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17 Insights

The QIAGEN Magazine 2017

Sample to Insight

We are living in an age of scientific discoveries and rapid progress into the building blocks of life – DNA, RNA and proteins.

These advances are improving our everyday lives, changing the way how people are treated for diseases like cancer, tuberculosis and other conditions, helping to find new medicines and even safeguarding the public.

But unlocking new answers from the incredibly complex world of biology – and turn-ing them into breakthroughs that impact our lives – remains elusive and challenging.

QIAGEN exists to support this quest, helping more than 500,000 customers around the world to gain the valuable molecular insights they need to improve healthcare and advance science. Our differentiated Sample to Insight solutions are used along the con tinuum from basic research to clinical healthcare and industrial applications to unlock insights easier, faster and more reliably than ever before.

Our passionate employees – known as QIAGEN ers – care deeply about the impact of their work. They are trusted advisors and experts committed to understanding the needs of our customers and tailoring our Sample to Insight portfolio to help them exceed their own expectations. We are embracing the spirit of digital transformation, working to improve our speed and agility in supporting our customers while creating even more value.

QIAGEN is tackling the bigger questions of our age and helping solve biological challenges that affect us all. This is an enormous challenge – but one that energizes us to excel.

It’s how we help our customers to advance from Sample to Insight and ultimately make improvements in life possible.

Contents

4 12 16 26

Diverse appeal

Cracking the code: how RNA may hold the answer

» The genomic revolution is still just at the beginning«

Enabling the fight against cancer

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30 36 42 48

Mapping a hidden world

»Like a smoldering ember that can

catch fire again«

Looking to the future of missing persons analysis with NGS

QIAGEN breaks new ground

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» What convinced us was the quality.«

Here are four experts in four countries at their four workplaces. What do their laboratories have in common? The QIAsymphony system.

Diverse appeal

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Company profile

GATC Biotech is Europe’s leading sequencing services provider with its own laboratories in Cologne and Constance, Germany. It offers DNA and RNA sequencing and bioinformatics solutions to customers from academia, health-care and pharmaceutical industry worldwide. The company’s mission is: ‘Improving the quality of life by analyzing nucleic acids.’ It contributes to the sequencing field with its own innovative products, scientific expertise and rig-orous quality. The customer-oriented R&D enables successful scientific collab-orations.

http: // bit.ly/GATCB iotech

1. What role does laboratory automation play at GATC Biotech?

Automation plays a very important role. We mostly use robotic systems because of their flexibility. In Cologne, we process about 50,000 Sanger sequencing samples a week – meaning approximately 10,000 every 24 hours. We have a very high automation grade, from sample arrival to data delivery. Every step is trackable in our LIMS, as the sam-ple barcodes are scanned immediately after sample arrival.

2. How is QIAsymphony used in GATC Biotech’s daily work?

It is used on a daily basis. We use it for the isolation of DNA and RNA for samples, which are analyzed by using next-generation sequencing. It is mainly used for blood and stool samples at the moment. Blood for applications like identification of cancer and other diseases, while stool samples, but also other sample material, are used for microbiome ana-lysis. We also process samples from swabs.

3. Why did you choose QIAsymphony?

What convinced us was the quality. GATC is a service provider, so we get a huge variation of samples, including blood that isn’t always stored as it should have been. Across this huge variety of incoming sample material and sample quality we found that QIAsymphony delivers the most stable results on quality and also on the amount of RNA we get from the isolates compared to other techniques.

4. How has QIAsymphony affected GATC Biotech’s workflow?

Thinking about our product as a service provider, from isolation to data delivery, the workflow has become more stable due to automation of the first step: the sample processing part. QIAsymphony helps to eliminate many manual steps and frees up staff time.

GATC Biotech, Konstanz

NameDr. Kerstin Stangier

Posit ionDirector of Production, GATC Biotech

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INSIGHTS | Diverse appeal

» We have to show the courthouse that our results are reliable.«

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Organization profile

Police of Finland’s forensic laboratory in Vantaa, Finland, is in charge of foren-sic and crime scene investigations nationwide. It is part of the National Bureau of Investigation police unit that operates throughout Finnish territory. The foren-sic laboratory has a staff of 125 people, including a DNA group with a team of 23 people. The lab’s DNA group receives roughly 27,000 crime scene sam-ples each year plus some 9,000 reference samples for database use.

http: //bit.ly/PolisFinland

1. How important is lab automation to your organization?

It is very important for us because our sample amount has increased by roughly 10 percent every year. Automation saves time. It means our sample batches can be big, and it also decreases human error so that our results are more consistent and reliable. Here, in Finland, we only work office hours, so people aren’t here in the lab after 4pm – but auto-mation can continue and the QIAsymphony can work independently overnight.

2. How is automation used in your team’s daily work?

We have different kinds of robots here to extract DNA from crime scene samples and do pipetting. The most common samples we have are ‘touch samples,’ which are skin cells you can’t see with the naked eye. We also have blood samples, saliva and semen. Automation helps us ensure that our sample processing is trustworthy. That’s very important because we have to show the courthouse that our results are reliable.

3. What has been your experience with QIAsymphony so far?

It’s nice and easy to use. We usually run 80 samples per extraction run and the extraction chemistry is very good. It is also effective with weak samples. That’s important for us because the ‘touch samples’ we usually get here are weaker DNA samples but the QIAsymphony is still able to process them.

4. What are the QIAsymphony system’s strengths?

Our collaboration with QIAGEN and its service works really well. QIAGEN gives us great customer service support for using the QIAsym-phony and other equipment. We’ve even named our QIAsymphony ‘Sibelius’ after the famous Finnish composer – it was a good fit with ‘symphony’!

Police of Finland, Vantaa

NameElina Hokkanen BSc

Posit ionTechnician, DNA examinations

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INSIGHTS | Diverse appeal

» It has made a significant, positive contribution to our workflow.«

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Organization profile

Virginia Commonwealth University’s (VCU) Molecular Diagnostics Services division is part of the Department of Pathology in Richmond, Virginia. The laboratory offers infectious disease and oncology testing as well as tests for inherited disorders and various gene abnormalities. The staff also helps the to train pathology residents and to educate medical students at both the under-grad and post-grad level.

http: // bit.ly/ VCUP athology

1. How important is lab automation to your organization?

Automation has been in place in my lab for about 10 years but we have seen with new instrumentation, in particular with the QIAsymphony, that our systems are now completely automated. This has been crucial for us. What has also been important to us as these automated systems have evolved is the improved ability to process different kinds of speci-mens and specimen tubes that work well for molecular diagnostics – and therefore without the template cross-contamination that could give us false positives.

2. How is QIAsymphony used in the laboratory’s daily work?

The beauty of the system is that it allows us to extract all the specimens at the same time. What’s more, the software is very user-friendly so we’ve been able to incorporate this in the testing with great results. More recently, we transferred all our genomic extraction to the QIAsym-phony. This has allowed us to streamline our processes and decrease the amount of professional time devoted to DNA or RNA extraction.

3. Why did the Molecular Diagnostics Services division opt to use QIAsymphony?

We selected the QIAsymphony because we have been working with QIAGEN products for many years and we have always been extremely satisfied with their high quality. When they came up with this automa-tion, we paid attention due to their very strong track record on product quality and providing us with excellent customer service. And they haven’t disappointed us.

4. How has QIAsymphony affected the laboratory’s workflow?

It has simplified our workflow significantly. We can extract all the spec-imens for different tests at the same time and then continue with all the different downstream processes. We can also load the instrument and let it run. It has made a significant, positive contribution to our workflow and increased the quality of the testing that we do.

Virginia Commonwealth University, Richmond VA.

NameDr. Andrea Ferreira-Gonzalez

Posit ionProfessor of Pathology and Chair of the Molecular Diagnostics Division at VCU’s Department of Pathology

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INSIGHTS | Diverse appeal

Organization profile

The Department of Animal Breeding and Genetics belongs to the Faculty of Veterinary Medicine and Animal Science at the Swedish University of Agricul-tural Sciences (SLU) in Uppsala. The department conducts research on domes-tic animals in the fields of molecular genetics and bioinformatics as well as quantitative and applied genetics. Its Canine Biobank, developed in collabo-ration between SLU and Uppsala University, is intended to increase knowl-edge of the biology of genetic diseases occurring in both dogs and humans. The research aims to improve canine and human health and support veteri-nary and human medicine. The laboratory also offers genetic services for ani-mals such as parental control or testing for inherited diseases.

http: // bit.ly/ SLUG enetics

1. How important is lab automation to your organization?

It is extremely important for our DNA extractions. We have around 3,000 samples per year, which is just too many to deal with by hand. We do DNA testing in a research setting, mainly for genetic variants associated with disease that our group has discovered. We’re constantly working on ways to increase the automation with different laboratory information management systems.

2. Why did SLU choose QIAsymphony?

We really wanted something that was ready to use ‘out of the box’ for DNA extractions. The QIAsymphony is easy to use and didn’t require any programming or optimization. We wanted something that worked, enabling us to focus on other things.

