Tecan Journal Edition 02/2014

Tecan Journal Life Sciences and Partnering Business

Edition 2/2014

Transforming therapeutic drug monitoring for transplant patients pages 20 - 21

Fluent™ – the new laboratory automation solution pages 4 - 5

Enhancing NGS sample preparation with automation pages 10 - 11

Biology meets engineering pages 22 - 23

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CEO WELCOME TECAN JOURNAL 2/2014

Welcome to the new Tecan Journal

Welcome

It is a very exciting time here at Tecan, with the addition of the Fluent™ laboratory automation family to our world-class liquid handling portfolio. Fluent has been a major development program for Tecan, and the introduction of this first wave of products underpins our brand values of quality, reliability and innovation. Our first Fluent solutions are designed to meet the needs of the rapidly growing cell biology market, and our test sites and assay partners have been impressed by its speed and capabilities.

This innovative new platform reflects the increasingly application-focused nature of the life sciences market, as scientists look to partner with equipment manufacturers that can provide this type of high quality and user-friendly technical solution, backed by knowledgeable and responsive application support. Tecan is committed to meeting these needs, combining our automation expertise with an in-depth knowledge of our customers’ applications to develop novel solutions which will help to shape the lab of the future.

This issue of the Tecan Journal also focuses on another major growth area within the industry – genomics – looking at the various ways automation can help to accelerate and simplify genetic testing workflows.

From comparative genomic hybridization microarrays to next generation sequencing, automation is playing an increasing role in sample preparation and processing, offering greater throughput and enhanced reproducibility. We also have details of some innovative biomaterials projects in both Germany and France, as well as news from our Partnering Business on the success of the Dako Omnis platform and the launch of the latest Cavro® Omni Robot at this year’s AACC Clinical Lab Expo.

I hope you enjoy the issue, David Martyr, CEO

Check pages 4 - 5 to learn more about Fluent

CONTENTS TECAN JOURNAL 2/2014

page 6

This versatile system allows instrument designers to optimize sensitivity for their applications 2

page 7

CEO Welcome

4 - 5 Fluent – the new laboratory automation solution 6 Around the clock monitoring

with CNS 6 Tecan launches new options for Cavro Omni Robot at AACC’s Clinical Lab Expo 7 Dako Omnis helping to accelerate cancer diagnostics 8 - 9 Tecan UK customers gather at historic Hinxton Hall 10 - 11

Enhancing NGS sample preparation with automation

12 - 13 A complete solution for ELISA processing 14 - 15 Reliability diagnosing cattle diseases 16 - 17

pages 24 - 25

Monitoring the effects of environmental pollutants on live organisms

Contents

pages 14 - 15

Shorter turnaround times for genetic testing

18 - 19 Automating clinical cytogenetics 20 - 21 Transforming therapeutic drug monitoring for transplant patients 22 - 23 Biology meets engineering 24 - 25 Looking out for the environment 26 - 27

Cyanobacteria see the light

28 - 29 Discovering more with less 30 - 31 GeT with the NGS program 31

Leading the debate

32 Events

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PRODUCT NEWS TECAN JOURNAL 2/2014

Fluent™ – the new laboratory automation solution

Fluent is a unique automation concept built around the application-specific needs of laboratories, delivering more capacity and increased speed. Initially focusing on the complete automation of cell-based and biochemical assay workflows, Fluent brings together all the modules and devices required for automation of these assays in a single efficient and easy-to-use platform. It offers higher throughput, greater precision and improved reliability, allowing researchers to concentrate on what really matters – the results.

The Fluent solution for cell-based assays is designed to take the complexity out of cell biology research. Completely new from the ground up, it is available in three sizes – offering deck capacities from 30 to 72 microplates – to suit the throughput requirements of almost any laboratory.

The patented Dynamic Deck™ uses a modular, multi-level design to offer exceptional deck capacity, allowing flexible integration of all the complementary devices required for cell-based research – including incubators,

Exceptional ease of use

Fluent’s touchscreen interface guides users with clear graphical instructions and alerts for optimum simplicity and performance

washers and readers – into a single, fully automated system.

Developed to meet the everyday challenges faced by cell biology laboratories, Fluent aims to make cell-based assay workflows faster and more efficient. Liquid handling and labware logistics have never been easier, thanks to the instrument’s three, task-specific arms which operate simultaneously to ensure timely completion of assays, minimizing the time cells spend outside of the incubator.

Perfect coordination of the robotic arms is guaranteed by the platform’s Path Finder™ move optimization technology, which continuously adapts to the changing topography of the workdeck, avoiding the need for laborious programming of individual arm movements, helping to accelerate both set-up and routine system use.

Even complex cell-based assays can be automated using the platform’s FluentControl™ software, freeing researchers to focus on other tasks. Fluent’s built-in touchscreen interface simplifies day-to-day

Unprecedented capacity, small footprint

The Dynamic Deck offers unrivalled capacity and optimum efficiency for device integration

activities by guiding scientists through routine set-up and operation of the system for consistent, reproducible operation. It can provide graphical instructions and prompts for every step of the set-up process, from the number and type of cell plates required to the exact location of compound plates and assay reagents, helping to ensure compliance with SOPs and assay protocols.

This is complemented by a PC-based programming environment which offers ‘drag and drop’ protocol development, 3D modeling and contextual checks to ensure rapid, easy scripting. FluentControl also offers straightforward integration and control of a wide range of Tecan and third-party devices, providing user-friendly, walkaway automation of virtually any cell-based assay workflow.

To find out more on Tecan’s new Fluent laboratory automation solution, visit www.tecan.com/fluent

Optimized cell protection

Simultaneous parallel movements of task-specific arms enhance speed and throughput

PRODUCT NEWS TECAN JOURNAL 2/2014

high productivity

cell protection

cell viability

apoptosis epigenetics GPCR

new

cell signaling

touchscreen

Improving productivity for complex cell-based research is a challenge.

Processes are complicated, space is in short supply, lab personnel are confronted with more and more difficult tasks, and greater accuracy is always demanded. With the launch of the Fluent laboratory automation solution, all that changes. World-class productivity and simplicity are now within the grasp of every lab.

Watch the To see how Tecan Fluent webinar is shaping the now lab of the future, go to our webinar www.tecan.com/webinars

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PRODUCT NEWS TECAN JOURNAL 2/2014

Around the clock monitoring with CNS Tecan’s Common Notification System (CNS) is now available for the Infinite® PRO series of microplate readers, allowing users to remotely monitor the status of any Infinite reader using Magellan™ software (v7.2).

With CNS, users can now easily check if their Infinite reader is performing a measurement, awaiting a predefined user action, or ready for the next assay plate.

CNS allows readers to be remotely monitored through any networked computer or mobile device, offering increased walkaway times and giving laboratory scientists the freedom to perform other tasks while their assays are

running. This innovative feature is particularly useful for overnight operations, such as long-term microbial studies with the patent-pending Gas Control Module (GCM™), ensuring greater process security and alerting the user if there is a problem, for example running low on oxygen or carbon dioxide. Together with the existing Freedom EVO® Remote for monitoring of liquid handling instruments, this latest addition to the CNS portfolio provides complete peace of mind for walkaway laboratory automation.

To find out more on Tecan’s CNS, visit www.tecan.com/magellancns

CNS helps users to stay informed around the clock

Tecan launches new options for Cavro® Omni Robot at AACC’s Clinical Lab Expo Tecan has extended the flexibility of its popular Cavro Omni Robot with the introduction of embedded control functions and the option to select single axis configurations. Unveiled with the launch of the Cavro Omni Robot Version 4.0 at the AACC’s 2014 Clinical Lab Expo, these latest updates will make it even easier to configure the Cavro Omni Robot to suit specific applications or instrument designs.

The robot’s new Embedded Command Processor Mode allows direct communication for precise control and coordination of axis movements and liquid handling operations.

This OS-independent command schema allows line commands to be sent directly to the robot using virtually any computer or

Perfection isn’t instant.

It evolves.

Tecan Cavro. 40 years of innovation.

custom control board, complementing the existing Windows®-based Command Processor Mode for greater integration flexibility.

of liquid handling options and finishes, provide exceptional flexibility for OEM liquid handling applications.

