Plate™ – a unique sample preparation tool for LC-MS

The AC Extraction Plate offers straightforward sample preparation for LC-MS

The recently launched AC Extraction Plate – based on Tecan’s proprietary TICE™ (Tecan Immobilized Coating Extraction) technology – is a convenient, automation-friendly solution designed to streamline sample preparation for LC-MS analysis of small molecules. The plate reduces the sample preparation process to a simple ‘pipette and shake’ routine, eliminating the need for laborious filtration, centrifugation and solvent evaporation steps.

The AC Extraction Plate is a 96-position, deep-well microplate, with the inner surface of each well coated with a highly controlled layer of TICE material. This coating efficiently extracts low molecular weight analytes – such as vitamin D and testosterone – from aqueous solutions and eliminates the need for protein precipitations and liquid-liquid separations. By avoiding these time-consuming and difficult to automate processes, the AC Extraction Plate provides a convenient and easy to automate solution for the preparation of biological samples and other complex fluids for LC-MS analysis of small molecules.

Mixing

Extraction

Wash

Elution

Prepare appropriate samples and controls

Add sample

Add wash solution

Add elution solution

Add appropriate extraction mix

Shake

Shake

Shake

Remove extraction mix

Remove wash mix

Typical sample preparation workflow using the AC Extraction Plate

To find out more about Tecan’s AC Extraction Plate, visit www.tecan.com/acplate

Transfer into plate/vial

Transfer eluate to appropriate vials or microplates

Components TECAN JOURNAL 1/2014

Extended flexibility of Cavro® Omni Robot fully integrated and optimized for use with the Cavro Omni Robot’s Universal Z arm, offering a number of additional benefits for OEM liquid handling. Its validated, maintenance-free design simplifies system integration, with on-board pressure-based liquid level detection (pLLD) and diagnostics to monitor correct operation. Together with the Cavro Omni Robot’s standard cLLD, these functions provide exceptional pipetting performance and enhanced process security.

As a self-contained, fully programmable pipetting option, the Cavro ADP is ideally suited to applications where access is restricted, and the module’s integrated tip ejection option makes it possible for the Cavro Omni Robot to perform fully automated tip re-racking for the first time.

The Cavro Omni Robot offers precise OEM liquid handling

Tecan has introduced two extra options for the Cavro Omni Robot; the Dual Z and the ADP (Air Displacement Pipettor). Available with a broad choice of lengths, orientations and options for all three axes, the Cavro Omni Robot is designed to combine precision OEM liquid handling with straightforward integration. The launch

The Cavro Omni Robot Dual Z option can be fitted with a choice of fixed or disposable tips

of these additional pipetting modules provides instrument designers with even greater flexibility in instrument design.

The Cavro Omni Robot Dual Z option offers two independent pipetting channels in a single housing, doubling the robot’s liquid handling capacity without having to mount an additional arm. This compact unit can be fitted with either fixed probes or disposable tip adapters, or a combination of both, with integrated capacitive liquid level detection (cLLD) and an adjustable pitch of 9 or 18 mm between channels. This elegant solution offers several potential advantages – especially where space is an issue – allowing instrument developers to increase throughput or perform additional operations without compromising on performance. For example, by fitting the Cavro Omni Robot Dual Z option with one fixed tip and one disposable tip adapter, it is possible to use the fixed probe for bulk reagent dispensing and disposable tips to pipette samples, avoiding the risk of cross-contamination while saving on consumables costs.

The Cavro Omni Robot is now also available with the Cavro ADP as an alternative to the existing liquid displacement pipetting technologies. Using pneumatic technology, this compact pipetting module has been

These additional pipetting modules further extend the versatility of the Cavro Omni Robot and, together with the system’s extensive choice of options and finishes, provide exceptional flexibility for OEM liquid handling applications.

To find out more on Tecan’s Cavro Omni Robot, visit www.tecan.com/omnirobot

The Cavro Omni Robot ADP option offers maintenance-free pipetting

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CORPORATE NEWS TECAN JOURNAL 1/2014

Monitoring the quality of beer – a unique collaboration Tecan has collaborated with HLFS Ursprung and the Stiegl brewery to optimize the HybriScan™D Beer method for the quality control of micro-organisms affecting the taste of beer on an Infinite® M200 PRO multimode reader.

it really stimulating for our students; they learn so much from taking part. They must plan and execute their project, requiring critical thinking and the ability to work to set deadlines, which is good training for the future. Students also have to present their work to an external jury and answer questions about the science involved, which is a whole new experience for them.”

Höhere land- und forstwirtschaftliche Schule Ursprung (HLFS Ursprung), based in Salzburg, Austria, is a residential school dedicated to providing a science-based secondary education focused on the fields of agriculture and environmental engineering.

Students from across Austria come to the school to study alongside others with a similar interest in science and, during the course of their studies, have the opportunity to take part in Jugend Innovativ, a highly regarded national competition that provides a platform for young scientists to present the results of novel research projects. HLFS Ursprung collaborated with Tecan Austria and the Salzburg-based Stiegl brewery to establish a rapid molecular test on the Infinite M200 PRO reader, achieving a creditable 3rd place from 32 entries in the science category of this prestigious competition. Bernhard Stehrer, a science teacher at HLFS Ursprung, explained: “In addition to their regular lessons, students can voluntarily undertake scientific projects, such as participating in the Jugend Innovativ competition, during their leisure time.

Those who participate are highly motivated and spend many hours working on their experiments; it is wonderful to see them getting so involved in science, and very rewarding. HLFS Ursprung has participated in the competition for many years, and we find

ideas and educational initiatives. Stiegl provided samples for analysis and showed us the methods used in its laboratory, which involve assessment of cultures under a microscope. It can take a long time to acquire sufficient experience to confidently assess cultures this way, and we felt that molecular methods might be faster and easier to learn.

To help us with this project, we needed someone familiar with modern techniques and cutting-edge technology, and so we contacted Tecan.”

s with ided the studentpli cations A brewery tour prov ap the practical an understanding of of the project “This year, we wanted to investigate the science behind food production, combining it with quality assurance of the end product.

As our students study molecular biology, we looked for a project that would allow them to explore a specific application in this area, and decided on the quality control of beer.

Micro-organisms are a necessary part of the brewing process, but they can also ruin the beer; careful control of micro-organisms is therefore crucial. We approached Stiegl, a large private brewery in Austria that we had previously worked with, as we knew that the Company was very open to new

Careful control of brewing process micro-organisms is vital to the

Julia Füreder, a Concept Engineer at Tecan Austria, took up the story: “I had previously worked with the school, and was happy to participate again. The students are really hard working and have an immense scientific knowledge; it is lovely to collaborate with them.

We did some research, and discovered the HybriScanD Beer assay (Sigma-Aldrich), a rapid molecular test using photometric detection. I immediately thought of the Infinite M200 PRO, and Tecan agreed to support the study.”

CORPORATE NEWS

sensitive and time saving and, from a technical point of view, easier to perform.

It also avoids the need for cultivation, generating results in hours, which is a huge benefit.”

valuable hands-on The students gainesady of running the as

experience

Julia continued: “Everyone was so enthusiastic. The students took full responsibility for the project, which took about two months to complete, with myself, a colleague from Tecan, Dr Katrin Flatscher, and the HLFS Ursprung teachers acting as mentors.

Students designed experiments to reduce the 24-hour pre-enrichment time, as well as a method for detecting foreign yeast, which causes the quality of the beer to deteriorate. Katrin and I worked with the pupils, showing them how to set up and use the Infinite reader, and they soon picked it up; by the end of the project, they were experts!”

The Jugend Innovativ

Ludwig Mühlhofer, Head Research and Development at Stiegl, added: “It was both interesting and important for Stiegl to work with the new molecular method, comparing it to microbiology, and it was really nice to see the enthusiasm and the effort of the

TECAN JOURNAL 1/2014

project team

“The wonderful thing about having this opportunity to work with Tecan and Stiegl is that the students gain experience of science in the context of work.” that the students gain experience of science in the context of work, enabling them to learn about targeted research and production processes, and to see that their work has a purpose and offers benefits for other people.