3. What are QIAsymphony’s main strengths?

QIAGEN is a huge organization that can support us if needed. If we run into a problem or a new kind of extraction, we contact QIAGEN to see if they have any tips on what to do. QIAGEN gets some strange questions from us, such as: Can we extract DNA from an insect’s intes-tines using the QIAsymphony or would a manual kit be better?

4. Which QIAsymphony features are most important to your work?

Its robustness, the integrity of the samples and not having any sample mix-ups. For us, perhaps the most important thing is minimizing the risk of mix-ing up samples that exists if you do everything manually. Everyone has experienced having to throw everything away and start all over again halfway through multiple extractions. The QIAsymphony prevents that.

5. How is QIAsymphony used in your laboratory’s daily work?

Our usage is extremely varied. The majority is for research purposes, such as DNA extractions from blood samples for disease testing and taking samples for the Canine Biobank. We also offer dog owners the opportunity to have DNA tests of their dogs. That’s semi-commercial because the dog owners pay and, more importantly, it gives us more samples for further research.

Swedish University of Agricultural Sciences, Uppsala

NameDr. Tomas Bergström

Posit ionAssociate Professor, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU)

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» QIAGEN is a huge organization that can support us if needed.«

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INSIGHTS | Diverse appeal

Conversation with CEO Peer M. Schatz on the exponential growth in genomic knowledge, achievements in 2016, and QIAGEN’s strategy to create value with Sample to Insight solutions for molecular testing – delivering insights into DNA and RNA, the building blocks of life.

» The genomic revolution is still just at the beginning«

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Why focus on molecular testing? Where is this field heading?

Molecular testing is experiencing disruptive growth. The genomic revolution is still just at the beginning, but the cumu-lative result of investments so far is creating a new age of sci-entific breakthroughs – with great promise to address some of the world’s most pressing challenges in healthcare and other areas of life. However, there are still many obstacles. Gain-ing molecular insights is a complex process that requires spe-cialized knowledge and resources to overcome big technolo-gy barriers. Just think of the large numbers of samples and the vast amounts of genomic data being created every day, challenging the capacities of scientists and clinicians to ana-lyze, interpret and apply the knowledge. We believe this growth creates significant opportunities for QIAGEN to pro-vide valuable contributions.

In which way?

What unites our more than 500,000 customers is the desire each one has to gain valuable molecular insights from a bio-logical sample, and to do so in a fast, reliable, standardized and efficient manner. Our teams at QIAGEN create value by seeking to understand the insights our customers are pursu-ing, and then developing solutions from our portfolio that exceed our customers’ expectations by helping them gain those molecular insights. We have a very diverse global cus-tomer base, ranging from basic research labs that are advancing humanity’s knowledge about life through to clini-cal laboratories performing what are now routine molecular tests. Each of our customer classes – Academia, Pharma, Applied Testing and Molecular Diagnostics – has various types of requirements and needs, and we can support all of them with our differentiated Sample to Insight portfolio of solutions.

So is your Sample to Insight framework about workflows?

Sample to Insight is more than just about providing smooth, end-to-end workflows. It’s a strategic framework that puts the needs and challenges of our customers front and center. It starts with understanding what insights are being sought and what would make the path to get these successful. We then help customers understand the value our solutions can offer, and how our workflows can enable them to accomplish their objectives. We want to identify key bottlenecks holding cus-tomers back and to deliver solutions so they can achieve greater success.

What is an example of how your Sample to Insight solutions enable new insights?

Just think of liquid biopsies, which are now enabling our cus-tomers to analyze cancer DNA fragments contained in blood samples or to perform important prenatal tests in a non-inva-sive way. This is a key technology that QIAGEN helped to develop and standardize in the 1990s; now we are creating liquid biopsy workflows that enable insights not even possi-ble five to 10 years ago. Working with our customers to implement solutions like these is how we achieve our vision of making improvements in life possible. This Sample to Insight framework has put QIAGEN on a new growth trajectory, transforming our company to focus even more on the value and impact of the solutions we offer, rather than just techni-cal features. The rewards of our work come in many ways, such as through contact with patients who have better out-comes due to molecular testing. Another way is when the Nobel Prizes are awarded – almost every year we see pic-tures of the winners standing in front of shelves full of QIAGEN products. These are great testimonials for how we contribute to advancing science and improving life. This is personally one of the most rewarding experiences for me, and a key motivator for our employees.

Can QIAGEN sustain its new growth trajectory?

Absolutely – our trajectory extends well into the future, as it is based on a multi-pillared portfolio of growth opportunities with long technology and application cycles. After investing strategically to accelerate sales in a few key areas, our 2016 results confirmed that we have started on a new growth path. We have also taken actions to deliver on the operating lever-age of growing sales, to optimize our balance sheet and to develop a more performance-driven organization. Looking forward to 2020, we aim to deliver compound annual growth excluding acquisitions of about 7-9 % in net sales at constant exchange rates (CER) and to grow our adjusted earnings per share above 12 %. We are also converting earnings into increases in free cash flow.

Why is testing for tuberculosis one of your targeted growth mar-kets?

The global need for TB prevention and diagnosis presents a huge opportunity for our novel Sample to Insight solution, QuantiFERON-TB. While tuberculosis is an ancient disease, it still strikes more than 10 million people a year and kills one

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INSIGHTS | » The genomic revolution is still just at the beginning«

Peer M. Schatz Chief Executive Officer, QIAGEN N.V.

every 18 seconds – making TB the no. 1 killer among infec-tious diseases. Global efforts to stop this disease have recog-nized that we not only need to treat patients with active TB but also attack latent tuberculosis infection. An estimated 2 to 3 billion people worldwide have latent TB infection, and up to 10 % of them will develop the active disease sometime in their lives. QIAGEN’s QuantiFERON technology is the mod-ern accurate test for TB infection, and more than 30 million of our tests have been administered to date. But penetration on a global scale is still low, and we estimate the address-able global market to have a volume of 65 million tests annu-ally. Our sales are growing at a sustained double-digit rate with the goal of exceeding $300 million by 2020, and we are rolling out the fourth-generation QuantiFERON-TB Gold Plus as an even more powerful tool to help fight TB.

What kind of impact can QIAGEN have in next-generation sequencing?

We are very excited, because QIAGEN is entering this fast-growing field just in time to shape the early days of NGS in the clinical markets. Our new GeneReader NGS System has garnered an enthusiastic reception from labs seeking a cost-effective, end-to-end solution for next-generation sequencing. Our focus is on the growing market for benchtop sequencers in oncology, and in GeneReader’s first year we exceeded our target of securing a 10 % market share for new placements in this application area. We expect this market to roughly dou-ble by 2020, and our goal is to capture at least a 20 % share of existing and new placements by then. Right now we are rolling out GeneReader system enhancements, plus at least five new expert-designed GeneRead QIAact panels and a

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hundreds of protocols for laboratory-developed tests, auto-mates sample processing for either PCR or NGS, and runs other specialized tests. Customers in Asia run a targeted menu of QIAGEN tests. Increasingly, we are seeing labs use both PCR and NGS platforms to address their varied needs, so both families in QIAGEN’s product portfolio can benefit.

How is QIAGEN evolving to keep up with rapid changes in the industry driven by digital technologies?

The pace of change in our industry has always been very fast, and we have three areas of focus to address this chal-lenge: our people, organizational setup and ways of doing business. People are the top priority – hiring the best in each field, training, advancing our knowledge as a company. We want customers to know that when they work with QIAGEN they are getting help from experts, and I am very thankful for the dedication and passion of our 4,700 employees world-wide. As we grow, we also make organizational changes as needed to remain agile and drive efficiencies. In the way we do business, we are decisively pursuing a digital transforma-tion. Our digital channels processed more than 30 % of sales in 2016, and we are aiming for 50 % by 2020. Our first wave of digital transformation focused on the customer expe-rience, and we are now in the midst of a major initiative called “Digitizing Sample to Insight.” We plan to digitize our entire value chain and establish an entrepreneurial, digital mindset across QIAGEN to innovate, simplify interactions and increase productivity.

Where do you see this business going in the future?

Whether you call it a genomic revolution, the Century of Biol-ogy, or just a disruptive change, molecular testing is growing rapidly. QIAGEN has a unique advantage because we have grown up helping research scientists break through to new insights, then collaborating with pharmaceutical companies and healthcare providers to bring needed solutions to market. QIAGEN is the only company that tailors just the right test for an experiment leading to breakthrough science and some-times even a Nobel Prize, and at the other end helps hospitals set up automated, cost-effective systems for routine molecular testing to improve patient outcomes. Some of the world’s most pressing challenges still lie in the future, and we continue to deliver innovative solutions to get answers faster, better and more efficiently. We’re making improvements in life possible by taking customers from Sample to Insight.

unique QIAseq custom panel service for a practically unlim-ited menu breadth in panels – all with very attractive techni-cal performance and economics. Customers are very com-fortable with QIAGEN as a vendor because we already supply sample technologies for more than 80 % of all NGS workflows and are present in almost every clinical laboratory. Our aim is to help drive the dissemination of NGS from elite research labs into widespread clinical use.