The modular design of the Cavro Omni Robot allows users to choose from various lengths and orientations of all three axes, including a choice of single or dual arm X-axis configurations. To ensure there is a Cavro Omni for virtually every application, it is now also possible to choose any combination of X-Y or Y-Z axes, offering instrument designers the option to create their own axes without the time and expense of developing a complete liquid handling solution. These latest updates further extend the versatility of the Cavro Omni Robot and, together with the system’s extensive choice

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

The Cavro Omni Robot offers exceptional integration flexibility

CORPORATE NEWS TECAN JOURNAL 2/2014

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Dako Omnis helping to accelerate cancer diagnostics

Dako Omnis.

A generation ahead in IHC & ISH.

Dr Hermann Herbst The Dako Omnis platform – developed and manufactured by Tecan – offers complete automation of both immunohistochemistry (IHC) and in situ hybridization (ISH) protocols.

Following the instrument’s launch in September 2013, this advanced staining platform is now helping clinical pathology

laboratories around the world to streamline their histology workflows, offering higher throughput and faster results for patients.

customer needs made the Company an obvious partner for the development of this advanced staining system.”

Featuring a wide range of functions designed to improve and simplify day-today operation – such as flexible loading, overnight running and fast turnaround times – the Dako Omnis is the result of combining Dako’s expertise in tissue-based cancer diagnostics with Tecan’s advanced technical knowledge. Britt Meelby Jensen, Dako General Manager and Agilent Vice President, commented: “Tecan’s extensive experience in the development of liquid handling technologies and in-depth understanding of clinical laboratory

To celebrate the success of Dako Omnis, Tecan invited Dr Hermann Herbst, Head of Pathology at Vivantes in Berlin, Germany – one of the first customers to receive their platform – to a special presentation on the shores of Lake Zurich. Dr Herbst described the changes to his laboratory’s workflow since the system’s introduction to an audience of Tecan employees and associates, highlighting the time savings and efficiency gains. Dr Herbst explained: “The Dako Omnis really is a state-of-the-art, fully automated IHC and ISH workstation, allowing us to run in either continuous or batch processing modes. It offers improved control over reagent use and staining and, by combining IHC and ISH on a single platform, it saves us considerable hands-on time in both processes.”

To learn more about the Dako Omnis platform, visit www.dako.com/omnis

3066 Dako Omnis A1 poster_Medica.indd 1

14-11-2013 08:58:10

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CORPORATE NEWS TECAN JOURNAL 2/2014

Tecan UK customers gather at historic Hinxton Hall The Tecan UK User Meeting 2013 provided the perfect opportunity for members of the automation community to network with other users, discussing a wide array of applications.

Towards the end of 2013, Tecan UK hosted a two-day user meeting at the Wellcome Trust Conference Centre, home to the world-renowned Sanger Institute, in Hinxton. Delegates at the state-of-the-art venue, located in over 100 acres of parkland on the banks of the River Cam, were able to enjoy the facilities of the purpose-built conference center and the historic Hinxton Hall. Held from the 5th to the 6th of November, the event provided the opportunity to hear speakers from many different fields – including the pharmaceutical, biotechnology and academic sectors – discussing the

“Feedback was very positive; delegates will be recommending the event to colleagues and attending again themselves.”

Photographed by Magnus Manske

wide variety of applications for which Tecan platforms are used, complemented by poster presentations and a display of some of Tecan’s automated solutions.

with a lively round table discussion, where customers and Tecan specialists debated the use of automation, its challenges and the solutions.

Presentations covered the adoption of automation in diverse areas such as lab­-scale protein production, high throughput ELISA, biobanking and protein-DNA interaction screening, as well as the challenge of incorporating sample collections obtained during company acquisitions into one standard format. A highly informative presentation on the theory behind optimizing liquid classes – supported by a presentation on the practicalities of implementation in the laboratory – was well received, and there were tips on maintaining Freedom® EVO systems and using Freedom EVOware®. Delegates also heard about the role of the Tecan Integration Group in providing customized solutions that are a little outside of the ordinary, as well as new Tecan applications. The event concluded

The success of the event was summarized

by Steve Hawthorn, Commercial Manager, Tecan UK Ltd, who said: “User meetings are about supporting our customers, bringing together the different branches of the life science market and creating an automation community where our customers can network and learn from each other’s experiences. The varied program attracted scientists from a broad range of backgrounds, and there was ample time for networking during the day and at the evening dinner.

Feedback was very positive; delegates will be recommending the event to colleagues and attending again themselves, and we have already been approached by a number of customers interested in presenting at future user meetings.”

CORPORATE NEWS TECAN JOURNAL 2/2014

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GENOMICS TECAN JOURNAL 2/2014

Enhancing NGS sample preparation with automation The University of North Carolina (UNC) has automated its major sample preparation protocols for next generation sequencing on a Freedom EVO® workstation, enabling more efficient processing.

sufficient to warrant investment in automation. After a year or two, our first Illumina HiSeq® instrument was introduced, and automation became a necessity. It made perfect sense to choose Tecan; I knew from personal experience that the Freedom EVO was a flexible platform, and I was already comfortable with the programming.”

The High-Throughput Sequencing Facility (HTSF), part of the Department of Genetics at the University of North Carolina, USA, is a full service sequencing facility providing state-of-the-art techniques for genetic and genomic research. The Department is involved in a number of important research projects, including The Cancer Genome Atlas (TCGA) project – a large-scale collaboration to characterize the genomic changes occurring in cancer – and UNCseq™, an internal study into the mutations triggering cancer to enable personalized treatment. UNC is also home to NCGENES (North Carolina Clinical Genomic Evaluation by NextGen Exome Sequencing), where semi-clinical studies encompassing exome capture and sequencing are undertaken.

The HTSF has turned to automation for standardization of its major sample preparation protocols, choosing a Freedom EVO platform.

Piotr Mieczkowski, Research Assistant Professor and Director of the HTSF, explained: “I was recruited to the HTSF six years ago, when the UNC was investing in a next generation sequencing (NGS) laboratory. It was an exciting time for me because of my interest in different technologies; I knew that NGS was going to be one of the biggest players in bioresearch, and that it would be very important in the future. Initially, we had a single, basic genome analyzer and no automation; the focus was on learning to use the technology. Over time, more analyzers were purchased, but throughput was still not

The HTSF is now developing and verifying a range of automated NGS protocols for the Freedom EVO platform in collaboration with Tecan and Illumina. The workstation is equipped with an eight-channel Air LiHa Arm, a Robotic Manipulator Arm, a temperaturecontrolled shaker, INHECO heat blocks with exchangeable plate adapters to accommodate 96- and 384-well microplates for thermal incubation, and a 96-position magnetic

Ewa Malc loads a microplate onto the Freedom EVO

separator for bead-based assays. The joint venture began with the automation of Illumina’s Nextera® Rapid Capture kits and, with these protocols now verified, the collaboration is focusing its attention on the TruSeq™ Stranded Total RNA and TrueSeq Nano DNA kits. Piotr commented: “We have learnt a great deal from Tecan, but it is also very good for Tecan to collaborate with universities; we have a variety of different instruments and the expertise required to run them, and we know what the market trends are in terms of the chemistry that needs to be used. Working with Tecan and Illumina has been the perfect combination.”

Many different types of sequencing – complete and targeted genome resequencing, small RNA sequencing, transcriptome

GENOMICS TECAN JOURNAL 2/2014

sequencing, ChIP-seq, bisulfite-treated DNA sequencing and metagenomic sequencing – are performed by the HTSF, and sample numbers can vary considerably, from just a few samples to perhaps 2,000 per year, depending on the project. Combining an automated liquid handling workstation with an NGS platform enables high throughput sample processing and allows more efficient data generation. The HTSF has successfully demonstrated this by automating parallel processing of up to 48 samples using Nextera Rapid Capture kits, providing an effective, robust, streamlined process for library preparation and exome enrichment. Sample throughput was increased compared to manual preparation – without any decrease in data quality – and minimal hands-on time was required, freeing staff for other tasks. But throughput is not the only issue.

Reproducibility is equally important, and automation removes the likelihood of operator-to-operator variation, as Piotr commented: “For high throughput, the benefit of automation is clear. But even for low sample numbers, we prefer to use automation if possible, as it ensures every step is performed in exactly the same way every time. This is especially true in clinical laboratories, where automation needs to be oriented towards low, but reproducible, throughput.”