They know that they have contributed to a process improvement, and that is a fantastic feeling.”

Tecan staff joine e HLFS Ursprung te as mentors for thde th achers project

“The results were really good, and compared well with those of the brewery.

Microbiological methods require culturing of micro-organisms, colony picking and microscopic examination, which takes days rather than hours. The students demonstrated that the new method is both

project team. In the future, it would be good to increase the degree of automation, further improving handling of the process.”

The success of the collaboration was summed up by Bernhard, who said: “The wonderful thing about having this opportunity to work with Tecan and Stiegl is

To find out more about Tecan’s Infinite M200 PRO reader, visit www.tecan.com/infinite200pro To find out more about HLFS Ursprung, visit www.ursprung.at To find out more about the Stiegl brewery, visit www.stiegl.at/en

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cell biology TECAN JOURNAL 1/2014

Automation paves the way for faster vaccine development Charybdis Vaccines in Italy has automated phage display/deep sequencing techniques on a Freedom EVO® platform, resulting in faster identification of bacterial antigens and protective antibodies. This system is helping to drive the development of new vaccines against pathogens of major worldwide concern.

Charybdis Vaccines Srl provides vaccine discovery, testing and development services to pharmaceutical companies through its diverse team of microbiologists, immunologists and molecular biologists.

Spun out from the University of Messina in 2011, the Company’s primary goal was to extend ongoing collaborations between the University and scientists and managers working for pharmaceutical and biotechnology companies. Professor Giuseppe Teti, Research Director at Charybdis, explained: “We are focusing on bacterial pathogens, using phage display techniques and animal models of infection to identify novel antigens of gram-positive bacteria, particularly group B Streptococcus and Streptococcus pneumoniae, which persist as major health problems worldwide. In phage

display, we ‘chop’ DNA extracted from these pathogenic bacteria into small pieces and insert them into phage genomes. These viruses then express fragments of bacterial proteins on their surfaces, allowing us to use the phages as bait to capture antibodies in patients’ sera. We can use this technique to identify bacterial antigens capable of producing antibody responses, which often turn out to be excellent vaccine candidates.

We have also used phage display methods to develop a breakthrough technology called PROFILER – Phage-based Representation OF ImmunoLigand Epitope Repertoire – that allows us to probe and categorize the antibody repertoire induced by infection or vaccination in humans or experimental animals.”

Staff at Charybdis Vaccines are helping to drive the development of new vaccines against pathogens of major worldwide concern. Left to right: Salvatore Benfatto, Veronica Lanza Cariccio, Deborah D’Aliberti, Maria Domina

cell biology TECAN JOURNAL 1/2014

In 2012, Charybdis decided to automate its workload to improve throughput, choosing a Freedom EVO 200 platform configured with Liquid Handling and Robotic Manipulator Arms, a six-position incubator, an Infinite® 200 PRO multimode reader for DNA quantification, a HydroSpeed™ plate washer, Te-Shake™, Te-MagS™ and Te-VacS™ modules, and labware carriers for tubes and plates, all controlled by Freedom EVOware® software.

“We chose Tecan automated systems because we liked the simplicity and versatility of the systems, as well as the ease of programming them for complex applications,” Professor Teti continued. “Another factor was the excellent help and advice we have had from Tecan to automate our techniques. Although we use the Freedom EVO platform for several different applications, the most interesting has been automating the antibody-based selection of phage display libraries, and for this we have worked very closely with the Tecan specialist team.”

Automation of the phage display technique begins with the addition of antibody-containing serum to protein G-coated magnetic beads in 96-well plates.

Serum and beads are then mixed with phage libraries containing bacterial antigens displayed on phage surfaces, followed by magnetic bead separation of antibody-bound phages from those without antibodies attached. This library selection procedure is followed by pre-sequencing steps on the Freedom EVO platform, including amplification of phage inserts from entire selected or unselected libraries, addition of Illumina® adaptors and amplicon purification.

Next generation sequencing on an Illumina

MiSeq® platform generates millions of DNA sequences daily from phage display. Professor Teti explained: “We developed this technique in collaboration with Professor Franco Felici (University of Molise) and Professor Concetta Beninati (University of Messina), and it is already opening up exciting possibilities in our work, particularly for vaccinology.

Until now, we have only been able to think about antibody response to vaccination or infection in terms of the quantity of antibodies induced. This new technique provides us with qualitative results, giving us a detailed picture of antibody specificities with information about the epitopes and/or protein fragments that are being recognized by the antibodies contained in individual serum samples.”

“We chose Tecan automated systems because we liked the simplicity and versatility of the systems, as well as the ease of programming them for complex applications.”

“We also use the Freedom EVO for automation of phage ELISAs,” he added. “The ELISA we run most frequently is for library selection; in this assay, coating of plates with anti-phage antibodies is followed by addition of selected or unselected libraries or individual phage clones, followed by addition of the antibody or serum sample

and appropriate secondary antibodies. After validation is complete, we plan to run up to 100 library selections daily, including same-day selection and sequencing. This huge workload would simply be impossible without the Freedom EVO platform, and automation has also reduced the volumes of sera we need to use; we often have only very small quantities of sera from laboratory animals, volunteers and patients, so this is very important. The high dispensing precision that we can now achieve is particularly important for our work, and factors such as human error and hands-on time – which are both major bottlenecks in any high throughput workflow – have been minimized.

Sample security, which is always an issue with human sera, is another major advantage of Freedom EVOware, as is data tracking; our main customers in the pharmaceutical industry greatly appreciate total traceability in the services we provide.”

Professor Teti concluded: “In the near future we plan to automate cloning and expression of the protein fragments identified by phage display. This will require ligation-independent cloning and automation of expression and purification of resultant proteins, but our experience has shown that the Freedom EVO is simple to use and to program – as well as very flexible – and we look forward to this next step in automating our workflow.”

To find out more about Tecan’s Freedom EVO platform, visit www.tecan.com/freedomevo To find out more about Charybdis Vaccines, visit www.charybdis.eu

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MICROARRAYS TECAN JOURNAL 1/2014

Faster and more reliable screening for cystic fibrosis mutations Alkor Bio has developed a rapid and accurate microarray-based diagnostic assay for cystic fibrosis using Tecan’s HS 400™ Pro Hybridization Station and PowerScanner™, allowing one technician to screen 10 patients for 25 cystic fibrosis mutations in under seven hours.

Alkor Bio, founded in 1992, is a large biotechnology group consisting of 12 companies in and around St Petersburg in Russia. Working in collaboration with hospitals and academic institutions both within Russia and across Europe, the group

develops, manufactures, distributes and markets medical diagnostics kits for detection of inherited, hormonal and infectious diseases, as well as allergies. The group has historically concentrated on ELISA-based testing – offering around 60 different diagnostic kits – but has recently developed its first DNA microarray-based assay, the CF-25 genomic test for cystic fibrosis (CF).

Caused by mutations of the CF transmembrane conductance regulator (CFTR) gene, cystic fibrosis is one of the most common autosomal recessive disorders in Europe, and is carried by one in 20 individuals of European descent. The CF-25 test is designed to identify 25 mutations which are frequently-occurring or associated with severe disease phenotypes. Alexander Pavlov, head of Alkor Bio’s Laboratory of Molecular Diagnostics, explained why the test was developed: “CF has traditionally been detected using biochemical markers and sweat testing, which are not always reliable and are characterized by a high incidence of false-positive results, creating a need for accurate DNA-based testing.

The CF-25 genomic test is based on reverse hybridization of fluorescently-labeled DNA probes to a microchip bearing mutant and corresponding wild type targets of the human CFTR gene. We have our own robotic printing facility to produce the microchips, and use an HS 400 Pro Hybridization Station and a PowerScanner, both from Tecan, to perform microarray processing and analysis.

This set-up only requires minimal amounts of DNA for analysis – we can even extract enough material from dried blood spots – and hands-on time is significantly reduced; one technician can screen 10 samples for 25 distinct CFTR gene mutations in six or seven hours.”