Several of your projects focus on emerging applications like liquid biopsies, metagenomics and single-cell sequencing. What’s the common thread?

Scientists around the world have long looked to QIAGEN for differentiated solutions to overcome challenges in sample technologies, where we are the undisputed market and tech-nology leader. These relationships enable us to identify the most dynamic areas of research and see their potential for further applications. Liquid biopsies are a prime example. QIAGEN, an early mover in processing samples from blood and other body fluids, now offers automated front-end work-flows for PCR and NGS, with a market share above 80 %. We also moved into metagenomics in a big way in 2016 by integrating MO BIO into QIAGEN and launching comple-mentary assays and bioinformatics for microbiome research. In single-cell analysis, QIAGEN’s innovative sample technol-ogies, assays and bioinformatics enable streamlined, cost-efficient solutions with great promise for future clinical use. Our core front-end strength helps scientists and clinicians get the most reliable results from molecular testing.

What about QIAsymphony? Is NGS making PCR obsolete?

No. Both technologies are highly synergistic, and in many cases they address different needs. PCR is significantly faster, simpler and far less costly than NGS, while NGS is more appropriate when looking for a significantly higher amount of data from a single sample. The QIAsymphony automation system surpassed our 2016 goal of 1,750 cumulative place-ments, driving double-digit growth in consumable sales. We expect to expand the installed base by more than 200 a year at least through 2020. QIAsymphony is such a versa-tile, broad-capability system that customers use it as a real workhorse. In Europe, labs run the QIAsymphony RGQ as a fully integrated molecular diagnostic platform using our tests for HIV, hepatitis, healthcare-associated infections and so on. In the United States, the QIAsymphony platform supports

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INSIGHTS | » The genomic revolution is still just at the beginning«

Enabling the fight against cancer

Cancer is one of the most devastating diseases in the world. In order to help clinical researchers understand it better and advance the development of new personalized treat-ments, QIAGEN introduced the GeneReader NGS System at the end of 2015 – the first true sample-to-insight workflow for next-generation sequencing that allows identification of clinically relevant cancer mutations. Shortly thereafter, the first system was installed at the research group of Prof. Kurt Zatloukal at the Austrian Competence Center for Biomarker Research in Medicine CBmed. His cooperation with QIAGEN helps to further advance the new system, fighting a scourge of humanity.by Hubertus Breuer

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17 17

Dr. Kurt Zatloukal, professor at the Institute of Pathology at the Medical University of Graz, sits slightly bent on a swivel chair looking at

a row of slides on a desk in front of him. Using his glasses, he points at a small spot of purple-col-ored tissue on one of the slides: “Here in the lymph node. At the edge, you can see metastases,“ he says. “If, as in this case, we have some time to determine the tissue more precisely, we can test the tumor cells for specific gene markers. The markers allow the physician to reach a more accu-rate diagnosis, and help him to understand the tumor better and make his choice of therapy.“

Through the large windows, early autumn light flows into the four-meter-high rooms of the Institute of Pathology. Inside, on the workstations next to Prof. Zatloukal, there are plastic boxes with tissue samples, coded with yellow, white, green and pur-ple tags and long numbers. They are samples from the liver, lung, colon and other organs – document to painful stories of sickness as well as testament to the hope of a cure.

The samples – per year no less than 100,000 – are sent to the Institute of Pathology by physicians after surgeries and biopsies to get answers, which may help to discover, e.g., how far a malignant tumor has grown or whether it has metastasized. Most of the samples are embedded in paraffin blocks, which are cut into fine slices and placed on glass slides such as the ones right under Prof. Zatloukal’s eyes. They can be structurally ana-lyzed in detail under the microscope, stained with

dyes to reveal their cellular pathology and used for genetic analysis.

Seamless workflow from sample to insight

In the past, traditional cancer genetics focused on single mutations in tumors. But thanks to various methods described as next-generation sequencing (NGS) that allow the massive parallel analysis of genetic material, today researchers can use gene panels to test multiple markers at once. This not only allows them to generate more genetic infor-mation, but also to explore the molecular nature of a tumor more quickly and affordably. What they mostly aim for are gene markers that allow them to understand the cancer better as well as which treatments have been associated with a specific marker. What has been missing until recently is a solution that integrates all the important steps from sample to insight in one seamless workflow: QIAGEN’s GeneReader NGS System.

Starting in spring 2016, based on the long-term research collaboration of QIAGEN with Christian Doppler Laboratory at the Medical University of Graz, the very first QIAGEN NGS system was installed at the recently established Competence Center for Biomarker Research in Medicine CBmed. The Christian Doppler lab, founded in 2011 and headed by Prof. Dr. Kurt Zatloukal, focuses on testing new technologies for processing biological samples. Since its beginnings, QIAGEN has been the lab’s corporate partner, an example of the widespread practice of the company to cooperate with scientists and universities on

View from the University Hospital towards the Med Campus Graz, including the new main building.

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people are newly diagnosed with cancer every year, accounting for more than 8 million annual deaths.

14 millionPreparation of formalin-fixed paraffin-embed-ded tissue sections for staining (above) and cutting of extremely thin slices with the help of a microtome (below).

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INSIGHTS | Enabling the fight against cancer

» What I particularly like is that no bioinformatics specialist is needed to interpret the results.«

Dr. Lisa Oberauner-Wappis

» Most tumors are heterogeneous. They probably have different variants active either in different parts or they change throughout its evolution – or both. It is a moving target which won’t be easily shot down, certainly not by a single bullet.«

Prof. Dr. Kurt Zatloukal

developing novel technologies and applications. As it happens though, Prof. Zatloukal also founded one of Europe’s largest biobanks at the Medical University of Graz, providing access to the tissues needed for testing new technologies. Furthermore, he also works closely with CBmed Graz, an Austri-an competence center developing customized solutions for biomarker research. “All that was rea-son enough for us to offer the GeneReader first to his team,“ says Yi Kong, Director Oncology Fran-chise at QIAGEN. “This way, we were able to get detailed feedback to optimize details of the work-flow, such as the interface displaying the results of gene analysis.“

Prof. Zatloukal, after giving a tour of the venerable Institute of Pathology, walks across campus to a grey 90’s building, where a small room with win-dows to a hallway houses the new GeneReader system. He is standing in front of desks ordered in a U-shape, on top of which are several QIAGEN-branded machines, all housed in silvery casings with dark blue semitransparent inserts. “I welcome any additional tool for understanding cancer bet-ter and fighting it, but this one especially,“ he says. “Over the last years it has become clear that with NGS, tumors can be analyzed, but the effort has been time consuming and difficult.“

He points out that to establish a good workflow one previously had to get machines from various vendors, which in turn had to undergo extensive testing in order to ensure that they meet quality standards – plus, they had to comply with various guidelines. “QIAGEN offers an integrated com-plete workflow. That saves time and money, helps to find answers more efficiently, and frees up time for researchers and lab staff to focus less on tech-nical issues and more on fighting cancer.“

Most cancers have polygenetic mutations

Still, even with a fully integrated workflow to obtain reliable results from NGS, answers are not a given. Thanks to NGS, today a human genome can be sequenced for under $1,000 in a matter of days. But big data collection alone is just one, albeit essential step. In order to develop a custom-tai-lored understanding of a patient’s illness the indi-vidual genetic markers have to be identified – and their biological role understood. To the degree that such knowledge exists, it is precious, considering that it is estimated that every human carries roughly three million individual genetic variants across their genome. Understanding these markers will allow for the ’personalized medicine‘ approach – tailor-ing any necessary combination of drugs, radiation and chemotherapy to a patient’s genetic profile.

In the case of monogenic diseases, the inheritance pattern is rather straightforward. Cystic fibrosis is a prime example: anyone harboring one defec-tive copy of the gene is not affected; but if both parents each pass on a mutant allele, their child will suffer from the disease. In contrast, most oth-er conditions such as Alzheimer’s or cardiovascu-lar disease are much more complex and cannot be associated with just one causal genetic variant.

The same holds true for cancer. The rare case of a single genetic alteration as a major cause of cancer and an accompanying treatment does exist – such as in chronic myelogenous leukemia. But by and large, most cancers are characterized by polygen-etic mutations. To deal with this complexity, QIAGEN’s GeneReader only uses panels that look for markers that have a known relevance for a tumor and its treatment. While some tumors with a specific variant may be resistant to certain agents, others can be particularly vulnerable to certain

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INSIGHTS | Enabling the fight against cancer

first, this may not sound lightning fast, but the whole workflow has now reached a capacity of 48 samples per run. That results in nearly 5,000 samples per year, even covering demands of high-throughput laboratories.