As sample throughput increases, so does the demand for data analysis, requiring a great deal of bioinformatics support. This may be from a single laboratory, or from a bioinformatics facility such as the UNC Center for Bioinformatics, led by Hemant Kelkar.

While single labs tend to be quite specialized and oriented towards one particular application, the Center covers all applications, which is ideal for the HTSF. “This type of

Left to right: The HTSF's Piotr Mieczkowski and Ewa Malc with Tecan's Jon Smith and the Freedom EVO system

support is essential to our research, since we generally need a broad range of applications; as new projects get underway, we decide how the data will be analyzed and then direct the researchers to the bioinformatics group which best fits their needs,” said Piotr.

He concluded: “Automation is becoming a critical tool, offering efficient, reproducible library preparation, and our aim is to automate all our library preparation protocols, whatever the technology platform; the Freedom EVO has proved ideal for this purpose.”

To find out more about Tecan’s NGS solutions, visit www.tecan.com/ngs To learn more about the HTSF, go to sites.google.com/site/htsfunc

“We prefer to use automation if possible, as it ensures every step is performed in exactly the same way every time.”

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CLINICAL DIAGNOSTICS TECAN JOURNAL 2/2014

A complete solution for ELISA processing MLM Medical Labs is taking advantage of the Freedom EVOlyzer® workstation’s optimized ELISA processing to help meet the complex laboratory support needs of clinical trials, increasing throughput and improving process security.

MLM Medical Labs is a specialized company with a global reach

MLM Medical Labs, based in Moenchengladbach, Germany, is an ISO15189:2007-accredited, GLP­-certified and CLIA-registered laboratory providing analytical services and biomarker analysis for pharmaceutical companies and contract research organizations (CROs) performing clinical studies. The Company offers the entire portfolio of service elements necessary for the laboratory support of clinical trials, as Professor Dr Stephan Wnendt, CEO of MLM, explained: “We are a central and speciality laboratory focusing entirely on the medical diagnostics that are necessary for safety analysis in clinical trials, including clinical chemistry, blood counts, serology and urine analysis. During a clinical study it is essential to closely monitor the safety of the individuals involved, to check that the patient meets the general inclusion criteria for the study, and then, during the study, to monitor how the drug affects their general health status.”

“Our clients are renowned CROs, biotech companies and global pharmaceutical

The MLM team

manufacturers in Europe, Asia and the USA, and we work across a broad range of therapeutic areas, including cancers, cardiac disease, high blood pressure and diabetes.

We use biomarkers to study the efficacy and side effects of candidate drugs, and many of these markers are analyzed by ELISA. Although we have been successfully using Tecan instruments – including a Sunrise™ microplate reader and a HydroFlex™ plate washer – as part of our manual ELISA protocols for many years, we wanted to fully automate the workflow to increase throughput, particularly for large-scale studies.”

“We looked at the various solutions on the market, and most offered a modular approach, with one system for plate set-up, another for running the ELISA, and a separate detection instrument. What impressed us about the Freedom EVOlyzer was the fact that all the functions we needed were brought together in a single instrument, controlled by one software program. This gave us a virtually ready-to-use, validated system that still had

CLINICAL DIAGNOSTICS TECAN JOURNAL 2/2014

the flexibility to be customized according to our exact needs. We were very happy with our existing Tecan instruments, so we were confident that the Freedom EVOlyzer would provide the quality we needed.”

“We bought our Freedom EVOlyzer in 2010, and immediately saw the benefits in terms of both throughput and reducing the number of pipetting and sample handling errors.

We are able to process far more samples in a day, and you don’t have to worry about misplacement of samples in wells or incorrect pipetting volumes. We also use disposable tips to avoid the risk of cross-contamination, which is obviously a key consideration for clinical trial samples.”

“Process security is further improved by the use of barcoded samples. The system has a direct link to our LIMS database, enabling each sample that is loaded onto the platform to be identified from its barcode, meaning everything is traceable from the moment it comes into the laboratory.

In a way, the Freedom EVOlyzer is not a standalone instrument, it is connected to the IT backbone of our Company, and we can retrieve the data at any time through the LIMS. Similarly, the integrated Sunrise reader has a direct input into our LIMS; the data is automatically pushed through to our server, and we can prepare the results reports from the LIMS system, which simplifies analysis and reporting.”

“We have one technician who is a specialist on the Tecan instrument and Freedom EVOlution™ software, with another who acts as their deputy. Once you are familiar with the software, it is easy to use, but the support we have had from Tecan’s applications team has also been very good. An application specialist from Tecan helped our technicians to set up the initial assays, and creating protocols for

“The Freedom EVOlyzer is not a standalone instrument, it is connected to the IT backbone of our Company.”

The Freedom EVOlyzer represents a validated solution for ELISA processing

new ELISA tests has been very straightforward.

Having a ready-to-go solution has been an advantage in this respect, and I think we would have lost that opportunity to some extent if we had chosen a more modular approach.”

“Automation of our ELISA processing with the Freedom EVOlyzer has been extremely helpful in meeting our customers’ needs and expectations, particularly for large-scale projects. For example, we had a study running last year where we had to analyze 8,500 samples for a certain insulin derivative.

Although it would have been possible to do

this manually, we would have been concerned about higher rates of errors and deviations, and the turnaround times would also have been much longer. Using the Freedom EVOlyzer we were able to analyze 300 to 400 samples a day – up to 3,500 samples a week – which simply would not have been possible previously.”

To learn more about the Freedom EVOlyzer, visit www.tecan.com/freedomevolyzer To find out more about MLM Labs, go to www.mlm-labs.com

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

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VETERINARY TECAN JOURNAL 2/2014

Reliability diagnosing cattle diseases A Freedom EVO® 150 workstation is providing the Central Diagnostic Laboratory at SAC Consulting with reproducible and reliable ELISA-based screening for Johne’s disease and other bacterial and viral pathogens in cattle. The system has increased the laboratory’s throughput by three-fold compared to manual processing, to an average of 1,000 samples a day.

SAC Consulting, part of Scotland’s Rural College, serves the farming community across Scotland and the North of England, providing laboratory testing, support and advice on all aspects of rural enterprise, from agronomy, livestock and dairy services to disease surveillance, farm animal diagnostics and environmental consultancy. SAC Consulting: Veterinary Services (SACCVS) – comprising eight disease surveillance centers and a Central Diagnostic Laboratory – offers a full spectrum of diagnostic testing services, including viral screening for cattle diseases such as BVD (bovine viral diarrhea), IBR (infectious bovine rhinotracheitis) and Johne’s disease.

To cope with its growing workload, the Central Diagnostic Laboratory has invested in a number of automated solutions to improve the throughput of its diagnostic assays, as Josh Bird, Senior Scientist at SACCVS, explained: “Ever-increasing biosecurity measures to prevent the spread of diseases harmful to the farming industry have led to a huge rise in the number of samples coming into the laboratory, and the throughput necessary was too high for successful manual testing to continue. It was the storage and tracking of samples, as well as the associated paperwork – rather than the assays themselves – that were causing issues, creating a logistical nightmare.

We looked at automation as a way of streamlining the laboratory workflow, and chose a Freedom EVO 150 platform to handle our ELISA-based testing, as this seemed to be the best system on the market for our needs.”

The workstation was delivered in late 2009, and was originally set up to perform Johne’s disease testing, the laboratory’s largest single test in terms of sample numbers at that time.

The platform is fitted with both a Robotic Manipulator Arm and an eight-channel Liquid Handling Arm using fixed tips, as well as a Sunrise™ microplate reader and a HydroSpeed™ plate washer, plus an incubator, hotels and, importantly, a PosID™ barcode reader. Josh explained: “As part of our Premium Cattle Health Scheme, barcoded labels are sent out to farmers or vets and put straight onto tubes when blood samples are collected, making it easy to match each sample to the associated paperwork.

“The main benefits of the Freedom EVO platform are its reproducibility, capacity for unattended overnight runs and reliable sample tracking, without any missed samples; we certainly feel we have got our money’s worth.”

These samples are booked into our LIMS database before we even receive them, so we can trace everything quite easily by using barcode scanners.”