Application specialist Anna Buyanova loading slides into the cassette

MICROARRAYS TECAN JOURNAL 1/2014

“We have been very satisfied with both instruments and the service and support we receive from Tecan, as and when we require it.”

Members of the Alkor Bio team. Left to right; Evgeniya Penzenceva, Alexander Pavlov, Nadezhda Seilieva, Ksenia Potarikina

Alexander continued: “We purchased the HS 400 Pro in 2011 to establish the right quality control steps and protocols for fluorescence-based protein and DNA arrays, and to standardize hybridization as much as possible. It automates all the processing steps – pre-hybridization, blocking, hybridization, washing and drying – with minimal need for manual handling of the microarray slides, and is fully programmable, offering a wide range of settings for precise time and temperature control. The software is also easy to operate; it was really easy to adapt the station to our hybridization settings and parameters, and to integrate it into our protocol.”

very important for us to have the scanner ready for use at any time, because we use it to perform quality control on new batches of microarray slides, and the Tecan system is proving to be very robust.”

“The CF-25 genomic test was licensed in Russia last year, and received the EU’s CE mark in early 2013. We are now planning to use this microarray platform to extend our repertoire of microarray-based tests to include other genes of interest, as well as an extended CF panel with an increased number of CFTR mutations. We have been

very satisfied with both instruments and the service and support we receive from Tecan, as and when we require it. As a result, we are happy to recommend the Tecan equipment to our customers as a good solution for improving reproducibility and accuracy, particularly for high throughput laboratories,” concluded Alexander.

To learn more about Tecan’s microarray solutions, visit www.tecan.com/microarray To find out more about Alkor Bio, go to www.english.alkorbio.ru

“Following hybridization, slides are transferred to the PowerScanner for analysis.

The main benefit of this instrument is its wide range of settings, allowing us to precisely tune the system to match the needs of our proprietary microarrays. It works with multiple microarray substrates and formats, and enables us to implement a wide range of applications; with 24 slides in the magazine, even high throughput protocols can be performed easily in automatic mode. Although we initially purchased this instrument because of its potential for research and development, we also wanted a high quality, reliable system that could withstand constant use. It was Olga Astasheva, Manager of Microarray, inserts the cassette into the PowerScanner

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liquid handling TECAN JOURNAL 1/2014

Speed and reliability for drug titrations GlaxoSmithKline’s quest for improved anti-malarial treatments has been revolutionized by the speed and reliability of the HP D300 Digital Dispenser. This innovative system has increased throughput for standard drug titrations and enabled combinations of candidate compounds to be tested much more easily.

Scientists working at the GlaxoSmithKline research center in Tres Cantos, Spain, are dedicated to fighting diseases of the developing world, primarily seeking better treatments for malaria and tuberculosis.

The Malaria Discovery Performance Unit (DPU) performs a wide range of in vitro parasitological studies investigating potential anti-malarial candidate compounds. Dr Laura Sanz, an investigator in the Malaria DPU’s Biochemistry and Parasitology Department, explained: “We assay structurally diverse molecules from different anti-malarial programs to determine their in vitro potency.

As part of this work, we prepare compound plates for on-site testing, and needed an instrument that could shorten this process.

We were looking for a system capable of increasing the speed of plate generation and reducing cycle times, as well as providing more versatility than our existing system.

It was also really important to have the

flexibility to accommodate a variety of plate layouts enabling us to generate product combination plates and explore synergies.”

“We have been working with the HP D300 since autumn 2012, and it has significantly increased our sample throughput. Plates can be prepared more rapidly and, consequently, compound evaluation can be initiated earlier.

This allows new experiments to be started sooner, increasing the rate at which a project progresses. It also saves a great deal of hands-on time and frees staff to undertake other laboratory activities.”

“A key feature of the HP D300 is its capability to dispense picoliter volumes to any well, regardless of microplate format. In drug discovery, particularly in the earlier stages, there may be very little of the compound of interest available. Dispensing smaller volumes into the plate wells saves precious

“The HP D300 has exceeded our expectations, helping us to find faster ways of achieving our goals.”

The HP D300 enables GSK’s Laura Sanz (left), Cristina de Cózar and Benigno Crespo to test combinations of compounds more easily

liquid handling TECAN JOURNAL 1/2014

sample material, and the HP D300 has

were limited to five plates per run, the

“Our quality standards are extremely high,

allowed us to reduce the amount of

latest updates enable us to dispense to an

and our priorities are speed and reliability.

compound required for plate generation.

unlimited number of plates for the same

The HP D300 has exceeded our expectations,

This also assists with assaying product

assay – we have recently prepared as many

helping us to find faster ways of achieving

combinations, helping us to elucidate

as 80 plates in a single day – which is a big

our goals and allowing us to do everything

the effectiveness of novel anti-malarial

advantage, helping to drive down costs per

we want to do. It’s a user-friendly instrument

combinations more easily. The HP D300’s

plate and per assay.”

that fits perfectly into our laboratory’s lead optimization operations, enabling us to test

small size was another key consideration, allowing it to be housed in a biosafety

Laura continued: “Our old system was

combinations of compounds more easily,

cabinet under the sterile conditions required

used to perform serial dilution assays, and

and providing a great opportunity to carry

for preparing plates and performing assays.

dispensed the same volume into each well

out investigations that were more difficult

This enables us to perform both activities in a

of the plate, meaning normalization of

to perform using the old system,” concluded

single cabinet, virtually eliminating the risk of

DMSO was not required. As the HP D300 can

Laura.

contamination.”

directly dispense different doses to different wells without the need for serial dilutions,

To find out more about Tecan’s

Scientist Cristina de Cózar added: “We

the final volume of DMSO in each well

HP D300 Digital Dispenser, visit

received support from Tecan while we were

varies. However, we tested the system with

www.tecan.com/digitaltitration

familiarizing ourselves with the system,

a range of compounds, with and without

although we hardly needed any training.

normalization of DMSO, and discovered that

To find out more about GlaxoSmithKline’s

The HP D300 is easier to use than our old

normalization was unnecessary under our

Tres Cantos research center, visit

titration instrument, saving us a lot of time,

current experimental conditions due to the

www.gsk.com/research/fighting-disease-in-

and the software is very easy to work with.

very low DMSO concentration per well, saving

the-developing-world.html

Although previous versions of the software

both time and reagents.”

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Cell biology TECAN JOURNAL 1/2014

Customizing automated colony picking Laboratory automation and LIMS specialist Mejoran Lab Automation has developed a customized method for automated fungal colony picking on a Freedom EVO® 150 platform with an integrated SciRobotics Pickolo™ colony-picker. This innovative colony picking method produces viable microinocula of consistent quality for downstream assays, reducing the time needed to select mutants for further investigation from one week to one day.

Freedom EVO worktable, where a digital image of the dish is captured and used to determine subsequent tip movements for colony picking and transfer to 96-well plates, creating microinocula for further fermentation for downstream assays.

Mejoran LIMS Consultant Francisco Arenal

Juan Bautista Crespo García, Laboratory Automation and Bioinformatics Director at Mejoran

Mejoran Lab Automation, based in Madrid, Spain, has developed a customized colony picking method for use in biofuel research in collaboration with Abengoa Bioenergy New Technologies in Seville, a supplier of innovative solutions for biofuel production. Ongoing biofuel research at Abengoa focuses on screening of cellulase-producing fungal strains that degrade wood. This process involves growing lignolytic fungi in Petri dishes at 37 °C, colony picking and transfer of mycelia to 96-well microplates for further fermentation, followed by downstream analysis of the mutant strains. To meet the demands of this project, Mejoran developed and optimized a novel colony picking method for high throughput screening of fungal strains. Screening was performed on a Freedom EVO 150 workstation equipped with an eight-channel Liquid Handling (LiHa) Arm with 200 µl disposable tips, a Robotic Manipulator (RoMa) Arm, a Multidrop® Combi nL (Thermo Scientific), plate hotels, and an integrated SciRobotics Pickolo module, housed in a biological safety cabinet.