The GeneReader in Graz uses a gene assay called the ’Actionable Insights Tumor Panel,’ which covers 12 targeted genes with 773 variants found in breast, ovarian, colon, lung and skin cancer – mankind’s most prevalent solid tumors. All these mutations have in common that they have been the subjects of several scientific publications, or are documented to be related to the outcome of specif-ic therapies. They have been selected using QIAGEN’s Ingenuity Knowledge Base, a unique resource for interpretation and selection of molec-ular content containing more than 13 million genetic findings. One example is a mutation on the ERBB2 gene, which can occur in lung, breast, ovary and bladder cancer. At the end of 2015, this variant was the topic of at least 27 scientific arti-cles. There is one report showing that a breast cancer patient with this variant had a positive response to a targeted treatment and that it appears in professional guidelines and is tied to Phase III clinical trials.

therapies, and mean that targeting a therapy spe-cifically to a cancer and prolonging the patient’s life is possible. Currently, drugs are targeting around 50 genomic variants in cancers.

“Knowing the genetic makeup of a cancer, and particularly actionable mutations, is a great bene-fit,“ says Prof. Zatloukal. “It can lead to a more substantive diagnosis and informed decision on which therapy to choose. But there are still many hurdles we need to overcome. This is what we work on in the Christian Doppler lab. For example: How do we sample and process a tumor properly in order to get accurate information on the cancer given that tumors happen to be very heteroge-neous? This is the kind of research we pursue.“

Careful selection of actionable cancer mutations

Then Prof. Zatloukal turns to his team to demon-strate the GeneReader itself. It has a transparent blue hatch in the middle. If one lifts it, one sees a turntable on which at any time several flow cells with multiple sample batches can be analyzed simultaneously or staggered, driven by random access and continuous loading of flow cells. It takes around five days from obtaining a solid tumor sample to getting an interpreted result. At

Watch Prof. Dr. Kurt Zatloukal discussing

the GeneReader NGS System

http: //bit.ly/ GeneReader

Working on the QIAcube to produce high-quality DNA libraries for the next steps of the GeneReader NGS System workflow.

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Improving outcomes with knowledge

One of QIAGEN’s unique resources is its own industry leading QIAGEN Ingenuity Knowledge Base compiled of multiple public and proprietary sources, such as drug labels, results from clinical trials, licensed exter-nal databases, professional guidelines and scientific literature. QIAGEN’s team of highly qualified Ph.D. and MD staff is dedicated to continuously conducting exhaustive curation of new primary literature and review of clinical cases to ensure that the database contains the most up-to-date information. Among other applications, the knowledge base powers ‘QIAGEN Clinical Insight‘ (QCI), a cloud based bioinformatics tool to interpret and report test results generated with the Gene Reader NGS System.

Furthermore, this knowledge base helps to design the gene panels used in combination with the GeneRead-er system themselves. The approach first selects tumors based on prevalence and potential health impact – such as breast, ovarian, colon, lung and skin cancer – and then turns to the knowledge base in order to look for genes and variants in these genes that are proven genetic biomarkers for these widespread tumor types, or that have evidence supporting their potential rele-vance to targeted therapies. The selection is conserva-tive in so far as it only uses data from professional guidelines, drug labels and clinical trials from the knowledge base – but not e.g. scientific literature, which is not primarily connected to actionable vari-ants. This in turn assures the relevance of the data.

The GeneReader workflow becomes manifest in the various QIAGEN devices that can be found alongside the benchtop sequencer itself. After DNA extraction and target enrichment at the Insti-tute of Pathology, library preparation, sequencing and interpretation including quality controls take place in this small room of CBmed. Unsurprisingly, there is also a computer screen on which the sam-ple report is displayed with the help of QIAGEN Clinical Insight (QCI), a continually updated, cloud-based clinical decision support solution spe-cifically designed for interpretation of NGS-based cancer test results.

Traffic lights guide lab work

The molecular microbiologist Dr. Lisa Oberauner-Wappis, who runs the QIAGEN setup with her team, is also quite impressed by the system: “What I particularly like is that no bioinformatics special-ist is needed to interpret the results,“ she says. In fact, the detected variants are marked in the color of traffic lights, indicating their relevance in a given disease context: red, orange or green. “Naturally, you first take a look at the ’red’ marked results,“ she says. The user-friendly design, of course, is one of the goals of the GeneReader NGS System: “At QIAGEN, we asked ourselves, ‘How do you

Automated clonal amplification on GeneRead QIAcube (above) and loading of the flow cell into the GeneReader benchtop sequencer for analysis (right).

23

Analysis and interpretation

tools

QIAGENKnowledge

Base

Drug labels

Clinical trials

Scientific literature

Clinical casecounts

Professional guidelines

External database

Actionablereport

address a pressing need in the clinical environment with a plug and play solution that can be adopted by any laboratory?,“ says Kong. “With an easy to use workflow, and easy to read results. For a wide spectrum of researchers, the complete sample to insight solution will certainly be a game-changer.“

The system also offers yet other advantages: The DNA of formalin-fixed, paraffin-embedded (FFPE) samples is often damaged. The sample preparation component of the QIAGEN system largely corrects this damage. Also, errors are often generated dur-ing the sample amplification steps. Once this pro-cess is completed, it is impossible to distinguish a unique DNA variant from a library construction error. The GeneReader system can be used to detect low-frequency variants with high confidence by barcoding DNA molecules before any amplifica-tion takes place – a proprietary technology known as digital sequencing – to distinguish unique DNA variants from PCR errors.

In addition, researchers and labs benefit from the single vendor model, says Kong: “Not only are they buying an integrated system that has been designed for fast and reliable output, if there is a problem, they can always pick up the phone and call support at QIAGEN.” Furthermore, commercial models such as price-per-insight options offer better cost management and low initial investment hurdles in the context of fixed-cost restraints. The success so far appears to underline the system’s attractiveness. By the end of 2016, the GeneReader NGS System had captured more than a 10 % share of the esti-mated global annual market for new placements of bench-top sequencer used for oncology.

Continuous improvement of the GeneReader workflow

Still, as good as the system already is, QIAGEN is continuously working on further targeted enhance-

ments and updates to increase its value for labora-tories. Six months after its launch, a GeneReader workflow was developed that can support analysis of liquid biopsy samples. For Prof. Zatloukal, this is important because it allows for a whole new approach to understanding the biological mecha-nisms of cancer: It has the potential to find traces of tumor cells or genomic molecules before a can-cer shows any symptoms or shows up with imaging technology. It can also be used to develop meth-ods for monitoring treatments and the progress of the disease, and help evaluate the genetic altera-tions in cancer metastases, which otherwise are not accessible in the body for molecular testing. In 2017, at least five new expertly curated gene pan-els are being added to the GeneReader, including two for lung cancer, a panel for breast and ovari-an cancer and one focusing on blood. Further-more, customers will soon be able to opt to custom design panels according to their specific needs creating a virtually unlimited menu breadth.

Prof. Zatloukal, now sitting comfortably next to the GeneReader and playing with his glasses in his hands, cautions that cancer is a notoriously com-plex disease. “Most tumors are heterogeneous. They probably have different variants active either in different parts or changing throughout its evolu-tion – or both. It is a moving target, which won’t be easily shot down, certainly not by a single bul-let. To fight it, we will most likely use panels testing more and more variants – and then attack them with a whole battery of drugs.” And to understand cancer? “We will need a systems biology approach, integrating all kinds of parameters, based on underlying principles which we don’t ful-ly understand yet – hopefully the GeneReader can help a little with that.“

25

INSIGHTS | Enabling the fight against cancer

Cracking the code: how RNA may hold the answer

Dr. John Martignetti is Associate Professor at the Icahn School of Medicine at Mount Sinai Hospital in New York City and Network Director of the Laboratory for Translational Research at the West-

ern Connecticut Health Network Biomedical Research Institute. Dr. Mar-tignetti is also a code breaker, and his success in deciphering these codes promises to benefit the health of mankind. Specializing in Genet-ics and Genomic Sciences, one of Dr. Martignetti’s missions is to unravel the mysteries of ribonucleic acid (RNA), currently one of the most excit-ing areas of clinical research. His insights bring the possibility of trans-forming the diagnosis, treatment, and survival of life-threatening condi-tions, including several cancers.

For decades, scientists trying to better understand genetics and molecu-lar biology focused almost exclusively on DNA; RNA was the forgotten relation. However, following clarification of the genetic code in the 1970s, it became clear that RNA plays important roles in mediating cell mechanisms, gene expression and helping control cell function. It is now a promising area of research in its own right.

Dark matter that really matters

Dr. Martignetti is excited by the prospect of revealing its secrets. “Think about the genetic material present in a cell or organism. Only a small fraction of it, around 2- 3 percent, codes for protein. The balance is non-

For many years, RNA research lagged behind investigations of DNA. Now, a growing understanding of RNA’s vital role in regulating normal physiology is attracting increasing interest. Research now reveals a powerful driver of both disease and health, with the potential for novel biomarkers and therapeutics.

by Colin Mackay

27

INSIGHTS | Cracking the code: how RNA may hold the answer

coding RNA,” he explains. “This has a function, but precisely what that function is, we don’t yet know. It’s part of what we are exploring.”

Increasingly, researchers believe that this non-coding RNA – known as ’dark matter’ – may be the key to unlocking the nature of disease. In some cases, it may even be the source of inherited disease itself. Future RNA research will target the precise location of disease traits within the human genome. It sounds simple, but in reality, Dr. Martignetti and his team are looking for – and finding – needles in a haystack.