“The typical throughput of the Freedom EVO is 12 plates per day, each containing 88 samples and eight controls, equivalent to nearly 1,000 samples. The platform is used in conjunction with a robotic microplate replication system, which uses our LIMS sample tracking software to automatically generate daughter plates for testing on the Freedom EVO, reducing the set-up time for a six plate run from 45 minutes to just 5 minutes. We are also hoping to directly integrate the Freedom EVO with our mother/ daughter plate system in the near future, giving us the capacity to do three or four runs daily, processing almost 2,000 samples.”

Josh continued: “As our testing requirements changed, we also automated both our BVD and IBR test kits on the Freedom EVO platform, and this gave us far more reproducible results compared to manual processing, with variability around 5 % over multiple runs.

In addition, we are validating our leptospirosis testing kit – an assay known for enormous variability between individual laboratory staff – on the Tecan platform, and have generated some very promising data. As it is computer controlled, processes are carried out exactly the same way every time, with incubation times accurate to the second, and this has certainly helped to improve the reproducibility.

VETERINARY TECAN JOURNAL 2/2014

We have never had any problem with carry-over between samples or assays using the fixed tips, and a weekly flush of the system with 50 % ethanol followed by distilled water prevents build-up of contamination.”

“The system is easy to use, and I really like the Freedom EVOware® software; it is very user­friendly and intuitive for scientists who have no IT background. Because there are separate commands for everything, once you understand the basics, you can build up complicated programs and create multiple options, depending on the requirements of your workflow. This is particularly useful in a veterinary testing environment, where we continuously have to adapt and change in response to upgrades in testing kits or new disease threats. There are two of us responsible for programming the system, with the aim of making it as easy as possible for the other staff; they can simply load the samples and select the correct options from the menu.”

“The main benefits of the Freedom EVO platform are its reproducibility, capacity for unattended overnight runs and reliable sample tracking, without any missed samples; we certainly feel we have got our money’s worth. All the people at Tecan that I have been in contact with are really nice and approachable, easy to get hold of and go out of their way to help us. They always respond within 24 hours, and our local Tecan engineer is usually at our laboratory the next morning if we require on-site help,” Josh concluded.

To find out more on Tecan’s veterinary diagnostic solutions, visit www.tecan.com/veterinary For more information on SAC Consulting, go to www.sruc.ac.uk/info/20005/sac_consulting

The Freedom EVO typically processes almost 1,000 samples a day

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GENOMICS TECAN JOURNAL 2/2014

Shorter turnaround times for genetic testing Ambry Genetics in California is taking advantage of the increased throughput, reliability and reproducibility of laboratory automation, using Freedom EVO® workstations to streamline its genetic testing workflows for cancers, cystic fibrosis and numerous inherited diseases.

Ambry Genetics, based in Aliso Viejo, California, USA, is a leading clinical diagnostics company at the forefront of genetic testing. It uses a wide range of technologies – including next generation sequencing (NGS), Sanger sequencing, microarrays and multiplex ligation-dependent probe amplification (MPLA) – to offer a portfolio of over 300 highly specialized tests for genetic diseases, including cystic fibrosis and hereditary cancers.

“Tecan’s offering was by far the best choice in terms of flexibility and software programming.”

The Ambry Genetics team

The Company prides itself on its state-of-the-art research and CLIA-approved, CAP-accredited laboratory, and continuously invests in cutting-edge technologies to provide a faster, more efficient service for its customers. This approach means that Ambry’s Research and Development Department needs the flexibility to run and assess a broad spectrum of technologies and assay protocols, as Joy Radecki, Associate Scientist, explained: “In R&D, we are always trying to find the best and most efficient technology on the market.

We are moving more and more towards NGS,

as is most of the genetic testing environment, however there are many assays which are not suitable for inclusion on NGS panels. As a result, we still do a lot of Sanger sequencing, microarrays and MPLAs, creating multiple workflows in the laboratory.”

Automation is vital to meet Ambry’s throughput needs and reduce turnaround times and, in 2011, the Company needed to upgrade its existing automated platforms to meet projected growth targets and increase capacity. Joy continued: “We attended demonstrations by eight laboratory automation companies, and Tecan’s offering was by far the best choice in terms of flexibility and software programming. The Tecan instruments could clearly satisfy all our automation needs, growing and changing with our workflow, and we could program the systems in house. We initially purchased Freedom EVO 150 workstations with MultiChannel Arm™ (MCA) 96s, Robotic Manipulator Arms and eight-channel Liquid Handling Arms. Since then, we have added multiple Freedom EVO 100 platforms with MCAs or eight-channel Air LiHa Arms.

The platforms are extremely reliable and reproducible, and transferring scripts such as liquid classes between machines is also very helpful for process development. All the workstations have the capability to perform DNA extraction, microarray set-up and sample preparation for Sanger sequencing and NGS, but we have found that it is more efficient to optimize each system to a specific workflow, while still retaining the flexibility to perform other tasks as required.”

“Our Tecan representative was invaluable in terms of the initial support he provided in choosing the correct instrument configuration, helping us to select the right arms and deck layout. We went through some of our standard operating procedures,

GENOMICS TECAN JOURNAL 2/2014

and worked together to build up the Tecan platforms. It was also recommended that we implement the Freedom EVOware® Normalization Wizard, as each NGS assay includes several normalization steps and needs samples to be normalized to specific concentrations. This application alone has been a lifesaver for us, saving several hours every day. By allowing us to simply specify the final target concentration for each well, the platform can quickly and easily prepare 96 samples for NGS, achieving in around 20 minutes what previously took two technicians an hour and a half. It is easy to modify; it only takes two minutes to go into the Wizard script to change the target concentration, which is very helpful for assessing new assays, each of which seems to need a different sample concentration.”

“We also have integrated PosID™ scanners on our workstations running DNA isolation protocols. This allows the technicians to simply load the samples onto the workdeck, and the system scans the barcodes and assigns an ID to each sample, creating an output file that can be easily converted and loaded onto our large DNA isolation instruments. This

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Intuitive touchscreen simplifies operation

eliminates the need for a second technician to check the sample labels, freeing up additional staff time and reducing a four-hour isolation process for 96 samples to just 90 minutes.”

“The Tecan platforms are extremely easy to set up and program, and the new Freedom EVO 100s also have the TouchTools™ graphical user interface. This has really helped with staff training, as I can program the

instrument to walk them through the deck set-up with photos and audio guides. The service from Tecan has always been extremely honest and helpful and, whenever we have encountered technical issues or challenges with day-to-day scripting, the Tecan team gets back to me with a solution within a day. I have also attended several of Tecan’s training courses; these were very useful for understanding the capabilities of the systems and, as a result of what I learned, we are hoping to move some of our scripts into Freedom EVOware Plus to help increase our capacity in the future.”

“The Freedom EVO platforms are perfect for our continuously changing protocols, because of their high flexibility and the numerous options available. They have had a huge impact on our throughput and turnaround times, ensuring reliable and reproducible results, which are crucial in a clinical laboratory,” Joy concluded.

To find out about Tecan's genomics solutions, visit www.tecan.com/genomics

TouchTools guides the user through instrument set-up

For more information on Ambry Genetics, visit www.ambrygen.com

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LIQUID HANDLING TECAN JOURNAL 2/2014

Automating clinical cytogenetics The Necker Hospital for Sick Children has automated its comparative genomic hybridization workflow on a Freedom EVO® workstation, increasing throughput more than 10-fold while significantly improving reproducibility and process security.

The Necker Hospital for Sick Children in Paris, France, was founded over 200 years ago, and remains at the forefront of pediatric medicine today. Acting as a European reference center for rare childhood illnesses, the Necker uses a wide range of cutting-edge genomic technologies for both its research and diagnostics activities, using current and historic samples to identify genetic markers that indicate disease or susceptibility. One of the diagnostic tools used at the Hospital is comparative genomic hybridization (CGH). This cytogenetic technique uses a competitive in situ hybridization method to compare DNA from a patient to a reference sample, providing a rapid method of identifying genetic variations which can affect prenatal or childhood development.

“In cytogenetics, we predominantly use CGH to study the genomic DNA of patients born with mental retardation and/or facial dimorphism, looking for any underlying DNA reshuffles causing imbalances in their genomes. CGH is also used for prenatal diagnostics where there is a risk of chromosomal abnormality due to a history of mental retardation in siblings, or if an ultrasound scan reveals physical abnormalities. Outside of this area, we use CGH for oncology and hematology – for small projects looking at imbalances in the genomes of various cancers – so we work with a variety of sample types, including blood, amniotic fluid, fresh and formalin-fixed paraffin-embedded (FFPE) tissues and bone marrow.”

