European Biotechnology News Special 4/2013 - Genomic Therapies & Diagnostics

European Biotechnology News Science & Industry

April 2013

II Genomic Therapies & Diagnostics and Diagnostics

SPECIAL

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Diagnostics & Genomic Medicine Intro

genomic fingerprints that predict cancer recurrence. In the US, however, regulatory paths for the co-development of CDx and (bio)-therapeutics are split – and North America is the place to establish CDx. Most developers establish their tests first via the CLIA, and only later apply for market authorisation at the FDA as a diagnostic.

Genomic medicine – based on diagnostics

Truly personalised medicine

Genomics is destined to become a real game-changer in drug development. Although currently less than 1% of all prescribed drugs require a companion diagnostic test, that situation is changing rapidly. Almost a third of the compounds now in late-stage clinical development, 50% of the Phase I candidates and 60% of preclinical drugs use a companion diagnostic (CDx) to identify responders by means of genomic biomarkers. Accordingly, market intelligence firm Kalorama is predicting huge growth for Personalised Medicine in the coming years. Its analysts estimate that current sales of US$28bn will grow to US$42bn. Development is being driven

by CDx firms like Roche, Abbott, Dako, Genomic Health, Leica and Qiagen.

Drug Response Dx, which has developed a CDx test that identifies non-responders to TNFa blockers, a US$20bn market.

Yet the future lies in evaluating not single biomarkers, but entire panels of genes – a challenge Schriek says will be addressed by next-generation sequencing platforms.

In March at the AGBT meeting, Qiagen entered the club that includes Roche, Illumina and Life Technologies – companies that offer bench-top next-gen sequencers. Other providers like Agendia or Genomic Health provide chip-based technologies to detect

© Xue Li / Christine Khammash / ETH Zürich

“At the moment, we are still in the lag phase of market growth. But the log phase is straight ahead,” says Ulrich Schriek, VP Business Development at Qiagen, one of the most active players in the CDx field.

According to market studies performed by Vision Gain, the current US$1.5bn market will more than double to US$3.5bn within the next two years. The biggest market is still cancer (see p. 28), but Schriek sees also market potential in autoimmune and neurological diseases. In February, Qiagen acquired a minority stake in Berlin-based

Analysing the individual metabolic fingerprint in exhaled air could help in the personalised monitoring of disease.

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For researchers though, genomic profiling may be only the first step on the road to better patient stratification. At Europe’s largest meeting of proteome researchers, the Proteomic Forum in Berlin, Stanford scientist Mike Snyder showed what the future can provide: his personal “Snyderome”. For over 14 months, the researcher monitored his own genome, transcriptome, proteome and metabolome together with physiological and clinical data and observed the manifestation of his genetic prediabetes risk after he had two infections. According to Snyder, only integration of genomic and phenomic data into “integrative personal omics profiles” can deliver reliable predictions about the risk of developing a complex disease.

Label-free biomarker monitoring Diagnostics biosensors for non-invasive, label-free monitoring of biomarkers (see p.

36) can pave the way to the multi­parameter analyses required for measuring such complex patterns of intracellular changes. Several innovations were presented at the 8th German Biosensor Symposium in midMarch. At the meeting, researchers from the lab of André Skirtach (Potsdam) presented new gold-coated carbon nanotube probes that act as signal enhancers. They significantly improved intracellular detection of biomarker fingerprints by surfaceenhanced Raman scattering. According to the researchers, the current detection limit in fibroblasts is in the nanomolar range.

With the progress in the fields of biosensors and companion diagnostics, the value of diagnostics is set to rise when it comes to reimbursement. “The value of a companion diagnostic has to move closer to the value of a therapy,” believes Drug Response Dx cofounder Jörg-Michael Hollidt.

F

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Diagnostics & Genomic Therapies Personalised Medicine

“Big Pharma will have to change” Although it’s been a recurring theme and media buzzword for years now, many issues relating to “personalised medicine” remain unresolved. This year’s “Science to Market” conference and partnering event took the opportunity to bring attendees up-to-date on many of them with the “Trends in 2013”. Organised by the European Association of Pharma Biotechnology (EAPB) and PROvendis GmbH – the service provider for the patent marketing association of the universities of North Rhine-Westphalia – the event taking place for the fifth time on 5-6 March attracted more than 100 participants to Cologne in Germany. At the city’s Chamber of Commerce, researchers from academia and industry, technology transfer specialists and patent licensing agents also came together to catch up on viable new business ideas, which were presented in pitches just five minutes in length. size-fits-all-approach,” he added. Empty pipelines and ever­-stricter regulatory requirements have caused drug development costs to skyrocket from US$800m on average in 2000 to US$1.6bn in 2010. Despite increased efforts in R&D, the number of new drugs isn’t rising. The rise in generics production is one manifestation of the winds of change, said Wolf, and personalised medicine will be the other. According to him, its advantages are clear: higher success rates for pharmacological inter-