Game-changing research

This is not only due to the constantly evolving nature of the ‘RNA world.’ “The biggest challenge is the large amount of data generated by our experiments and how to make sense out of it,” explains Dr. Martignetti. “We need bioinformatic tools, which analyze data generated by, for example, coding RNA, messenger RNA, small nuclear RNA, so that we can see patterns and understand relationships across data sets.”

This can be a challenging yet extremely rewarding task. In one instance, Dr. Martignetti’s team used RNA to understand how cancer cells

» RNA is a key to understanding how we will diagnose and treat many different diseases in the future, but it will also be vital in understanding normal physiology and health.«

Dr. John Martignetti

28

responded to a specific treatment, a novel class of chemotherapeutics recently entered into Phase I I clinical trials. Using cancer cell lines derived from patients with ovarian cancer, the researchers examined their transcriptomes to determine which pathways were affected by the novel drug. This enabled the team to identify signatures associated with patients likely to respond to the proposed treatment, and those who were not likely to respond. The ultimate goal: a precision medicine approach of giving this novel agent specifically to patients whose tumors will be sensitive and respond, while not giving it to those patients whose tumors are unlikely to respond.

In another study, the scientists looked for the cause of an inherited form of bone cancer across a number of families from around the world. “By analyzing these families, we identified that a single mutation resulted in the showering of new hybrid RNA molecules that change the function of a critical metabolic enzyme,“ explained Dr. Martignetti.

Breakthroughs from bioinformatics

According to Dr. Martignetti, breakthroughs like these would be virtual-ly impossible without advanced bioinformatics tools. “It’s a bioinformat-ics issue. We need software that helps us to make sense of the data in a meaningful way, and the QIAGEN software products we’re using are very powerful analytical tools.”

In his research, Dr. Martignetti primarily turns to QIAGEN’s Ingenuity Pathway Analysis (IPA) software. IPA allows him and his team to ana-lyze complex genomic data in real time – within days rather than weeks – without depending on other bioinformaticians for help. “It’s not some-thing we could do manually. We would not see these kinds of relation-ships we’ve seen in our previous studies without IPA,” Dr. Martignetti explains.

Dr. Martignetti believes that his area of research is only now beginning to realize its immense promise; so far, it has only scratched the surface. He predicts major advances in using RNA to improve the understand-ing, diagnosis, and treatment of disease. There is the prospect of a vir-tuous circle, with new insights leading to increasing opportunities to har-ness RNA in furthering research and improving healthcare.

For Dr. Matignetti (on the right), breakthroughs in RNA research are primarily driven by advanced bioinformatics.

Watch Dr. John Martignetti discuss-ing challenges in

RNA research

http: // bit.ly/ RNAresearch

29

INSIGHTS | Cracking the code: how RNA may hold the answer

Mapping a hidden world Scientists around the globe have embarked on an ambitious project to chart and better understand the microbiome, pushing the frontiers of life sciences.by Steffan Heuer

For the average New Yorker, the local subway station is a waypoint to quickly get to work. For Dr. Chris Mason, however, it’s the gateway to the hidden world of the

microbiome. When the Associate Professor of Physiology and Biophysics and of Computational Biomedicine at Weill Cor-nell Medicine in Manhattan entered the 68th Street stop for the number 6 train on a recent morning, he whipped out a handful of nylon swabs to run over the handrails, turnstiles, benches and even electronic info boards above the platform to collect samples. Back in his lab, he ran the samples through assays to identify the genetic material collected in the urban wild.

New York is but one of 72 large cities around the world where scientists like Dr. Mason are chasing insights into the microbiome. They’ve come together under the roof of the Meta SUB International Consortium to map and better under-stand the interactions between microbes that permeate virtu-ally every aspect of human life.

“Every time we touch an object or breathe, we make contact with millions of microscopic organisms such as bacteria, viruses, fungi, protozoa and even algae that have colonized every surface on Earth and made a home inside our bodies,” says Dr. Mason. Experts estimate that every human holds a total of 100 trillion microbial cells, which likely outnumber the number of cells in the human body.

The microbiome has a far-reaching impact on life. On the one hand, it’s responsible for infectious diseases such as cholera or the avian flu. On the other hand, microorganisms act as a live shield to protect humans from pathogens, aid with diges-

of urban populations use public transpor-tation, making it one of the most shared spaces of the urban environment.

~30 %

of the world’s 7.4 billion people live in urban areas.

>50 %

32

tion, process drugs, and promote overall health and well-being. Understanding the myriad of interactions is therefore considered one of the most exciting and dynamic new fron-tiers of life science. It promises to bolster public health defens-es, develop new therapeutic applications and even improve disciplines such as forensics, city planning and architecture.

So far, humans have not fully grasped the size and diversity of this parallel world. In 2013, Dr. Mason started a project called PathoMap that collected samples from the New York City subway yielding the first detailed metagenomic profile of a large metropolis in 2015.

Meta SUB will take this microbial sleuthing to the global scale. In June 2016, Weill Cornell Medicine led a myriad of other scientists, researchers and trained citizen scientists who started to collect and analyze samples of DNA and RNA in

Every human hosts about 100 trillion microbial cells, making up around five percent of our body weight.

As part of the Meta SUB project, Dr. Mason and other scientists around the globe will collect thousands of samples from the public transportation system.

33

high-traffic areas of several dozen large cities around the world. The Meta SUB project, headed by Dr. Mason as prin-cipal investigator, will run for five years. “Our goal is to drill into longitudinal profiles of the world’s major cities and study how their genetic makeup, pathogen load and even antimi-crobial resistance change over time”, explains Dr. Mason.

Getting to know the hidden world around us promises big pay-offs. Researchers hope to better understand the relation-ship between bacteria that colonize our bodies and condi-tions like obesity, metabolic syndrome or even mental condi-tions such as anxiety and attention deficit hyperactivity disorder (ADHD).

15microbes are shared by a person with our environment every hour – our microbial fingerprint.

million

34

This work requires a standardized protocol and platform to make sure the results can be reliably gathered, interpreted and then compared. QIAGEN therefore provides the consor-tium with its DN easy PowerSoil as well as QIAseq FX DNA kits to process genomic materials for analysis and preparing the sequencing libraries. “Understanding the various microbi-omes and their impact on human health and environment is a key area of interest for our company,” says Michael Kazinski, QIAGEN’s Senior Director Molecular Preanalytic Technolo-gies. “We want to support basic research and medical devel-opment with technology that a researcher can use who’s nei-ther an expert in bioinformatics or genetics.”

With technological advances and rapidly emerging knowl-edge on the microbiome, researchers increasingly generate insights that are applicable to public and environmental health. For Dr. Mason, the microbiome could even propel the idea of personalized medicine forward. He considers the rich microbial world around us a “phalanx of friends” that should be harnessed to design an individual, “geospatially-informed treatment” plan. In the not-too distant future, a physician could use it to check on any past antimicrobial resistance and implement the best antibiotic for an infection.

It’s a vision worthy of scouring the entire world.

Watch Dr. Christopher Mason discussing

the PathoMap project

http: // bit.ly/ PathoMap

of all DNA present on the sub-way’s surfaces identified by the PathoMap project did not match any known organism.

50 %QIAGEN supports the Meta SUB project with technologies for processing of samples and preparation of sequencing libraries.

35

INSIGHTS | Mapping a hidden world

»Like a smoldering ember that can catch fire again«

How the leading TB Assay can help tackle Japan’s high infection rates and the world’s top infectious disease killer.by James Simms ll

Japan’s rate of tuberculosis puts it in the middle range of countries around the world, rather than at the expected bottom. According to the WHO, the nation lags behind

other industrial economies like the U.S., which has a TB rate one-sixth that of Japan. TB rates in Japan increased after World War II and with its aging population. Most of the new cases of active TB are attributed to disease transformation from latent tuberculosis infection (LTBI). That hidden form of TB infection is asymptomatic and not contagious, but it can reactivate months to decades later into its active contagious form.

Experts say the key to accelerating the TB rate decline and preventing outbreaks is treating LTBI among the most vulnera-ble to developing the active disease, namely children under age 5 and the elderly. The WHO says LTBI treatment can reduce the risk of developing the active form by 60 % to 90 %.

Accurate and economical medical tests are crucial when deter-mining who needs treatment for LTBI. The century-old tubercu-lin skin test (TST) is still being used to detect latent TB infec-tions. But the technology has several shortcomings, frequently producing false negative results among the elderly and false positive results among individuals with BCG vaccinations, which are still given to over 90 % of the children worldwide.

That’s why leading experts increasingly endorse the use of interferon gamma (IFN-g) release assays (IGRA) to aid detec-tion of a TB infection. IGRA s work by using highly specific antigens of M. tuberculosis that don’t cause false reactions from BCG vaccination or common environmental mycobacte-ria. With over 30 million tests sold to date, QIAGEN’s QuantiFERON-TB test is the leading IGRA worldwide.