“My role is to transfer our manually-developed CGH protocols onto our automated systems,

which include a Freedom EVO 100 liquid handling platform and an integrated Infinite® 200 PRO microplate reader, ensuring that transfer of the technology follows good biological practice and satisfies the high quality standards necessary for our work.

When samples arrive in the hospital, we automatically extract the genomic DNA with a Qiagen Autopure LS® instrument, and measure the optical density ratios (OD260/OD280 and OD260/OD230) using our Infinite 200 PRO multimode reader. We then normalize the DNA concentrations based on these ratios, and check the quality of the extracted DNA by gel electrophoresis using the Freedom EVO 100 platform to ensure that it is not too degraded to analyze. Samples meeting the quality criteria for CGH are loaded onto the Freedom EVO platform in 96-well plates. Each patient’s DNA is then labeled with a fluorophore using a random

CGH can be used to identify both physical and cognitive problems, as well as a variety of cancers, as Jean-Michel Lapierre, a biology engineer for the Historic Embryology Cytogenetic Service at the Necker, explained:

“Our Tecan equipment has given us the reproducibility and process security which we need.”

From left to right: Jean-Michel Lapierre, Sylvie Nusbaum, Sophie Fontaine and Catherine Ozilou

LIQUID HANDLING TECAN JOURNAL 2/2014

priming technique, and transferred back to the Infinite reader to check the labeling efficiency by fluorescence analysis.”

Jean-Michel continued: “The principle of CGH is to compare the fluorescence intensities of the patient DNA with control DNA that has been labeled with a different fluorophore.

The patient and control samples are therefore hybridized on microarrays representing the entire human genome; the more oligonucleotide genomic DNA sequences that are deposited on the microarray slide, the more the resolution of the technique increases. After hybridization, there is a wash step to remove any unbound genetic material from the arrays, then the slides are transferred to our scanner for analysis. This instrument determines the fluorescence intensities of the two fluorophores at each point on the array, and our software compares the fluorescence patterns, showing any copy number variations (losses or gains) in the patient genome relative to the control.

This data is then used to try to determine the genotype-phenotype relationship between the genomic abnormalities detected by CGH and the clinical signs; if there is no clear correlation, we continue investigating with a higher resolution or with other molecular techniques. If a copy number variation is detected, we confirm this result using a complementary technique such as fluorescence in situ hybridization (FISH) or quantitative PCR, and use the Freedom EVO platform to generate the library of hybridization probes.”

“We chose Tecan’s Freedom EVO platform because its open architecture gave us the flexibility to perform many different

The Freedom EVO offers high throughput and excellent process security

protocols on a single instrument. Both this platform and the Infinite 200 PRO are now essential in our work; they are easy to use and we can trust them to perform routinely without any problems. Before automation, we had to do everything by hand, resulting in a low sample throughput of around 500 to 700 samples annually, as well as issues with errors and reproducibility. Since we began using the Freedom EVO platform, we now handle approximately 1,800 samples annually, including postnatal (75 %), prenatal (20 %) and onco-hematology diagnosis (5 %), with a team of three technicians. Our Tecan

equipment has given us the reproducibility and process security that we need, with the potential to process 2,000 to 2,500 samples a year without increasing the size of our team.”

To find out more about Tecan’s genomics solutions, visit www.tecan.com/genomics To learn more about Necker Children’s Hospital, go to www.hopital-necker.aphp.fr

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MASS SPECTROMETRY TECAN JOURNAL 2/2014

Transforming therapeutic drug monitoring for transplant patients A Freedom EVO® 150 is being used to full effect by scientists and doctors at the University Hospital of Padova in Italy, preparing samples for LC­-MSMS to monitor immunosuppressant drugs in transplant patients.

The University Hospital of Padova is a prominent 1,000-bed hospital in Italy that serves as a specialist center for surgery and liver, heart, kidney and lung transplantation.

The Department of Laboratory Medicine in the hospital employs 100 technicians, performing around nine million tests per year. A dedicated emergency laboratory for urgent tests also operates 24 hours a day, carrying out an additional million and a half tests annually. The department’s clinical chemistry section has recently overhauled the way it monitors immunosuppressant drugs, choosing LC-MSMS over immunoassays for its better specificity and sensitivity, and its ability to measure several compounds in a single analytical run.

Dr Martina Zaninotto, supervisor of the clinical chemistry section, explained: “Previously, we monitored immunosuppressant drugs using immunoassays but, as assay performance was disappointing, we looked at mass spectrometry as an alternative. Accuracy is of course fundamental to our work and this technique offered us better specificity, to distinguish between drugs and their metabolites, and improved sensitivity for times when we are looking for very low concentrations of drug in a sample.”

Dr Mariela Marinova has been closely involved in the method development, in the first instance for determining levels of the immunosuppressants everolimus and sirolimus. She added: “Although mass spectrometry gave us better sensitivity and specificity, manual sample preparation of up to 150 samples a day was proving far too labor intensive. It was clear that we needed to automate this part of the process and, after testing three different systems, we decided that the Tecan workstation offered the best analytical performance for our requirements.”

Dr Carlo Artusi, a chemist in the laboratory, described the current set-up: “Preparation of the sample matrix in whole blood is based on protein precipitation, so our Freedom EVO 150 is equipped with Te-Shake™ and Te­VacS™ modules to handle 96-well filtration and collection plates. We are currently integrating these stages into our LIS, using the barcode reader on the Freedom EVO to improve sample tracking within the laboratory. Our Agilent 1200 Series LC system coupled to an Agilent 6430 triple quadrupole mass spectrometer with an electrospray ionization interface then runs each sample in just two minutes, creating a very fast, optimized workflow.

We are able to analyze our samples far more quickly. Using our previous manual extraction

MASS SPECTROMETRY TECAN JOURNAL 2/2014

protocol, sample preparation would take up to two hours, but the Freedom EVO has reduced this to 40 minutes, leaving the technicians free to perform other tasks.”

Dr Marinova added: “We are a certified laboratory and time-to-results is an important aspect of this certification; it is vital for patients and clinicians alike to have a quick turnaround of results, and is key for efficient workflows within the laboratory.”

Dr Zaninotto concluded: “Automation has really improved the reproducibility of our assays; inconsistencies caused by manual errors have reduced significantly and, in our

experience, we haven’t needed to repeat a single test since we changed to automated sample preparation. The drug doses given to patients are getting progressively lower, and it is only with the combination of automated sample preparation and mass spectrometry that we can guarantee accurate monitoring of these concentrations. This is especially true for pediatric samples where the drug concentrations are extremely low and, for this reason, we also use this protocol to measure tacrolimus in these patients. We are now developing similar methods for other drugs, including metanephrines in plasma and cortisol in saliva.”

The protocol developed by the team at Padova is described in detail in: Marinova, M; Artusi, C; Brugnolo, L; Antonelli, G; Zaninotto, M; Plebani, M. Immunosuppressant therapeutic drug monitoring by LC-MS/MS: workflow optimization through automated processing of whole blood samples. Clinical Biochemistry (2013), 46, 1723-1727

To find out about Tecan’s mass spectrometry sample preparation solutions, visit www.tecan.com/lcms For more information on the University Hospital of Padova Department of Laboratory Medicine, visit www.medlabpd.it

The clinical chemistry team (left to right): Martina Zaninotto, Mariela Marinova, Prof Mario Plebani, Carlo Artusi, Giorgia Antonelli

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TECAN INTEGRATION GROUP TECAN JOURNAL 2/2014

Biology meets engineering The High Throughput Omics Platform is an advanced microbial cultivation and sampling system designed to accelerate the development of novel biotechnology applications.

Created as a collaboration between LISBP and the Tecan Integration Group, this unique system is being harnessed to investigate potential biofuels, biomaterials and biochemicals.

The Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) is part of the French National Institute of Applied Sciences in Toulouse, and uses a multi-disciplinary approach to develop novel solutions to real-world problems across the material science, environmental and life science sectors. Working closely with a wide range of academic and industrial partners, both within France and internationally, LISBP has the flexibility and the diverse skill-base necessary to exploit the metabolic

pathways of micro-organisms for innovative biotechnological processes.