Petri dishes containing the fungal colonies are transferred from the hotels to the

Juan Bautista Crespo García, Laboratory Automation and Bioinformatics Director at Mejoran, explained: “The new picking method proved crucial. Manual screening processes are costly and time consuming, and so we developed an automated protocol for picking fungal colonies. A particular drawback of manual colony picking is the lack of control over how much fungal mycelium is transferred to the individual microplate wells; if too much mycelium is picked the plates will become overgrown. In contrast, automated colony picking using the Freedom EVO platform and integrated Pickolo module is very precise,

with much more control over the quantity and quality of the microinocula. This enables picking and transfer of uniform amounts of mycelium specifically from the perimeter of the colony, where growth is more efficient.

Using a novel tip-touch picking method – a sideways movement of the tip slightly below the surface of the agar, mimicking the action of manual picking processes – we were able to generate excellent quality, identical microinocula with close to 100 % further growth efficiency for subsequent experiments.”

Mejoran LIMS Consultant Francisco Arenal added: “Our general laboratory automation experience, combined with a close collaboration with SciRobotics, allowed us to develop this innovative colony picking method suitable for any fungal strain in just five months. As the Petri dishes are

Graphical representation of Mejoran’s automated tip-touch colony picking method

Cell biology

TECAN JOURNAL 1/2014

“We were able to generate excellent quality, identical microinocula with close to 100 % further growth efficiency for subsequent experiments.” filled manually, there is some variation in the volume of agar, and so we needed to determine its exact position. New camera settings were established to capture the best possible images of the growing fungi, and the Freedom EVO’s flexibility allowed us to switch between different tips to choose the most appropriate size and type for the application. We also created a bespoke worklist, selecting individual movements one at a time to optimize the position and behavior of each tip in each piece of agar.

This is what makes the Freedom EVO special.

It enables us to work with the instrument codes on a line-by-line basis, defining the exact movements required to correctly position each tip in each Petri dish, with no software-imposed limitations. The system can also successfully integrate a range of third-party instruments, offering maximum flexibility; the Pickolo software is easy to integrate with the Freedom EVOware®,

Mejoran developed a unique colony picking procedure on a Freedom EVO with an integrated SciRobotics Pickolo module

and the platform communicates very well with the Thermo Multidrop dispenser too.”

Juan concluded: “The automation of colony picking gives us a huge advantage. With efficient automation, laboratories can increase their colony picking and screening throughput significantly. Manual selection of a minimal number of mutant fungal strains may take five or six people a week to perform; using the Freedom EVO with the Pickolo module, one person can select the same number of

mutants in just one or two days. This frees staff to focus on testing new processes to avoid border or geometry effects in the microplates, as well as improving downstream assays to develop different cellulose-producing fungal strains.”

To find out more about Tecan’s colony picking applications, visit www.tecan.com/colonypicking To find out more about Mejoran, visit www.mejoran.es

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GENOMICS TECAN JOURNAL 1/2014

Sample preparation: the heart of NGS The Albert Einstein College of Medicine is using a Freedom EVO® platform to automate sample handling and library preparation for next generation sequencing.

The flexibility and throughput offered by this workstation enable straightforward processing of a wide range of genomic and epigenomic studies, providing high quality libraries for sequencing using the College’s two Illumina HiSeq® 2500 analyzers.

The Albert Einstein College of Medicine

The Albert Einstein College of Medicine of Yeshiva University, New York, has a strong focus on research, and is dedicated to the use of innovative biochemical techniques to improve medical understanding. As part of this multidisciplinary approach, Einstein has developed a number of core genetic facilities which provide expert support and services to researchers across the entire College. David Reynolds, Director of the Genomics Core, explained: “We have had a genomics core for over 15 years, originally providing Sanger sequencing and microarray-based services, and became interested in next generation sequencing (NGS) in 2008. We quickly learned that library preparation for NGS is a very labor-intensive process, so looked at automation as a way of expanding our throughput.”

“We had a good idea of what we wanted to achieve with an automated solution, and none of the existing instruments for NGS sample preparation offered us the freedom to develop our own protocols and applications; the Freedom EVO gives us the flexibility to evolve the platform as our protocols and

“We are still exploring the full capabilities of the instrument… but the flexibility of the Freedom EVO makes it easy to adapt our scripts and update protocols.”

Zeineen Momin loads samples onto the Freedom EVO

requirements change. Dr John Greally, Director of the Center for Epigenomics at Einstein, recognized this, and was an important advocate for bringing the system into the lab.”

The Genomics Core chose a Freedom EVO 200 workstation with eight-channel Liquid Handling (LiHa), Robotic Manipulator (RoMa), and Pick and Place (PnP) Arms. The system is also equipped with a PlateLoc™ Thermal Microplate Sealer (Agilent), an S2 Focused-Ultrasonicator (Covaris) and a TRobot Thermocycler (Biometra), as well as an integrated Infinite® 200 PRO multimode reader for nucleic acid quantification and a bespoke magnet for bead-based nucleic acid purification using AMPure® beads (Agencourt) in deep-well plates. This set-up – known as SARGE (Sample Automation Robot for Genomics and Epigenomics) – enables rapid automated processing of samples in a 96-well microplate format.

David continued: “Our initial goal was to automate our manual bead-based protocol using TruSeq® library kits (Illumina) for basic

GENOMICS

TECAN JOURNAL 1/2014

DNA library preparation. Although this was less straightforward than we first expected – library kit manufacturers did not have recommendations for automation of their protocols at the time – the Tecan Integration Group (TIG) was very proactive in developing the workstation to meet our needs, modifying difficult to integrate modules and creating custom tube racks for the workdeck of the Freedom EVO.” Zeineen Momin, an R&D technician in the Genomics Core, added: “The system is very user friendly, and the software is straightforward to program. Although we did not have previous experience with Tecan instruments, we were able to start optimizing the scripts after some basic on-site training. The Helpdesk also proved very useful for immediate support if we had any issues, and we attended a Tecan training course in North Carolina to help us further optimize our protocols.”

David commented: “Once we had established the initial method for generating TruSeq DNA libraries, the experience we gained made it much easier to develop new applications, and we have now developed a second workflow based on KAPA Biosystems NGS reagent kits.

Creating these new scripts was extremely easy, requiring just minor changes to the liquid classes, reaction volumes and timings of the various steps to achieve excellent DNA yields. We have also moved away from whole genome sequencing – which isn’t commonly performed at Einstein – to exome, amplicon, RNA and cDNA sequencing, and use KAPA kits for all of these applications. For RNA-seq we use a custom directional protocol upstream, followed by KAPA with a modified enrichment master mix, while exome-seq is performed using the Roche NimbleGen™ SeqCap™ EZ kit.

This work was a collaboration with Shahina Maqbool, Director of the Epigenomics Core,

Zeineen Momin and David Reynolds with Einstein’s Freedom EVO

who helps to develop protocols and ensure high quality sequencing data. We have been very happy with the results. The flexibility of our platform allows all of these applications to be set up and performed very rapidly, processing up to 48 samples per run.”

“We have also been impressed by the robustness of the protocols, enabling a wide range of sample types to be used for library generation. Although we perform quality control testing on all samples before library preparation, and ask for a minimum of 1 µg of nucleic acid, we are a core facility, and researchers come to us with a wide range of starting materials. For example, we were recently supplied with yeast samples for whole genome sequencing which were supposed to be at least 1 µg. When we tested them, there was actually only 10 to 25 ng of genetic material per sample. The researcher was happy to proceed on the understanding that we might not be successful, but the library generation worked perfectly without having to change the protocol.”

“We are still exploring the full capabilities of the instrument, and are constantly

evolving our workflow, but the flexibility of the Freedom EVO makes it easy to adapt our scripts and update protocols. There are also several applications which are currently being performed manually that we would like to automate, and we are hoping to use TouchTools™ to enable more people to run basic scripts,” said David.

Dr Greally concluded: “Massively-parallel sequencing is something of a commodity now, so we have recognized that the future lies in our ability to develop unique approaches to library production, especially in the fields of epigenomics and single cell genomics. These custom protocols, coupled with the Freedom EVO, will allow the Genomics Core to drive innovative research here at Einstein.”