37

INSIGHTS | »Like a smoldering ember that can catch fire again«

QuantiFERON-TB Gold Plus (QFT-Plus) marks the fourth gen-eration of the most accurate test for detecting TB infection, offering the ability to capture a much broader picture of an individual’s immune response to TB infection. Following its CE-marking in Europe and regulatory submission in the U.S. in 2015 and 2016, respectively, QIAGEN intends to submit QFT-Plus for regulatory approval in Japan in 2017.

To better understand TB and the potential role that QFT-Plus can play in disease management, we talked to Dr. Kiyoyasu Fukushima, M.D., Deputy Chief of the Japan Red Cross Nagasaki Genbaku Isahaya Hospital and respiratory section head. His hospital has the largest number of TB beds in the prefecture, and five respiratory doctors, with 10 to 15 active TB patients at any given time.

A nationally recognized TB expert, Dr. Fukushima conducts research on QFT-Plus and has extensively evaluated previous generations of the assay.

Why is TB so high in Japan?

Dr. Fukushima: After WWII, there were many patients who had TB and cleared the disease on their own. But 70 years

later, their immune systems are weakened, and so there have been TB relapses.

While declining – though still high, what is Japan’s TB outlook?

Dr. Fukushima: The slope is becoming less and less steep. For active TB, I would liken that to a burning fire that you have to douse with water. But latent TB is like a smoldering ember that can catch fire again. Japan’s way of dealing with TB is to find those embers and snuff them out. It is possible to become a low TB country by 2030 as long as we properly continue on the current path.

What’s the best way to deal with TB?

Dr. Fukushima: Early detection and early treatment. From my point of view, we should employ IGRA and low-dose comput-erized tomography scans to detect both latent TB infections in high-risk populations and patients with early, active TB. For developing countries with limited healthcare resources, I would recommend a combination of x-rays and IGRA. Treat-ment is the same worldwide. If done properly – meaning not stopping treatment mid-way – we can cure ninety-some per-cent of the cases.

Dr. Fukushima’s hospital has the largest number of TB beds in the prefecture, with 10 to 15 active TB patients at any given time.

38

– Manual in-vivo test with significant inter-reader variability

– Lower sensitivity than IGRAs and high level of false positive results due to cross-reaction with BCG vaccines and other bacteria

– Two patient visits required, negatively affecting patient compliance

+ Fully automated in-vitro test providing objective and standardized results

+ Most accurate test for TB infection, not affected by BCG vaccine

+ Reliable results with only one patient visit

QIAGEN is working with healthcare authorities and non-governmental organiza-tions worldwide to reach the WHO’s goal

of reducing the incidence of active TB by 80 % and the number of associated

deaths by 90 % by 2030.

1/3 of the world’s population is estimated to carry latent TB.

<–10 % of people infected will

develop active TB during their lifetime.

10.4 million

new cases of active TB were registered worldwide

in 2015.

people succumbed to TB, making it the leading cause of death among infectious

diseases globally.

1.8 million

The global fight against TB

TST QFT

…with a weakened immune system, e.g.

patients suffering from chronic disease.

…with a higher risk of TB contact, e.g. healthcare profes-

sionals.

…from countries with a high TB

incidence.

2030 goal

2

Screening and treating high-risk populations for latent TB is

increasingly recognized as a key element in reducing the global

burden of tuberculosis. Risk groups include Individuals …

QuantiFERON-TB is the most accurate test for TB infection and has several advantages over the more

than 100-year old tuberculin skin test.

Data sources: WHO, QIAGEN.

1

3

What’s the advantage of IGRA versus TST in latent TB testing?

Dr. Fukushima: Several factors favor IGRA s. The biggest is that IGRA s aren’t affected by BCG vaccination, which leads to false positive results with the tuberculin skin test. IGRA s also have a higher specificity and sensitivity, allowing to find 90 % of the true positives. They’re also highly objective, so they’re not affected by the person analyzing the results, and patients only have to come in once. For TST, in contrast, you are supposed to have specialized training to accurately assess them. Even I haven’t had that.

For example, at my hospital, I tested 36 TB patients with the second generation of QuantiFERON ten years ago. That had 86 % sensitivity and tuberculin’s was 86 % too. But for healthy people, 78 staff at my hospital, QFT produced only 9 % pos-itive test results in contrast to 94 % false positives with TST. That means the specificity for tuberculin was only 6 %, and 91 % for QFT.

The new QuantiFERON-TB Gold Plus represents a key milestone in the devel-opment of diagnostic tests for latent TB infection.

40

What’s the main difference between QFT-Plus and the former test generations in your view?

Dr. Fukushima: The biggest difference between QFT-Plus and former generations is the incorporation of CD8+ T-cell response data in addition to the measurement of CD4 T-cell response. This allows the test to measure a broader range of immune response.

What are the technology’s potential benefits?

Dr. Fukushima: When we test someone positive for LTBI, at this point nobody knows whether we are facing a recent or older infection. Early research suggests that, thanks to the CD8+ data, going forward it might be possible to differenti-ate this. Meanwhile, we might be able to identify individuals who have a higher risk to progress to active TB.

Another point is that the CD8+ technology promises to deliv-er higher sensitivity and specificity in patients at greatest risk for TB infection, particularly individuals co-infected with HIV and elderly patients with lower levels of CD4, i.e. a weaker

immune system. About 30 % to 40 % of elderly patients have non-functioning immune systems and will thus likely test negative for LTBI even if infected. And the older a patient gets, the lower the CD4 level, which makes it more difficult to detect TB infection regardless of the method used.

Is this also reflected in your research results?

If a person is 80 years or younger, I found the test results generated with QFT and QFT-Plus to be comparable. They had a sensitivity of 91 % and 94 %, respectively. But for those 80 years or older, QFT-Plus seems to provide better perfor-mance. Here, QFT-Plus shows a sensitivity of 83 % compared to 74 % for the third-generation – and I think the difference would be more pronounced in a larger patient sample with several thousand over 80.

What’s the difference between QFT-Plus and other IGRA s?

Dr. Fukushima: It’s obvious. I’ve found both QFT and QFT-Plus to be significantly more sensitive both in the overall patient population and in individuals over 80.

41

INSIGHTS | »Like a smoldering ember that can catch fire again«

Looking to the future of missing persons analysis with next-generation sequencing

Under the watchful eye of Thomas Parsons, the International Commission on Missing Persons has become the global reference in forensic human identification. As the ICMP establishes its new headquarters in The Hague, it presents the opportunity to raise its expertise to the next level.

To the average passer-by, the entrance to the new ICMP headquarters is just another polished door on a pleas-ant main street in a quiet, neat Dutch city. It would be

difficult to guess that the three-storey facility that lies behind will soon host a cutting-edge laboratory, working to bring solace and comfort to families that have lost loved ones through armed conflicts, disasters or migration.

A unique opportunity

On the third floor, ICMP Director-General Kathryne Bomberg-er sits at her desk in a quiet corner, watching the new offices take shape around her. She is quietly excited by the reloca-tion. “The Hague is ultimately the ICMP’s natural home,” she says. “It provides a unique opportunity to reinforce the impor-tance of what we do. The proximity of the other peace and justice institutions will enhance the awareness and perception of the ICMP.” She believes this wider recognition will be an important contribution in making the case for a global response to the problem of missing persons.

However, the ICMP is more than an institution of justice. It has built a reputation based on leveraging technology and establishing solid evidence; its new headquarters will build on this. It offers the organization the possibility of developing a new scientific approach to tackling the challenge of miss-ing persons. The new facility will combine the latest in DNA sequencing technology with the ICMP’s established knowl-edge base and expertise in areas such as forensic genetics and the logistical and data handling needs for missing per-sons investigations.

A definitive center of excellence

Responsible for creating this facility will be Thomas Parsons, the ICMP’s Director of Science and Technology. Quiet-spo-

ken and precise, Parsons leads the ICMP’s team of experts in forensic anthropology, forensic archeology, DNA profiling, genetic kinship matching and informatics. Although his new laboratory space is still at a very early stage, his vision for it, and what it can deliver, is clear. “This is the opportunity to establish a definitive center of excellence for DNA-based human identification,” he says.

At the same time, he also wants the facilities in The Hague to benefit from the mindset that helped the ICMP achieve so much in former Yugoslavia. In Sarajevo, Parsons explained, his team pursued a single-minded approach to problem solv-ing. It was this mindset that drove many of the advances that DNA laboratories around the world now benefit from. “We continuously updated our techniques, with unrelenting focus. We regularly asked ourselves ’What is currently holding us back? How do we address it?’ Once we had solved one issue, we would repeat the process to tackle the next.”

Answering fundamental questions

However, Parsons is quick to stress that although the science is important, ultimately it’s about the difference that it makes to families and individuals. He and his team are hugely motivat-ed by the consequences of their work for families of missing persons. “Our efforts bring a degree of resolution for these anguished people. We may not cure anything, but in many instances we can answer some of their most fundamental ques-tions and resolve some of the causes of their ongoing trauma.” But equally importantly, Parsons appreciates what ICMP’s work contributes to justice. “Where perpetrators believed they would be able to remove people from the human experience, we provide irrefutable forensic evidence of identity. This means that perpetrators can be held accountable.”