LISBP’s MetaSys team, headed by Jean-Charles Portais, is a core facility offering the tools, expertise and support necessary to engineer micro-organisms for the conversion of renewable resources into useful end-products – biofuels, biomaterials and biochemicals.

Working primarily with E. coli as a ‘cell factory’, the team designs synthetic metabolic pathways for the consumption or production of molecules of interest, using ‘omics’-based approaches to understand and optimize how these pathways operate within biological systems.

Stéphanie Heux, a researcher in the MetaSys team, explained: “Our work requires the creation of a large number of microbial strains with synthetic modules that convert renewable carbon resources into biomolecules of interest for wider applications, such as biofuel production.

We originally analyzed these metabolic pathways manually, but were very limited in the number of cultivations we could perform in parallel. We needed a high throughput platform for rapidly processing engineered bacterial cells on a larger scale, to analyze large numbers of bacterial strains under different conditions more efficiently.”

The High Throughput Omics Platform offers rapid, large-scale processing of cell cultures

“In 2009, we approached a number of laboratory automation companies to design a bespoke system that would meet our needs.

The Tecan Integration Group (TIG) provided us with a clear outline of the proposed solution, with a detailed and precise project specification document that enabled us to understand exactly how the robotic platform would look and operate. The Tecan offering was also very compact and flexible – with

TECAN INTEGRATION GROUP TECAN JOURNAL 2/2014

three robotic arms on a single workstation – and this, combined with the level of technical support on offer, made the choice easy for us. We worked closely with the TIG team to develop the concept further, with both parties suggesting changes to improve speed and efficiency, and the High Throughput (HT) Omics Platform is the result of this work.”

Controlled by Tecan’s advanced Pegasus software, the HT Omics Platform has a range of modules to enable precise and flexible operation, including a custom bioreactor block, an eight-channel Liquid Handling Arm, a Pick and Place Arm, a Robotic Manipulator Arm, a HydroFlex™ plate washer, a Sunrise™ absorbance reader, a centrifuge and a barcode scanner. The system also has both heating and cooling devices, as well as carriers and storage racking for microplates and labware. Stéphanie continued: “We run several types of metabolomic and fluxomic experiments on the platform, all of which can be carried out on up to 48 cultivations in parallel. We can perform direct measurement of physiological parameters

such as growth, oxygen and pH, monitor and analyze extracellular metabolites by HPLC, analyze intracellular metabolites by mass spectrometry, and study isotope patterns in metabolic end-products using NMR.” “TIG tailored the Pegasus software to fit each application, as the sampling process is closely linked with the growth of each E. coli strain within the bioreactor, which cannot be easily predicted. The HT Omics Platform carries out large-scale analysis of the activity of each strain; preparing, running, monitoring and controlling the fermentations, and adjusting the pH, temperature and stirrer speed for 48 micro-scale (10 ml) fermentations in parallel. The robotic system also features fully automated metabolite harvesting and extraction for downstream analysis.”

“The system is highly reliable and easy to use, and automating the whole process has greatly improved throughput and robustness, avoiding the errors inherent in manual operation. It operates 24/7, offering continuous parallel processing for 48 E. coli

The custom bioreactor block can be accessed by the system’s LiHa Arm

strains with little human supervision, including overnight analysis, and releases the equivalent of five full-time staff to develop and analyze even more bacterial strains. It was really nice working with the TIG team, because they were always available to respond to our numerous requests, and had the creativity and biological and technical backgrounds needed to understand our expectations. We are very happy with the system,” concluded Stéphanie.

To find out about the Tecan Integration Group, go to www.tecan.com/tig For more information on LISBP, visit www.lisbp.fr

“It was really nice working with the TIG team… they had the creativity and biological and technical backgrounds needed to understand our expectations.”

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ENVIRONMENTAL ANALYSIS TECAN JOURNAL 2/2014

Looking out for the environment Monitoring the effects of environmental pollutants on live organisms is now much faster thanks to a technique developed by researchers in France, who are using an Infinite® F200 PRO microplate reader to screen aquatic model organisms.

of interest is activated. Using early stage larvae rather than adult organisms means we are effectively combining the advantages of seeing what is really happening in an in vivo model with the simplicity, sensitivity, automation, low costs and ethical advantages of an in vitro approach. We can rapidly screen a large number of molecules far more cost effectively and on a much smaller scale, reducing the need for aquariums or dedicated laboratories. This approach also significantly cuts the time required for tests, typically to 24, 48 or 72 hours compared to 21 days for adult organisms.”

Andrew Tindall and Petra Spirhanzlova with WatchFrog's Infinite F200 PRO

WatchFrog, a small biotech company based in Paris, is a spin-off from the comparative physiology research department at the French Museum of Natural History. The Company develops, manufactures and markets tests to detect a wide range of potential pollutants, including pesticides, plastics, cosmetics, food additives and pharmaceutical residues. WatchFrog’s technology is based on physiological changes that occur within aquatic model vertebrate organisms, amphibian larvae or fish fry, when exposed to these contaminants. These models primarily reveal changes in endocrine signaling, where abnormal hormone levels can disrupt normal sexual function, brain development and metabolism, and can be followed using fluorescence-based genetic reporter mechanisms.

Robotized imagery is the traditional method of reading experiments of this kind; photographing each larva over time and quantifying the images. However, WatchFrog has developed a microplate reader protocol which is considerably faster, easier and less expensive and, importantly, can be standardized between different laboratories. Andrew Tindall, a researcher in WatchFrog’s research and development team, explained: “The underlying principle behind our tests involves exposing small, intact, translucent, vertebrate larvae to the contaminants in question. These larvae have endocrine systems that are physiologically close to humans and they harbor genetic constructs, typically containing green fluorescent protein (GFP), which cause them to fluoresce when the biological pathway

Following poor results with another microplate reader, and encouraged by good reports from collaborators using Tecan equipment, WatchFrog chose an Infinite F200 PRO reader in 2012. Andrew continued: “We knew from experience that Tecan equipment is robust and well built, and the Infinite F200 offered some particular features that we consider vital for biological screening, most notably, reliable temperature control; there is no danger of overheating the reader chamber even after multiple measures of each well on a series of plates. Bottom reading is also very important, because it allows us to measure the free swimming models in 96-well plates, taking multiple readings on the same larvae over time without the need for anesthesia, which could potentially interfere with the results.”

“One larva 2-3 mm long is placed in a small amount of water in each well of a clear bottom plate, where it swims freely without any further preparation. The plate is then placed in the reader at a temperature appropriate to the organism, and the instrument is programmed to read at given times. The excitation light illuminates the well, causing the GFP produced by the larvae to emit green fluorescent light. The fluorescence in each well is then quantified

READERS TECAN JOURNAL 2/2014

by the Infinite F200 PRO, with the results interpreted by staff to determine the sample’s biological activity. We can then conclude whether the tested sample has an effect on the hormonal axis of interest, helping us to make informed decisions on the risk of the test substance to the environment or the public.”

Andrew concluded: “Now that the technique is well established, we are discovering many more advantages to the Infinite F200 PRO; it is very robust, ideal for long read times and very easy to use. It also allows hands-free operation, releasing staff for other tasks and reliably running unattended, even overnight.

WatchFrog is a partner of the EDA-EMERGE publicly-funded project to train young scientists to meet the major challenges in the monitoring, assessment and management of toxicants in European surface and drinking water. As part of this project, my colleague Petra Spirhanzlova successfully reduced the time taken to scan one 96-well plate from 40 minutes to only seven, improving our throughput considerably. We now have a reliable method that can be reproducibly used by our partner laboratories all over Europe, which is a condition for the validation

of our tests by the Organisation for Economic Co-operation and Development, and a great advantage to monitoring pollutants in this context.”

To find out about the Infinite F200 PRO reader from Tecan, visit www.tecan.com/infinite200pro For more information on WatchFrog, visit www.watchfrog.fr

Fluorescence from medaka fry is monitored using the Infinite reader

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MICROBIOLOGY TECAN JOURNAL 2/2014

Cyanobacteria see the light Scientists at Berlin’s Technical University of Applied Sciences Wildau have established a screening platform for phototrophic organisms on a Freedom EVO® 200 liquid handling platform equipped with an Infinite® M200 PRO microplate reader.