To find out more about Tecan’s sample preparation solutions for next generation sequencing, visit www.tecan.com/ngs To learn more about the Genomics Core at Einstein, go to www.einstein.yu.edu/ departments/genetics/resources/genomicscore.aspx

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tig TECAN JOURNAL 1/2014

Integrated nanoliter dispensing aids drug discovery Scientists in the ADME Screening, Enzymology and Automation Group at Roche, Switzerland, have successfully integrated a mosquito® nanoliter liquid handling instrument with a Freedom EVO® platform, enabling accurate, precise pipetting at very low volumes. to integrate a liquid handling system capable of dispensing nanoliter volumes with one of these workstations to enable pipetting of sample volumes of less than 1 µl; the mosquito nanoliter liquid handling instrument (TTP Labtech) proved ideal. As the first ever integration of such a system with a Freedom EVO platform, this required a driver to enable communication between the two instruments. We have a very good relationship with the Tecan Integration Group (TIG); the team wrote a driver in just a couple of weeks.”

Pascal Schenk with the Group’s Freedom EVO system

The Roche ADME Screening, Enzymology and Automation Group, based in Basel, relies heavily on laboratory automation to efficiently deliver high quality experimental data. Accurate and precise pipetting, sometimes of nanoliter volumes, is required to perform the Group’s assays, as Automation Specialist Pascal Schenk, explained: “Test compounds are delivered in DMSO, and this has implications for our enzyme assays, where the overall DMSO concentration must be less than 0.5 %; the total volume of your experiment is dependent on the minimum volume of DMSO that can be accurately and precisely dispensed.”

Pascal continued: “Our department has six Freedom EVO 200 platforms, each equipped with a MultiChannel Arm™ (MCA) 96, as well as Te-Stacks™ for nested disposable tips and microplates. We needed

“Integration of the mosquito with a Freedom EVO was a really straightforward process, and was carried out in house. We validated the system by testing a range of liquid classes – including DMSO, acetonitrile, methanol, and aqueous buffer solutions – with both the Liquid Handling (LiHa) Arm and the MCA, as well as calibrating the mosquito for DMSO, checking the accuracy and precision of pipetting to ensure that the correct volumes were dispensed. For our current assays, we use a sample volume of 250 nl, which is easily achievable with a CV of 1 % for both accuracy and precision, and the mosquito’s positive displacement pipetting also allows us to dry dispense as little as 25 nl of our test compounds.”

“We use the system to prepare assay-ready plates, dispensing 100 nl aliquots of test compounds directly into microplates for screening, as well as generating standard curves. The enzyme reagents used for these procedures can be very expensive and are sometimes in short supply. Integrating the mosquito with the Freedom EVO has enabled the total assay volume to be reduced, significantly decreasing the amount of test compound and other reagents required.

Through careful selection of labware and the use of appropriate tips, we had already

tig TECAN JOURNAL 1/2014

“TIG wrote a driver in just a couple of weeks.”

managed to reduce compound requirements from 200 µl per assay to 20-50 µl. Using the mosquito system, just 5 µl is now sufficient to enable serial dilutions to be prepared, delivering further material and cost savings.”

“In addition to enzyme assays, we also assess compound solubility. For the final step in the process, samples are diluted at least 1,000-fold for analysis by mass spectrometry, and the integrated system is ideal for this,” Pascal added. The plate containing the samples for dilution is placed directly on the mosquito, along with a second 384-well plate from the Freedom EVO’s Te-Stack, transferred to the system by the Robotic Manipulator (RoMa) Arm. A low volume of test compound is dispensed into the second plate before the RoMa transfers it to the workdeck of the Freedom EVO, where dilution is performed using the MCA. The MCA allows us to add 200 µl of reagent to the sample, enabling dilution to be performed by dispensing just one large volume of the dilution solvent, rather than by serial dilutions.”

“The driver TIG developed allows us to control everything from Freedom EVOware®, including initializing the mosquito scripts and specifying which of its five deck positions the RoMa should transfer a plate to. To oversee the status of a run, we simply open the mosquito software and the Freedom EVOware side-by-side on the monitor, enabling us to observe both instruments. We have been using the system for almost a year now, and

it is working very well. The project has been a great success,” concluded Pascal.

For more information on TTP Labtech’s mosquito, go to www.ttplabtech.com

To find out more about Tecan’s customized solutions, visit www.tecan.com/tig

To learn more about Roche, visit www.roche.com

The mosquito system has been fully integrated into the Freedom EVO workstation

The mosquito provides positive displacement pipetting down to 25 nl

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Forensics TECAN JOURNAL 1/2014

Bespoke forensics Two Freedom EVO® platforms are speeding up processing of DNA evidence at the Miami Valley Regional Crime Laboratory, improving efficiency and helping staff to eliminate a six month backlog of cases since coming online. needs. Several manufacturers offered systems capable of automating DNA processing, but the Freedom EVO platform was the best fit for our laboratory and workflow.”

Mark Squibb with the DNA section team

“The Freedom EVO’s modularity has allowed us to build a system that will precisely match our workflow, both now and in the future.”

Miami Valley Regional Crime Laboratory (MVRCL) is a forensic science facility based in Dayton, Ohio, US. The MVRCL provides a full range of forensic services – including fingerprinting, DNA profiling, trace evidence, firearms, document testing, drug chemistry and toxicology – to a population of over a million people in the Montgomery County community and surrounding counties. In 2012, the Center’s DNA section implemented automated liquid handling, using two Freedom EVO platforms to help staff deal with the laboratory’s ever-increasing workload. Mark Squibb, Laboratory Supervisor and DNA Technical Leader for the section, explained: “We identified that automating certain elements of our workflow would be beneficial, eliminating hands-on processing for repetitive tasks. We wanted to develop an automated solution that could be integrated with our existing data management software to avoid the need to completely revalidate our workflow, and began looking at liquid handling workstations that met our specific

The MVRCL chose two Freedom EVO workstations to perform a range of repetitive tasks, eliminating some of the laboratory’s previous bottlenecks and freeing up staff to begin processing new cases. Mark continued: “We have a Freedom EVO 200 equipped with both Liquid Handling and Robotic Manipulator Arms that is geared towards nucleic acid extraction, quantitation and amplification set-up. Samples are then transferred to our Freedom EVO 150 platform, which automatically carries out the DNA amplification reactions. The amplification set-up and reactions are performed in microplates, but our Freedom EVO 200 also has the capacity to work with either tubes or microplates, giving us the flexibility to load samples onto the workstation in a variety of formats.”

“The Freedom EVO’s modularity has allowed us to build a system that will precisely match our workflow, both now and in the future, and process security is obviously enhanced by eliminating many of the manual processing steps. Because we funded the automation project through several successive rounds of federal grants, the platform’s open architecture gave us the option to implement automation in stages, with the flexibility to adapt to changes in our workload over time.

The forensic DNA community is ever-changing in terms of the technologies it uses, and we needed to make sure that our automated system could accommodate these changes, allowing us to implement new techniques as required.“ “Although we have not yet fully automated the entire DNA processing workflow, we are already seeing the benefits in terms of

Forensics TECAN JOURNAL 1/2014

throughput and turnaround times. Before automation, the backlog of new cases – cases that had not yet been started – was from several weeks up to three months. Cases are now processed within a week of receipt in the laboratory, usually within a couple of days.

The efficiency gains from releasing staff to perform other tasks – many of which cannot be automated – have also been significant.

This had led to an increase in throughput from around 50 cases a month to over 80.”

“Automation has also made the paperwork involved in processing each case easier, freeing up even more staff time. All of the Freedom EVOs’ sample handling and pipetting logs are automatically exported to our in-house software, ensuring a comprehensive audit trail and avoiding the risk of transcription errors. Although we have not yet chosen to implement automated barcode scanning for sample identification,

we have space on the decks of both instruments to do this in the future, should our sample numbers increase further.”