Learn more about the ICMP’s work in Bosnia to identify the victims of the

Srebrenica massacre:

http: // bit.ly/ ICMPSrebrenica

44

ICMP: Destination The Hague

Founded in 1996, since 2001 the International Commission on Missing Persons (ICMP) has provided the benchmark for DNA identification techniques, combining forensic archeological and anthropological techniques with state-of-the-art DNA matching processes. To date, it has assisted national authorities in resolving the fate of some 70 percent of the 40,000 people who disap-peared during the war in former Yugoslavia, with DNA assisted identifications of over 20,000 individuals worldwide; an unprece-dented achievement.

In 2015, the ICMP entered a new phase as an internationally rec-ognized, treaty-based international organization and moved its base from Sarajevo, Bosnia and Herzegovina, to its new head-quarters in The Hague in the Netherlands. There, the ICMP will sit alongside other institutions including the International Court of Justice and the International Criminal Court.

QIAGEN’s R&D team in Frederick led by Eric Lader, Senior Director BRC Product Development (on the right), supports the ICMP in the development of SNP-based assays for human ID applications.

45

INSIGHTS | Looking to the future of missing persons analysis with NGS

Thomas Parsons, the ICMP’s Director of Science and Technology, hopes to establish the new headquarters in The Hague as a definitive center of excellence for DNA-based human identification.

» Where perpetrators believed they would be able to remove people from the human experience, we provide irrefutable forensic evidence of identity. This means that perpetrators can be held accountable.«

Thomas Parsons

With the new laboratory in The Hague, Parsons and his team hope to build on these capabilities. He is eager to leverage the potential of next-generation sequencing (NGS), which he believes will address many of the existing challenges in delivering large-scale missing persons identification. Parsons explains: “There are three problems that currently hold us back; the unit cost per test; the difficulty of working with highly degraded samples and the amount of genetic informa-tion needed to confirm identity via distant family members. Advancements in next-generation sequencing clearly offer the potential to address these issues.”

Turning the promise of NGS into reality

To turn the promise of NGS into reality, Parsons and his team are focusing on developing novel Single Nucleotide Polymor-phism (SNP)-based testing methods. These will identify singu-lar mutations in the human genome and provide greater pow-er for establishing kinship when used in large numbers. The objective is to develop highly homogeneous and cost-effec-tive laboratory mechanisms that can be applied irrespective of the level of sample degradation. Ultimately, he hopes to make this feasible at around one tenth of the current cost by pooling samples using molecular barcoding mechanisms.

Many in the field of forensic genetics foresee that an SNP-based approach may best capitalize on the strengths of NGS, and Parsons believes that with carefully directed effort it may even replace STR analysis as the standard approach in current human ID applications. Certainly, he views NGS as the way forward, not only for the ICMP but also for the entire forensic community, allowing it to address some of the major existing challenges in missing persons investigations.

At the forefront of human identity testing

The new laboratories in The Hague mark another step in the long-standing collaboration between the ICMP and QIAGEN. The relationship dates back to the ICMP’s initial work in Bosnia and Herzegovina, where QIAGEN helped the organization implement highly efficient approaches for isolating DNA from bone. The next phase will see QIAGEN provide support in developing SNP-based assays. The new ICMP laboratory will also take delivery of the QIAGEN GeneReader NGS System, the first fully integrated NGS workflow solution.

For QIAGEN, the collaboration with the ICMP is a unique opportunity. “The ICMP is at the forefront of human identity testing around the world, pioneering methods and principles for analyzing challenging samples,” says Keith Elliott, QIAGEN’s Senior Global Product Manager in Applied Test-ing. “What makes the ICMP so special is their commitment to leveraging science to uphold basic human rights and justice for missing persons and their families. Working with Thomas Parsons and his team in developing Sample to Insight next- generation sequencing is a huge privilege for QIAGEN.”

Parsons believes that within the next three to five years capa-bilities will advance substantially from where they are today. He is dedicated to maximizing the impact of these technolog-ical advances on the ICMP’s mission. “This is a worldwide crisis on many levels; economic displacement, mass disaster, terrorism, post-conflict, ongoing conflict, all of these. We have already demonstrated some of the possibilities; now we want to expand those as broadly as we can. Our coopera-tion with QIAGEN is a major benefit for this objective.”

QIAGEN’s GeneReader NGS System will help the ICMP to harness the power of NGS tech-nology for missing persons identification.

47

INSIGHTS | Looking to the future of missing persons analysis with NGS

QIAGEN breaks new groundFour stories, four QIAGENers break-ing new ground in their work: bring-ing much-needed medical treatments to Africa; thinking out of the box in digital sequencing; employing big data expertise to create more benefi-cial processes; enabling personal-ized healthcare. Their pioneering work is opening up new growth and devel-opment fields for QIAGEN.

48

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1

Dr Leonardo Di Matteo, Senior Data Scientist, Hilden

SmarterDr. Yexun (‘Bill’) Wang, Senior Director R&D, Frederick, MD.

Faster

Chris Bray, Director of Regula-tory Affairs, Manchester

Safer

Agnieszka Oles, Senior Account Manager Africa, Dubai

Further

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October 2016: Arrival in Dubai. I always wanted to live here since my first visit years ago. You either love or hate Dubai – I love it! Why come here? After eight years in Germany, I wanted a change and a new challenge. I love Africa, the people, the culture – so when QIAGEN decided to open a sales office for Africa in Dubai, I jumped at the chance.

November 2016: Stayed in a hotel so far, but soon to move into my own apartment. Smooth acclima-tization thanks to great help from our office man-ager. She has looked after documentation, driven me around & helped me find a nice apartment in just two days – with 20 to choose from! Dubai is very easy for expats and a great hub for flights to Africa.

QIAGEN hasn’t really been active in Africa before – apart from South Africa and distributors in Kenya and Nigeria. So we’re building up a whole sales network from scratch. With some competition strong and well established, we’re looking for experienced distributors and partners. That’s my big but exciting challenge in 2017! It’s why I wanted this job.

December 2016: Our priority countries are Kenya, Tanzania, Nigeria and Ethiopia. The last two are a bit tricky right now. The volatile Nigerian naira makes life difficult for distributors, and there’s polit-ical unrest in Ethiopia. My job involves looking at

a country’s potential, healthcare system and set-up (both public and private), finding distributors expe-rienced in life sciences and molecular diagnostics, and evaluating their potential. I get my information from German Chambers of Commerce or medical attachés.

Traveling in Africa can be a challenge. For a meet-ing just 120 miles or 200 km north of Lagos, I was on the road for 11 hours – traffic jams, gigantic potholes, cows and goats blocking your way. Such burdens are common for African patients, who often have to travel a long way for medical treatment. With the scarce healthcare resources, new and innovative approaches to tackling wide-spread diseases are needed. Seeing the impact molecular technologies are having on the quality of life in Africa is hugely motivating for me.

January 2017: With AIDS still a big problem in many African countries, our HIV assays are vital, and our QuantiFERON-TB test for tuberculosis is really needed. In Nigeria, there’s a big demand for our forensic products and paternity tests too.

Our Dubai team is great – my boss, my colleagues, the work atmosphere. All totally focused on the challenge of creating something from scratch and improving people’s lives. That’s what drives me. The further I go, the better it gets.

FurtherAgnieszka Oles, Senior Account Manager Africa, Dubai

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INSIGHTS | QIAGEN breaks new ground

Research is generally a very slow process, but Bill Wang and his team have delivered a tidal wave of results fast in recent years: six patent applications, five papers, three digital sequencing product lines since 2013. For clinical researchers around the world, the most important breakthrough is proba-bly his work on digital sequencing technology, a novel meth-od that can count and differentiate individual DNA mole-cules during the next-generation sequencing (NGS) workflow.

The brain behind this technology grew up in China and acquired the nickname ’Bill’ in school English lessons. In 1998, he moved to Minneapolis where he earned a PhD at the University of Minnesota. He first worked for SAB ioscienc-es, a company acquired by QIAGEN in 2009, and gained a reputation as a courageous, unconventional mind. “I’m an out-of-the-box thinker,” Bill says, “but I’m also a perfectionist. I never take blind risks and do lots of thinking and calcula-tions before I undertake something.”

Bill’s pioneering work began with a critical evaluation of the first NGS panels: “They had certain deficiencies, for example it was impossible to differentiate between artificially induced bias and genuine mutations.” Bill and his team then analyzed academic papers on how molecular barcodes can be used to overcome this problem. “We saw molecular barcodes as a

potential game changer,” Bill says. “The challenge for us was to modify our system to fit these academic findings and scale them up for industrial implementation.” After QIAGEN sepa-rated research from development in Life Sciences, Bill and his team were able to concentrate all their efforts on their research work – with impressive results.