Germany’s Technical University of Applied Sciences Wildau (TH Wildau) is the largest university of applied sciences in the state of Brandenburg. Historically, with its origins in locomotive construction, TH Wildau was an engineering university, but today it has developed to offer a wide range of modern, forward-thinking courses, including biosystems technology and bioinformatics.

Professor Marcus Frohme’s Molecular Biotechnology and Functional Genomics group is engaged in several studies including one in collaboration with an industrial partner, Algenol Biofuels, looking at adaptive evolution in cyanobacteria. The University’s researchers have established a screening platform for phototrophic organisms on a Freedom EVO workstation with an integrated Infinite M200 PRO for this project. Ulrich M. Tillich, a PhD student based at TH Wildau, explained: “Our group needed a screening platform for phototrophic organisms for the cyanobacteria study. Although commercially available cultivation platforms for

heterotrophs and eukaryotes exist, there was nothing suitable for phototrophic organisms, and so we designed and tested a custom-built system.”

Ulrich continued: “Initially, we used a Genesis™ RSP 150 liquid handling system with a GENios™ Plus plate reader, but this instrument was old and had been superseded by more advanced liquid handling platforms; system support was also ending. We then invested in a Freedom EVO 200 workstation equipped with Robotic Manipulator (RoMa) and Liquid Handling (LiHa) Arms, an Infinite M200 PRO reader, a HydroFlex™ washer and a Hettich® ROTANTA centrifuge, all controlled by Freedom EVOware®, and integrated a custom-built cultivation chamber that can accommodate two 96-well plates. The main advantage of the new platform is its flexibility; it provides a simple user interface for day-to-day operation, as well as allowing in-depth programming, enabling a broad range of

“Instead of taking a whole day to calculate values for two 96-well plates, everything can be done in around two hours.”

The Molecular Biotechnology and Functional Genomics group integrated its custom-designed incubation chamber into a Freedom EVO workstation

MICROBIOLOGY TECAN JOURNAL 2/2014

Nick Wolter (left) and Ulrich M. Tillich with the Freedom EVO-based screening platform

different requirements to be accommodated.

We can also add additional modules, such as a 96-channel pipetting head, at a later date if necessary. It is a great improvement on the old liquid handling system. The analytical capabilities of the Infinite M200 PRO are also good; with a monochromator-based system you are not tied to the available filters, which allows for more experimentation. You can just try things and see if you get the result you need, without spending a lot of money on a filter that you may never use again.”

Nick Wolter1, a specialist for automation in life sciences at TH Wildau at the time, took up the story: “The system is used to monitor cell growth, chlorophyll content and cell vitality, to prepare samples for MALDI-TOF analysis and to make back-ups of the cultures – small agar plates for use in the immediate future allowing results to be rapidly validated, and 96-well plates for longer term cryopreservation. Initially, we found it harder than expected to keep the cultures in suspension and tried using different shaking patterns – bi-linear and circular – but always had problems with cell sedimentation; adding glass beads to each well of the microplate was the answer.”

“Our screening platform includes an automated dilution step, and it is important to minimize any errors due to evaporation.

The RoMa removes the microplates from the cultivation chamber at least once a day, to allow any loss of liquid due to evaporation to be determined by the LiHa’s conductive disposable tips, before it automatically refills the wells to full volume with sterile water. This eliminates the potential for errors due to evaporation during subsequent optical density (OD) measurements and dilutions; the OD is used to determine the cell density, and this value forms the basis of the automated dilution. Previously, we had to take the measurements and then manually input the values for the dilution.

With Freedom EVOware, the process is fully automated, which saves a lot of work; instead of taking a whole day to calculate values for two 96-well plates, everything can be done in around two hours.”

deep-well plates in the integrated cultivation chamber, while controlling parameters such as light intensity, carbon dioxide, temperature and plate shaking. Currently we can handle a maximum of two 96-well plates, although it should be very easy to scale this up further.” Nick concluded: “Before automation, we were screening for temperature-tolerant mutants in small cell culture bottles by a more traditional method, and had a maximum throughput of just 27 cultures; automation makes high throughput possible.”

Ulrich added: “The screening platform is essentially a proof of concept, establishing that the process can be fully automated. We have successfully used the system to screen a pool of mutants for strains with the highest thermal tolerance, culturing cyanobacteria in

1Nick Wolter

To find out more about Tecan’s cell biology solutions, visit www.tecan.com/cellbiology To learn more about the Molecular Biotechnology and Functional Genomics group, visit www.th-wildau.de/molekularbiologie is now an application specialist at GFE Blut mbH, working on robotic systems for automated analysis of blood donations.

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BIOPROCESSING TECAN JOURNAL 2/2014

Discovering more with less Global biopharma company UCB has increased the throughput of its antibody purification pipeline, using a flexible Freedom EVO® workstation to miniaturize its chromatography applications. As a result, the Company is able to investigate far more parameters in a fraction of the time, while consuming significantly less material.

UCB is a global biopharmaceutical company, with operations in approximately 40 countries. It focuses on antibody-based drugs for the treatment of autoimmune diseases, such as Crohn’s and rheumatoid arthritis, and conditions affecting the central nervous system. UCB’s immunology hub is based in Slough, UK, where the majority of the Company’s antibody research and early development takes place.

Research teams at UCB identify novel targets and specific antibodies using two different cell-based approaches for protein production, E. coli and Chinese hamster ovary (CHO) cells. Antibodies are then handed over to development teams to progress through the pipeline. Jonathan Symmons, Development Scientist at UCB, explained: “Our role is to develop the best processes for generating large amounts of the antibody drug product in house, and we are closely involved in both Phase I and Phase II clinical trials, where the process is still open to change and further development.”

cell cultures and microbial extracts. They are constantly looking at ways to scale this process down to reduce the amount of material used, giving them the opportunity to perform more experiments with the amount of protein available. This is partly to do with cost, but also because they are frequently working with very small sample sizes. For example, in early phase projects they might screen a few similar but slightly different constructs of an antibody. At that stage, the fermenters are not optimized to produce huge amounts of material, and only milligrams of antibody are coming through.

“We had been looking at Atoll’s MediaScout® RoboColumns® for some time, and specifically at how to implement them into an automated protocol. Atoll and Tecan had worked together closely on this, and it made sense to look at this option; the support we subsequently had from both companies in setting up and optimizing the system was

excellent. We soon realized how flexible the Tecan system is and eventually chose a configuration that would not only allow us to switch between chromatography and ELISAs, but would also still keep our options open for other potential assays. Our Freedom EVO 200 is equipped with a Te-Stack™, a Liquid Handling Arm with eight fixed tips, a Robotic Manipulator Arm, a Te-Shake™, a HydroSpeed™ plate washer and Infinite® 200 PRO microplate reader. We also have a Te-VacS™ vacuum manifold module, and are looking to implement the 96-well PreDictor™ filter plate chromatography format (GE Healthcare) to further reduce the amount of material required and potentially provide a screening technique for even earlier-stage products.”

The workflow varies from day to day; the group may be looking at different loading conditions, varying the pHs, conductivities, etc. for a single column type, or screening

Purification is a significant stage of the manufacturing process, and the UCB team primarily uses chromatography techniques to purify the products from the harvested

“The sheer volume of experiments we can now perform simultaneously is brilliant.”

Left to right: Jonathan Symmons, Chris Morris and Mariame Dami

BIOPROCESSING TECAN JOURNAL 2/2014

resins with different loading material. More and more people at UCB are being trained to use the Freedom EVO for applications at all stages of the development process, and there have recently been two Masters’ students performing a large Design of Experiments (DOE) study to assess the Freedom EVO for the chromatography capture steps in early phase process development. Full analysis of the project is not yet complete, but early indications suggest that this approach is comparable to previous methods.

Thanks to the Freedom EVO platform, the

DOE study was on a far larger scale than had ever been practical for the development team to undertake before. Jonathan continued: “The sheer volume of experiments we can now perform simultaneously is brilliant. We can do eight chromatography runs at once using the RoboColumns, but the DOE project was even more impressive. We have been able to perform full factorial DOE – previously this would have been performed as a fractional factorial providing less than a third of the data points – and we could never have even attempted that without the Freedom EVO and RoboColumns; there simply would not have been enough

material or time in the early phase of a project.”

Time is also a critical factor for EngD student Chris Morris, who is using the liquid handling capabilities of the Freedom EVO to look at precipitation as a purification method. This project compares different permutations for precipitating the target protein from the process impurities, and requires mixing hundreds of combinations of buffers. This would take days to perform manually at the bench, but only takes hours in a microplate on the Freedom EVO, again using smaller sample volumes.