“Our Tecan workstations are now central to our DNA workflow. Automation has tackled several issues with a single solution, allowing us to eliminate many of the hands-on processing steps needed prior to sequencing DNA. Analysts now simply load samples onto a robotic workstation for processing, enabling them to address other bottlenecks within the laboratory. As a result, samples can now be collected, preserved and processed within a week,” Mark concluded.

To find out more on Tecan’s forensics solutions, visit www.tecan.com/forensics To learn more about the Miami Valley Regional Crime Laboratory, go to www.mcohio.org/government/mvrcl/

MVRCL’s Freedom EVOs eliminate several bottlenecks in the laboratory

Freedom EVOware® provides robust process security

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GENOMICS TECAN JOURNAL 1/2014

Deciphering the epigenetic code UK-based Oxford BioDynamics has automated its proprietary biomarker discovery platform, EpiSwitch™, on a Freedom EVO® 150, helping to establish a NGS, CGH-array and PCR-based pipeline for the discovery of novel biomarkers, as well as a PCR protocol for biomarker-based diagnostic testing.

“Automating the EpiSwitch process with the Freedom EVO and Air LiHa has improved reproducibility and enabled us to increase our throughput.”

Oxford BioDynamics Limited (OBD), a healthcare service company spun out from the University of Oxford, focuses on molecular biology investigations into gene expression and epigenetics. Its unique EpiSwitch platform, based on Chromosome Conformation Capture (3C), enables the discovery, development and validation of epigenetic biomarkers, aiding the identification and further development of biomarker panels for diagnostic and prognostic purposes. OBD has successfully automated its EpiSwitch NGS, CGH-array and PCR-based discovery pipeline and PCR test procedure on a Freedom EVO liquid handling system, improving both reproducibility and throughput.

Howard Womersley (front) and the Oxford BioDynamics team with the Freedom EVO

Dr Alexandre Akoulitchev, co-founder and Chief Scientific Officer of OBD, explained: “Epigenetic biomarkers are very informative, providing a clear indication of whether – and how – a patient’s gene expression profile has changed, as well as the progress of disease progression. In cases where objective biomarkers are required to help identify which patients fit into a particular cohort, we use existing knowledge of the epigenetic deregulation of well-known genes to assess whether any informative biomarkers are present. As an extension of our EpiSwitch platform, we have also developed a number of applications that involve deep sequencing and microarrays. This allows us to carry out investigations at the biomarker discovery

GENOMICS TECAN JOURNAL 1/2014

Marker 1

Marker 2

Marker 3

Marker 4

Screening for epigenetic markers to detect hepatocellular carcinomas. Diseased individuals are marked with +, healthy donors are marked with -; The sizes of markers 1-4 are 328bp, 324bp, 213bp and 261bp respectively. The electrophoresis was done on a PerkinElmer LabChip GX

stage in an unbiased manner, looking at quite complex disease phenotypes where very little information is available. This approach allows us to identify and filter out specific information about deregulation at the epigenetic level. By combining individual biomarkers and powerful statistical tools, we can develop biomarker panels that deliver good cross-validation with clinical results.”

“When developing this technology, we paid particular attention to compliance with industry-standard procedures, and so our methodology has been carefully designed and perfected. Our ISO-certified reference laboratory, based in Oxford, is responsible for R&D and quality control, as well as the transfer of technology. This enables us to provide customers with a fully validated set of biomarkers, together with a technology that can be licensed and used in house for either diagnostic or prognostic testing in

hospitals and clinics, or for high throughput screening in the pharmaceutical industry.”

Automation is fundamental to the OBD business model, and the Company recognized the importance of developing processes that are efficient and cost effective in a low throughput diagnostic laboratory, but which can also be easily scaled-up and translated onto an automated platform for high throughput applications. “At any one time, we will have several ongoing projects, and flexibility is essential to enable us to switch between them as and when necessary,” said Chief Operating Officer Dr Phil Jordan. “Initially, most projects involved manual processing of quite small numbers of samples but, as we progressed further, we needed methods that offered better reproducibility and higher throughput.

Automation was clearly the answer, and we acquired our first liquid handling system – a

Freedom EVO 100 – in 2010. Even then, it was obvious that we would eventually need higher throughput still and, two years later, we invested in a Freedom EVO 150, which enables us to look at roughly 600 markers a day.”

Dr Howard Womersley, Associate Director, Platform Development, added: “We looked at a number of liquid platforms before settling on a Freedom EVO 150 equipped with a MultiChannel Arm™ 96 and an eight-channel Air LiHa, controlled by Freedom EVOware® software. The system is faster than the other platforms that we looked at, and its versatility allows us to switch between different types of labware – 96-well plates, PCR tubes and 50 ml tubes – while its Air LiHa gives us the pipetting accuracy we need over a larger volume range, from 1 to 1,000 microliters. Our requirements change on a daily basis, and the Freedom EVO gives us the flexibility to cope with a dynamic workflow, changing between R&D applications and biomarker screening. Freedom EVOware is quite impressive too; it can do pretty much everything you need, and the scripts can be as simple or as complicated as necessary.”

Dr Akoulitchev concluded: “EpiSwitch is a unique assay looking not just at ordinary DNA and PCR products, but at intact epigenetic biomarkers. Automating the process with the Freedom EVO and Air LiHa has improved reproducibility and enabled us to increase our throughput; the system handles this challenging technology very well.”

To find out more about Tecan’s genomics solutions, visit www.tecan.com/genomics To find out more about Oxford BioDynamics Limited, visit www.oxfordbiodynamics.com

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Liquid handling TECAN JOURNAL 1/2014

High throughput nanoliter pipetting with the MCA 384 Scientists working in the Screening Unit at the Institute for Molecular Pharmacology in Germany are finding the low volume pipetting capability of the MultiChannel Arm™ 384 beneficial for the investigation of siRNAs and small molecule compound screening.

“The MCA 384 can accurately and reproducibly pipette down to 300 nl without the need to use any special techniques.”

The Leibniz-Institute for Molecular Pharmacology (FMP), based in Berlin, Germany, is an academic center offering open access RNAi and small molecule compound screening. FMP’s Screening Unit has automated these processes on a Freedom EVO® platform, taking advantage of the low volume pipetting capability of the MultiChannel Arm (MCA) 384. Martin Neuenschwander, automation scientist at FMP, explained: “We have been using laboratory automation for small molecule screens for several years, and have four Freedom EVO 200 platforms equipped with a variety of liquid handling arms, including MCA 96, MCA 384 and eight-channel Liquid Handling (LiHa) Arms, as well as Robotic Manipulator (RoMa) Arms. For compound screening, material is often limited, and it is also important to keep the DMSO concentration below 1 %. We needed to pipette volumes down to 300 nl, and invested in a new Freedom EVO platform optimized for this work.”

Katina Lazarow and Martin Neuenschwander with FMP’s Freedom EVO workstation

“The new workstation is equipped with an MCA 384, a Carousel LPT 220 EVO™, a wash station, a HydroSpeed™ plate washer and a Safire2™ microplate reader, as well as two small LiCONiC incubators. Using the 15 µl tips, we performed some experiments pipetting two different colored dyes in DMSO, adjusting the liquid classes as necessary to achieve linearity down to 300 nl. In a second study, these adjusted liquid classes were used to demonstrate pipetting reproducibility, taking a fresh tip box for each experiment.

These studies showed the MCA 384 can accurately and reproducibly pipette down to 300 nl without the need to use any special techniques, allowing us to reduce our assay volumes to just 30 µl while still maintaining a DMSO concentration of less than 1 %.”

Martin continued: “Another big advantage of the system is that we can perform serial dilutions within individual plates, which is ideal for IC50 determinations. With our previous system, we had to copy the entire plate, performing dilutions across several different plates. With the MCA 384, we have the capability to select just one column, allowing us to perform dilutions in the same plate. We can do everything with just two plates now, whereas before we always had at least 20 to measure. In addition, the layout of the Freedom EVO workdeck is easily reconfigured in house, enabling us to add additional carriers to meet future needs – for example to accommodate 1,536-well plates – or to integrate other modules such as readers or incubators into the workstation. It gives us so much more flexibility.”