QIAGEN’s current NGS research panels are significantly more reliable than alternative technologies in detecting DNA mutations in cancer samples. Their sensitivity has been improved to <1 %, which allows detection of even extremely rare genetic variants or tumor fragments in large volume liq-uid biopsy samples. This improvement was validated by an extensive study Bill’s team conducted using 6,000 reported mutations. Besides this high analytical sensitivity in mutation detection, enhanced digital sequencing also brings the bene-fits of low noise and improved reproducibility of results. But Bill isn’t satisfied with the improvement to <1 %. He and his team are already pushing the accuracy of mutation detection in cancer samples towards 99.9 %, while also working to simultaneously analyze DNA and RNA via digital sequenc-ing, and applying the molecular barcode in other applica-tions, e.g. single cell analysis. “I like to work on difficult things,” Bill admits. “And most time I get them done.” Not least thanks to faster, out-of-the-box thinking.

FasterDr. Yexun (‘Bill’) Wang, Senior Director R & D, Frederick, MD.

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INSIGHTS | QIAGEN breaks new ground

Why is the seemingly boring topic of Regulatory Affairs so important?

We enable QIAGEN to sell its products. It’s as simple as that!

How did you get into Regulatory Affairs?

While working for a start-up supporting the clinical trials of pharma companies, we began developing companion diagnostic tests to help them obtain regulatory approval for their products in the U.S.

What exactly are companion diagnostics?

A companion diagnostic test provides information to a health care professional that is essential for the safe and effective use of a corresponding drug.

What does your job involve?

I’m responsible for a team that spends around 80 % of its time supporting projects that are devel-oping companion diagnostics. The regulatory requirements vary from country to country and are always changing. We need to prove to regulatory authorities that our products are safe and effective. Up to now, only the U.S. and Japan required co-approval of a companion diagnostic to register a corresponding drug. But in 2017, the new EU IVD regulation will contain specific companion diag-nostic requirements. Registration in the big markets can be complex, expensive and take a long time.

What do you see as one of your biggest successes?

In 2012, the FDA approved our therascreen KRAS test for detecting seven KRAS mutations in colorec-

tal cancer samples. Back in 2008, the FDA had lit-tle experience with the regulatory requirements for companion diagnostics but we worked collabora-tively with them and found creative ways of deal-ing with certain issues. Subsequently, the FDA has published two guidelines related to companion diagnostics. We played our part in this success story, which is ultimately about helping cancer patients live longer.

What kind of challenges do you face?

One big challenge is sample availability for devel-opment studies. For example, the FDA wants us to test 1,000 samples, but we only have 100 avail-able. That’s when creative thinking is needed.

What’s next on your pioneering horizon?

NGS plays a key role in personalized healthcare, and we want to enable any lab to take advantage of this powerful technology. The GeneReader NGS System was the first, but by far not the last milestone in this journey. We want to change the paradigm of NGS -based biomarker testing and not only make the entire workflow even simpler while ensuring the highest quality standards, but also develop new test panels that add further test-ing options in addition to the current ‘one test – one drug’ approaches. There are several align-ment and regulatory challenges that we need to address on the way, but overcoming these hurdles is what makes being a pioneer so rewarding.

SaferChris Bray, Director of Regulatory Affairs, Manchester

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INSIGHTS | QIAGEN breaks new ground

“People often ask me why I moved from academia to healthcare and from particle physics to data science. After obtaining an MSc in Milan, I did my PhD in particle physics at CERN, the European Organization for Nuclear Research. Those were exciting times. You must have heard of the Higgs Boson, that elusive elementary particle in the Standard Model of particle physics. It was first thought to exist in the 1960s but only recently has its presence been confirmed – and I was privileged to be part of that team. In my post-doc at MIT, I was looking for dark matter, the ‘Holy Grail of particle physics.’ After that, I kept on looking for the next challenge – and joined QIAGEN as a Senior Data Scientist in June 2015.

So what’s the link between particle physics and QIAGEN? Well, particle physics is basically all about interpreting masses of data and searching for anomalies. That gave me a good skill set for my present job. At CERN and MIT, I acquired the intellectual techniques you need to tackle a project in the right way – and those techniques are the same wherever the ‘Big Data’ comes from. I actually prefer to talk about ‘Smart Data’ because the focus is on handling data optimally rather than blind processing. My current job involves extracting insights from the masses of data we generate every day, e.g. about customers’ purchasing behavior. We have developed techniques to spot anomalies in data and play them back to our sales people. Our recently introduced, award-winning Sales Cockpit, an evo-lutionary operational analytics tool, is an incubator of new ideas and generator of insights into sales and customer behavior data. That way, we can tell our sales reps what a customer might be interested in buying, for example, or look at what cus-tomers have published in the research field, interpret that data and then predict their potential demand. We’re turning data into customer and business value.

And where are we heading? One way to look at data is to think of it as a deep, dark pool rich in insights awaiting the right analyst to be revealed. I always get amazing help from data visualization, which acts like a flashlight in this analogy and guides our research in the midst of such deep waters. Our vision is inspired by other data-driven giants like Amazon, where the challenge of analyzing vast amounts of retailing data was overcome so successfully it gave rise to a new business model where digital services play a primary role. I believe that QIAGEN is taking huge steps in digitizing the entire value chain and moving into a best-in-class position in our industry. We want to be the spearhead of QIAGEN’s new data-driven services that will improve our customers’ lives in the future, and ulti-mately empower them to access new scientific insights hidden in the many data sets collected by using our products.”

SmarterDr. Leonardo Di Matteo, Senior Data Scientist, Hilden

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INSIGHTS | QIAGEN breaks new ground

CORPORATE COMMUNICATIONS

For InvestorsPhone worldwide: + 49 2103 29 11711 Phone U.S.: + 1 240 686 2222 Email: IR@QIAGEN.COM IR.QIAGEN.COM

For MediaPhone worldwide: + 49 2103 29 11826 Phone U.S.: + 1 240 686 7425 Email: PR @ QIAGEN.COM PR.QIAGEN.COM

QIAGEN ON THE WEB

www.QIAGEN.com www.facebook.com / QIAGEN

www.twitter.com / QIAGEN www.linkedin.com / company / QIAGEN www.youtube.com / QIAGEN

Imprint

CREDITS

Concept and Design3st kommunikation, Mainz www.3st.de

PrintingEberl Print GmbH www.eberl.de

PhotographyAndreas FechnerRoberto WestbrookCelia PetersonKo Sasaki

EditorPrzemyslaw Jedrysik

PUBL ICATION DATE

March 2017

TRADEMARKS

Our name together with our logo is registered as a trademark in the United States and a number of other countries: QIAGEN®.

For a complete list of QIAGEN’s trade-marks and disclaimers, please refer to QIAGEN’s webpage under www.QIAGEN.com / trademarks_disclaimers.aspx

In this annual report, QIAGEN uses the term molecular diagnostics. The use of this term is in reference to certain countries, such as the United States, limited to prod-ucts subject to regulatory requirements. As of February 2016, QIAGEN molecular diagnostics products included 16 FDA (PMA approved or 510k cleared) products, 16 clinical sample concentrator products (13 kits and 3 instruments), 64 EU CE IVD assays, 18 EU CE IVD sample preparation products, 18 EU CE IVD instruments for sample purification or detection, 38 China CFDA IVD assays and 9 China CFDA IVD instruments.

This Annual Report may also contain trade names or trademarks of companies other than QIAGEN.

© 2017 QIAGEN, all rights reserved.

This document contains detailed financial information about QIAGEN prepared under generally accepted accounting standards in the U.S. (U.S. GAAP) and included in our Form 20-F annual report filed with the U.S. Securities and Ex change Commission. QIAGEN also publishes an Annual Report under IFRS accounting standards, which is available on our website at www.QIAGEN.com.

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QIAGEN at a Glance

Product Categories Percentage share of 2016 net sales

Molecular Diagnostics Physicians, hospitals and health care providers use QIAGEN technologies to save lives and fight disease. Our products support disease prevention such as screening women for risk of cervical cancer; profiling patients to pinpoint many diseases; personalized healthcare to guide treatment decisions; and point-of-need testing to provide on-site diagnosis.

Academia Researchers at life science laboratories around the world depend on QIAGEN to advance our understanding of the molecular basis of life. Customers include universities and research institutes.

Applied Testing Professionals in fields such as human identification and forensics, food testing and veterinary medicine use QIAGEN technologies in commercial applica-tions beyond human healthcare. Our products are helping to solve crimes, secure food supplies and detect potentially devastating livestock diseases.

Pharma Scientists in the phar maceutical and biotechnology industries look to QIAGEN to advance gene-based drug discovery and development, supporting the crea-tion of new medical breakthroughs.

Instruments are used with consumables, enabling customers to automate processes from the preparation of clinical samples to the delivery of valuable results.

87 %

13 %

Consumables and related productsare specialized kits that contain all necessary materials to support the use of sample and / or assay technologies as well as bioinformatics solutions for analysis, interpretation and reporting of biological data.

50 %Molecular Diagnostics

9 %Applied Testing

19 %Pharma

22 %Academia

Customer Classes Percentage share of 2016 net sales

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