Jonathan concluded: “The whole industry is moving towards a ‘Quality by Design’ approach to development, and the Freedom EVO fits this model perfectly.

It enables us to perform large DOE studies with smaller amounts of material, in a shorter amount of time, resulting in a greater understanding earlier in the development phase and potentially minimizing the number of changes to the process later on in the pipeline. We are doing things that we never would have attempted before, which is a huge step in the right direction.”

To find out more on Tecan’s drug discovery solutions, visit www.tecan.com/bioprocessing

UCB’s Freedom EVO workstation offers flexible automation for assay design and optimization

To find out more about UCB, visit www.ucb.com

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GENOMICS TECAN JOURNAL 2/2014

GeT with the NGS program The GeT genomics facility near Toulouse has been developing a series of automated NGS protocols in collaboration with Tecan – including Illumina’s TruSeq® DNA and RNA kits, as well as Bioo Scientific’s NEXTflex™ PCR-Free Modules – on two Freedom EVO® workstations, helping to improve throughput and reliability for a wide range of projects.

now have two Freedom EVO workstations at the center of our sequencing workflows, reducing hands-­on time, increasing throughput and improving the reproducibility of our data.”

Johanna Barbieri (left) and Marie Vidal operating one of GeT’s Freedom EVO systems

France’s National Institute of Agricultural Research (Institut National de la Recherche Agronomique, INRA) has sites around the country, with active research projects in virtually every area of agriculture. The INRA’s Génome and Transcriptome (GeT) facility in Castanet-Tolosan, on the outskirts of Toulouse, is a core facility providing a full range of genomics services for French laboratories, national and international collaborations.

Next generation sequencing (NGS) forms an ever-increasing part of GeT’s workload, as Olivier Bouchez, research engineer and NGS team manager at INRA, explained: “We are a public institute, and so perform sequencing projects on behalf of a wide variety of research groups from across France. A majority of our workload is genomic DNA sequencing for plants and animals of agricultural interest

by NGS, but we work on almost all types of organisms, performing over 150 projects each year with a team of 15 researchers.”

GeT’s workflow begins with the receipt of purified DNA or RNA into the laboratory, where it undergoes quantification and quality control

screening using an Agilent BioAnalyzer, with 3 µg of material required for PCR-free protocols, and 200 ng for PCR. Samples are then loaded onto the laboratory’s Freedom EVO 200 – equipped with eight-channel Liquid Handling (LiHa) and Robotic Manipulator Arms – for pre-PCR library preparation. Post-PCR processing is performed on a recently purchased Freedom EVO 150 equipped with both an eight-channel LiHa for classical library purification, and a MultiChannel Arm™ (MCA) 96 for higher throughput amplicon sequencing workflows. Olivier outlined the Group’s reason for choosing automation: “As a core facility, we need the flexibility to run numerous different chemistries and assays, depending on the needs of individual research groups. We have two HiSeq® and one MiSeq® sequencing systems, so manual preparation of libraries would be a major bottleneck in our workflow. We first invested in laboratory automation over 10 years ago, and have been using Tecan liquid handling workstations ever since, as the flexibility of these instruments is very well suited to our needs. Our two original Genesis™ platforms are still in use, and we

As a core facility, the GeT works with a wide range of chemistries, including Illumina’s TruSeq DNA, TruSeq RNA, TruSeq Nano DNA and TruSeq Stranded mRNA kits – as well as Bioo Scientific’s NEXTflex PCR-Free Modules – and has developed a range of library preparation and purification protocols for the Freedom EVO workstations in collaboration with Tecan’s application specialists. Olivier continued: “Depending on the size of the project, we process up to 50 samples a day for classical DNA or RNA libraries, or 170 samples a day for amplicon sequencing. Our protocols have to be very flexible to allow us to run just a few samples each for multiple projects in parallel, or a large number of samples for a single project. We are constantly updating and optimizing our processes, as well as developing new applications – such as bisulfite and mate pair sequencing – and the ease of script writing in Freedom EVOware® makes it very simple to create these protocols.

Regardless of the chemistry being used, we prepare the reagents for each assay, then load everything onto the Freedom EVO platforms for processing, freeing up staff time to perform other tasks.”

“We have worked with Tecan for a long time, and have always been very happy with the liquid handling workstations and support.

The platforms are very robust and, if I have a question, I can always contact the Tecan team for a quick answer,” Olivier concluded.

To learn more about Tecan’s genomics solutions, visit www.tecan.com/genomics To find out more on the INRA’s GeT core, go to get.genotoul.fr

TALK TO TECAN TECAN JOURNAL 2/2014

Total RNA

NanoDrop™ control

BioAnalyzer control

mRNA purification (poly-T beads)

Fragmentation

First strand cDNA synthesis

Second strand cDNA synthesis

Bead purification

3’ adenylation

Adapter ligation

Bead purification + PCR set-up

PCR

Bead purification

BioAnalyzer validation

qPCR quantification

(Libraries pool)

Sequencing run

Leading the debate In an ideal world, scientists want to load their samples onto an automated workstation and press a single button to start the relevant protocol. The complexity of modern assay systems makes this increasingly difficult to achieve, but instrument manufacturers can still help to overcome the difficulties in automating some applications by providing highly integrated, user-oriented solutions. Hardware and software elements should work in harmony to minimize the automation knowledge required for day-to-day operation of the system, while still providing the flexibility necessary to adapt to changing laboratory requirements. As automation becomes increasingly prevalent across virtually every area of life sciences, laboratories are turning towards more application-focused liquid handling solutions which can provide an accessible and practical route to automating complex protocols.

Cell-based assays is one area now benefitting from increased automation, in an effort to deal with increasing workloads and largerscale screening projects. By integrating all the necessary modules and devices into a standardized solution, dedicated systems such as Tecan’s new Fluent™ cell-based assay solution (pages 4 - 5) can provide high throughput, walkaway automation and allow scientists to focus on the fundamental cell biology. This can be further enhanced by useroriented graphical interfaces to simplify the set-up and operation of the instrument, helping to ensure reliable and reproducible performance and accelerate research.

To share your thoughts on other applications that could benefit from user-friendly automation, e-mail talk@tecan.com

Key: Performed on Freedom EVO/Genesis

Bronwen Forster, Senior Product Manager for Liquid Handling Robotics

Performed on thermocycler/offline

Workflow for Illumina TruSeq Stranded mRNA

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EVENTS 2014 TECAN JOURNAL 2/2014

Meet Tecan at these events Americas AACC 2014 Annual Meeting and Clinical Lab Expo

Chicago, USA

29 – 31 July 2014

2nd International Inspection Technology and Equipment Expo

Beijing, China

31 July – 02 Aug 2014

2014 National Congress of Biochemistry and Molecular Biology

Xiamen, China

21 – 23 Aug 2014

Asia and Pacific

24 Annual Combined Biological Sciences Meeting

Perth, Australia

02 – 03 Sept 2014

JASIS 2014

Chiba, Japan

03 – 05 Sept 2014

Analytica China 2014

Shanghai, China

24 – 26 Sept 2014

th

Australasian Genomic Technologies Association (AGTA)

Melbourne, Australia

12 – 15 Oct 2014

Matrix Biology Society of Australia and New Zealand

Queenscliff, Australia

26 – 29 Oct 2014

SMAP Congrès Français de Spectrométrie de Masse et d'Analyse Protéomique

Lyon, France

29 Aug 2014

ELRIG Drug Discovery 2014

Manchester, UK

02 – 03 Sept 2014

MSACL EU Mass Spectrometry Applications to the Clinical Lab

Salzburg, Austria

02 – 05 Sept 2014

20th ICRAV (International Conference of Racing Analysts and Veterinarians) Conference

Republic of Mauritius

20 – 27 Sept 2014

Europe, Middle East and Africa

British Society of Genetic Medicine Conference 2014

Liverpool, UK

22 Sept 2014

MipTec 2014

Basel, Switzerland

23 – 25 Sept 2014

Biospain 7th International Meeting on Biotechnology

Santiago de Compostela, Spain

24 – 26 Sept 2014

World of Technology and Science

Utrecht, Netherlands

30 Sept – 03 Oct 2014

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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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.

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