Martin added: “We control almost everything from Freedom EVOware®, which is perfect for rapid, high throughput screening using fairly simple worklists, while still allowing the more complex programming for assays where the timing is crucial. In addition, we can carry

Liquid handling

out longer experiments needing overnight measurements, for example cell-based assays monitoring fluorescence intensity, ensuring that there are no gaps in the data.”

Katina Lazarow, a scientist from the RNAi screening core facility, added: “The Screening Unit is also responsible for RNAi screening, and has two libraries of siRNAs stored in 384-well microplates. The new Freedom EVO is also used to perform transfections for these screens, which involves transferring the siRNAs into assay plates, adding the cells and, at a later date, changing the medium. The system also prepares the plates for reading, removing the medium and adding other solutions as necessary. Previously, we used

A

fixed tips for all our liquid handling protocols, but disposable tips are more suitable for siRNA and semi-sterile processes. We are able to use the MCA 384 with 125 µl disposable filter tips to pipette 4 µl volumes, and have demonstrated a CV of below 1 % with good reproducibility across the plate. The MCA is also particularly suitable for assays where cells do not adhere well. By pipetting very slowly, we can ensure that the cells are not disturbed, which is critical for microscopy applications.”

“I only began using the Freedom EVO about a year ago, but very quickly learnt how to write the scripts and use the workstation; it is really good to work with. The big advantage of the Freedom EVO workstation is that it

TECAN JOURNAL 1/2014

makes it possible to perform high throughput whole genome screening in 384-well plates.

The system is very reproducible and accurate, and using the MCA with disposable tips allows very clean working, eliminating any risk of cross-contamination,” Katina concluded.

To find out more about Tecan’s MultiChannel Arm 384, visit www.tecan.com/mca384 To find out more about the Screening Unit at FMP, visit www.fmp-berlin.info/core-facilities/ screening-unit/screening-unit/intro.html

Linearity of pipetted volumes below 500 nl

Pipetted volume (nl)

500

C Heat map of pipetted volumes at individual positions

450 400 350 300 250

B

500

50

100

150 200 Dilutor volume (nl)

250

300

Row

0

Reproducibility across different tip boxes

450

Pipetted volume (nl)

400 350 300 250 200 150

A B C D E F G H I J K L M N O P

1

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24

100

Column

50 0

1

2

3

4 5 Tip box number

6

7

8

0.0

25.0

A: Pipetting performance showed good linearity at volumes of less than 500 nl. B: Excellent pipetting reproducibility was achieved at 300 nl.

C: The high reproducibility of pipetting across a microplate is clearly shown by a heat map of % CVs

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Liquid handling/Forensics TECAN JOURNAL 1/2014

Building a case of precision pipetting The DNA Section of the Orange County Crime Laboratory has recently taken delivery of its first Air LiHa equipped Freedom EVO® workstation for DNA quantitation and amplification reaction set-up. Complementing the laboratory’s existing liquid displacement Freedom EVO platforms for DNA extraction, this new instrument will help to streamline the workflow and improve pipetting precision.

“Although we are only in the validation phase at the moment… the pipetting precision of the Air LiHa is very good.”

Forensic scientists Jennifer Jarrett, Robert Binz and Heather Pevney (left to right) with one of the DNA Sections’ Freedom EVO workstations

The Orange County Crime Laboratory (OCCL) in California, USA, is a full service, internationally accredited laboratory providing forensic analyses to law enforcement and fire protection agencies throughout Orange County. OCCL’s DNA Section collects and profiles DNA from a variety of sources – including samples taken

from victims or suspects and DNA trace evidence from items – processing around 15,000 samples a year. To help deal with this large caseload, OCCL has invested in a number of automated laboratory solutions, including two Freedom EVO 150 workstations for DNA extraction. Robert Binz, a Forensic Scientist at OCCL, explained their approach:

Liquid handling/Forensics

“We purchased our first Freedom EVO in 2010 to speed up DNA extraction, and originally chose the HID EVOlution™ because it was already optimized and validated for use with the Applied Biosystems PrepFiler® Forensic DNA Extraction Kit (Life Technologies). Using this platform, we can process up to 80 samples per run – to match our downstream processes – and it was so successful that we purchased a second platform within a year.”

“More recently, we began looking to acquire a new system to replace the third-party workstations used to automate the quantitation, normalization and amplification steps of our workflow. As we do not use the Applied Biosystems Quantifiler® Duo chemistry for the quantitation step, the HID EVOlution package was not an option.

We decided that an air displacement liquid handling system was the best fit for our needs, providing accurate and reliable low volume pipetting with disposable tips. Several manufacturers offered such systems, but none of the others offered the versatility of the Tecan instruments, making a Freedom EVO workstation equipped with an Air LiHa the obvious choice. Although we were not familiar with the Air LiHa itself, our existing relationship with Tecan was good, so we were optimistic that the system would offer the precision and reliability we needed.”

Robert continued: “The workstation itself is fairly simple, with just the Air LiHa pipetting arm and carriers for tubes, plates, troughs and pipette tips on the deck of the instrument. The key consideration for our quantitation and amplification protocols is accurate liquid transfers at low volumes, allowing us to pipette from 1 to 15 microliters

with high precision. Quantitation is performed in 96-well microplates, into which we transfer 14 μl of master mix reagent and 10 μl of buffer, followed by 1 μl of sample from either a tube or microplate. We need to do this for up to 80 samples per plate, plus standards and controls, so reliable and reproducible transfers are vital to avoid false negatives which could potentially impact on a criminal case. The quantitation plates are then transferred to an Applied Biosystems 7500 for analysis, while the sample tubes or plate remain on the Freedom EVO. The results of the quantitation are automatically uploaded to our LIMS, which then instructs the Freedom EVO to perform sample normalization and amplification as required via a worklist.”

“Amplification set-up is the most complex part of our liquid handling workflow. Initially, 15 µl of master mix reagent is transferred to the amplification plate. The workstation then cherry-picks the samples for amplification – avoiding those extracts with insufficient DNA for typing – and adds between 1 and 10 µl of either neat or normalized DNA to the amplification plate based on the quantitation results. This is followed by the addition of reciprocal volumes of TE buffer to make the total volume in each well up to 10 μl. Again, accurate liquid transfers are vital for this application, as the amplification process is very sensitive to the amount of DNA present.”

TECAN JOURNAL 1/2014

volume was increased to 10 μl, which we are extremely happy with.”

Robert concluded: “When the new workstation was first installed, we worked with Tecan’s application development team to set up some of the basic scripts for our two major protocols, then continued the development of these scripts in house.

A colleague and I have both attended the Freedom EVOware® Standard and Liquid Handling Basic training course at Tecan’s North Carolina site, and this, combined with our previous experience of the liquid displacement Freedom EVO platforms, has enabled us to exactly match the system to our workflow and LIMS requirements.”

To find out more on Tecan’s Air LiHa, visit www.tecan.com/airliha To learn more about the Orange County Crime Lab, go to www.occl.ocgov.com

“Although we are only in the validation phase at the moment, we have performed numerous calibration protocols, and the pipetting precision of the Air LiHa is very good. For 1 μl transfers we are achieving CVs of 1-5 %, dropping to 1-3 % when the The Air LiHa offers precision liquid handling down to 1 μl

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OEM TECAN JOURNAL 1/2014

Pooling resources Novartis has a long history of working with Tecan’s Partnering Business for the development of automated workstations for blood banking applications. The latest Procleix SP® System offers a flexible, high throughput solution allowing sample pooling and archiving on a single instrument.

Novartis Diagnostics’ Procleix® portfolio of nucleic acid testing (NAT) blood screening instruments has been providing reliable laboratory automation to blood banking facilities around the world for nearly 15 years.

Designed to offer walkaway automation for blood screening applications – including pooling, testing and archiving – these instruments eliminate the need for time-consuming manual processing by providing proven and reliable liquid handling and analysis.

wanted to offer customers a single platform that combined both pooling and archiving activities. Bradley Sherrill, Director of Global Marketing at Novartis, explained: “We wanted an advanced pooling instrument that would allow laboratories to migrate from time-consuming and laborious manual pipetting processes to a highly automated system that could perform all the pipetting and sample manipulations, as well as offering full process monitoring and software control.”

Pooling blood samples prior to testing – aliquoting multiple patient samples into a single master pool tube for infectious disease testing – is performed in many blood banks, and is one of the routine applications that has benefitted from laboratory automation.

In addition to pooling samples for testing, many laboratories also archive aliquots of each individual patient sample in case further testing is required, and Novartis

“Our partnership with Tecan – a company well known for producing state-of-the-art liquid handling platforms – goes back to one of the first automated pipetting systems, the Tecan Genesis RSP 150/8, and extends to our most recent pipetting and archiving system, the Procleix SP System. The technology developed in partnership with Tecan allows blood screening laboratories to choose between 4-, 8- or 16-sample master pool

The Procleix SP combines blood pooling and archiving on a single instrument

The instrument’s 8-channel Liquid Handling Arm offers efficient throughput

formats, and provides end-to-end automation of the pooling and archiving process; operators can simply load the racks of sample tubes onto the deck, and the instrument and software-guided interface take care of nearly everything else. Newer platforms, such as the Procleix SP, use Tecan’s Pressure Monitored Pipetting (PMP™) system to provide real-time error detection and further improve process security. We also use Tecan’s high quality disposable tips to ensure optimized instrument performance, and these have been well received by our customers.”

Bradley continued: “Direct control of the platform is handled by the Tecan software, but we have developed the user interface in house, allowing the pooling workstations to integrate seamlessly with other instruments from the Procleix portfolio. This approach allows us to draw on our existing software validation and expertise as a leading blood screening company, and on Tecan’s knowledge and experience in laboratory automation to present a comprehensive product offering to our customers.”

Talk to Tecan TECAN JOURNAL 1/2014

“Tecan is a great instrument development and technical partner.”

“We provide all of the operator training, customer support and on-site maintenance of instruments ourselves, but we rely on our close relationship with Tecan’s technical personnel for their liquid handling and instrument expertise. From the clients’ perspective it’s a single service, but in the background it’s a real partnership, so working with a company that has a global reach is obviously very important. In my own experience, this approach has been very successful; Tecan is a great instrument development and technical partner, and the Company’s staff have always been very responsive to requests for information or assistance. Overall we are very happy with our relationship with Tecan.

It is certainly a long-term partnership, and we look forward to developing further instruments with Tecan in the future,” Bradley concluded.

To find out more on Tecan’s Partnering Business, go to www.tecan.com/oem To learn more about Novartis Diagnostics’ Procleix portfolio, visit www.novartisdiagnostics.com/ products/instruments The Procleix SP System is not available for commercial sale in the United States. Performance characteristics have not been evaluated by the FDA. Approvals and commercial availability for the Procleix SP vary by region.

Dr Klaus Lun, Executive Vice President, Head of Corporate Development

Leading the debate The laboratory automation sector is changing, with an ever-increasing focus on complete solutions to simplify individual protocols and streamline entire applications. Instrument manufacturers need to move beyond the traditional boundaries of hardware and software, exploring new ways of innovating customer workflows.

Despite the many and varied applications of liquid handling workstations, there are a few key processes that are routinely performed across multiple disciplines, and it is these ‘common’ tasks that can be best served by the development of more intelligent automation solutions. The creation of truly complete solutions – incorporating hardware, software, consumables and reagents in a single package – represents a real benefit for customers, adding value in terms of ease of use, process security and reproducibility. However, simply packaging together the existing components that customers can source from various individual suppliers is not enough.

Instrument manufacturers need to really look at the liquid handling tasks that are being commonly performed in life science laboratories around the world, and offer customers a better, faster and more convenient way of achieving their goals. The recently launched AC Extraction Plate™ is an example of how a ‘smart’ consumable can benefit the end user, combining Tecan’s liquid handling expertise with a novel extraction device to offer a genuine alternative to laborious sample preparation.

The key to achieving this kind of progress is to really understand what customers are using their automated systems for, and working with expert partners to develop new solutions to make those applications easier.

To share your ideas of how Tecan can streamline your workflow, e-mail talk@tecan.com

Use of disposable tips virtually eliminates the risk of cross-contamination

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EVENTS 2014 TECAN JOURNAL 1/2014

Meet Tecan at these events Americas SLAS Society for Laboratory Automation & Screening 2014

San Diego, CA, USA

18 – 22 Jan 2014

MD&M West – Medical Design & Manufacturing

Anaheim, CA, USA

11 – 13 Feb 2014

AAFS 66 Annual Scientific Meeting – American Academy of Forensic Sciences

Seattle, WA, USA

17 – 22 Feb 2014

MSACL 2014 – The Association for Mass Spectrometry: Applications to the Clinical Laboratory

San Diego, CA, USA

01 – 05 Mar 2014

Pittcon® Conference & Expo 2014

Chicago, IL, USA

02 – 06 Mar 2014

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ABRF 2014 – Association of Biomolecular Resource Facilities

Albuquerque, NM, USA

22 – 25 Mar 2014

SOT 53rd Annual Meeting and ToxExpo™

Phoenix, AZ, USA

23 – 27 Mar 2014

The 10th Annual PEGS – the essential protein engineering summit

Boston, MA, USA

05 – 09 May 2014

ISBER 2014 Annual Meeting & Exhibits

Orlando, FL, USA

20 – 24 May 2014

The 2014 Annual Meeting of Japan Society for Bioscience, Biotechnology and Agrochemistry

Kawasaki, Japan

28 – 30 Mar 2014

CMEF China International Medical Equipment Fair Spring 2014

Shenzhen, China

17 – 20 Apr 2014

Arab Health

Dubai, UAE

27 – 30 Jan 2014

ArabLab 2014

Dubai, UAE

17 – 20 Mar 2014

Analytica 2014

Munich, Germany

01 – 04 Apr 2014

27 Tumor Cytogenetic Workshop 2014

Cologne, Germany

22 – 24 May 2014

Asia and Pacific

Europe, Middle East and Africa

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Tecan are pioneers in automated liquid handling and innovative life science solutions. For over 30 years we continue to enable and support our customers to make the world a healthier and safer place.

Headquarters: Tecan Group Ltd., Seestrasse 103, CH-8708 Männedorf, Switzerland T +41 44 922 8111 F +41 44 922 8112 info@tecan.com

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www.tecan.com

Tecan Journal, Customer Magazine of Tecan Trading AG., ISSN 1660-5276 Design: OTM/London www.otmcreate.com Photography: Günter Bolzern/Zürich www.bolzern.net Editor in Chief: Tecan Trading AG, Cornelia Kegele Project Lead: Tecan Trading AG, Cornelia Kegele/Antonietta Allocca Editor: kdm/UK www.kdm-communications.com Print: DAZ Druckerei Albisrieden AG/Zurich www.daz.ch Address: Tecan Trading AG, Marketing Communications, Seestrasse 103, CH-8708 Männedorf, Switzerland, journal@tecan.com, www.tecan.com To register for the Tecan Journal please go to www.tecan.com/journal © 2013 Tecan Trading AG, Switzerland, all rights reserved.

Tecan Group Ltd. makes every effort to include accurate and up-to-date information within this publication, however, it is possible that omissions or errors might have occurred. Tecan Group Ltd. cannot, therefore, make any representations or warranties, expressed or implied, as to the accuracy or completeness of the information provided in this publication. Changes in this publication can be made at any time without notice. All mentioned trademarks are protected by law. In general, the trademarks and designs referenced herein are trademarks, or registered trademarks, of Tecan Group Ltd., Mannedorf, Switzerland. A complete list may be found at www.tecan.com/trademarks.

Product names and company names that are not contained in the list but are noted herein may be the trademarks of their respective owners. For technical details and detailed procedures of the specifications provided in this document please contact your Tecan representative.

This journal may contain reference to applications and products which are not available in all markets. Please check with your local sales representative: www.tecan.com/contact