© PROvendis GmbH

“Picking up 2011’s topic ‘Personalised Medicine’ is definitely not a disadvantage,” clarified EAPB President Wieland Wolf.

“Within two years a lot of new things have happened in this rapidly-developing area of research.” ​​ The keynote address given by Wolf (for Thomas Gottwald from Tübingen University, who was ill) stressed that the road to personalised healthcare is set in stone – that there is no way to return to the blockbuster age. A lack of drug efficacy and patient compliance have doomed the “one-

The meeting’s popular social event took place at the “Bayer Kasino” in Leverkusen.

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ventions, therapies with fewer side effects and for the first time the advent of targeted instruments of disease prevention. However, biological systems are complex, and we still know too little about them. There are innummerable undiscovered target proteins, he said, as well as key elements and pathways regulating ADMET effects (absorption, distribution, metabolism, excretion and toxicity). Even more important is the selection and validation of suitable bio­ markers. This idea was taken up by Marion Rudolph from Bayer Pharma AG. Only 100 biomarkers are currently used in medicine, she claimed, although research papers suggest an astonishing 150,000 play biological roles. In her opinion, the reason for this discrepancy is the lack of a precise definition of what makes a good biomarker.

Rudolph suggested proactively integrating a biomarker strategy in the preclinical phase of a project, since search and inclusion are currently largely ad hoc. Whether as a surrogate endpoint in a clinical trial or as a benchmark for internal decision processes, she said this strategy needs to be guided by the intended use of the biomarker, following as she dubbed it “a holistic, fit-for-purpose approach”.

Cells as clinical trial biomarkers Andrea Groenewegen from Novartis Pharma AG agreed that separating patients into groups based on biomarkers depends first of all on finding reliable ones. She reported on a standard method in the lab – flow cytometry – that has made the leap from bench to bedside. A method used in clinical trials, she added, must be above all selective, robust, sensitive and inexpensive. Until recently, tests based on soluble materials such as ELISA (an immuno­assay) dominated clinical diagnostics. Thanks to flow cytometry, whole cells can now be used as reliable biomarkers that can provide information about pharmaco­dynamics, disease state or patient stratification. Novartis had to establish the validation of the method for clinical use from scratch, she emphasised, as no international guidelines existed. Now Groene­wegen and her team routinely use the method in the pharma giant’s trials.

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Diagnostics & Genomic Therapies Diagnostics

research group, the label-free technique is designed for use in Point-of-care (POC) set­ tings. Another format for POC biosensing of pathogens was presented by Sebastian Kersting (IBMT, Potsdam), who combined isothermal amplification of bacterial genes with their probe-based detection on lateral flow strips. Such DNA sensors are gaining importance in infection diagnostics because they shorten the time necessary for path­ ogen diagnosis from weeks (for antibody­based verification) to mere hours.

Biosensors extend diagnostic range Dr. Anke Kopacek, DiagnostikNetBB, Hennigsdorf

Bio­sensors are gaining ground in laboratory diagnostics. Frost & Sullivan is expecting the market to grow at annual rates of between 12%-14%, up from the current US$10bn to US$14bn by 2016. The largest segment (45%) is point-of-care testing (POC). An update on the latest developments in the field was provided at the 8th German BioSensor Symposium in mid-March. The developments presented there range from improved spectro­ scopic sensors to novel probes to practical medical applications.

“Biosensors for the specific detection of bio­ markers – particularly in a label-free format – are opening the door to an era of person­ alised medicine,” stressed the organiser of the symposium Fred Lisdat, who also chairs Biosystems Technology and is a member of the advisory board for Diag­nostikNetBB. The network of 35 research and indus­ try partners is dedicated to the develop­ ment of in-vitro diagnostics and biosensors.

One example presented at the meeting was new gold-coated carbon nanotube probes, which were developed in the lab run by An­ dré Skirtach (Potsdam). They significantly improve intracellular detection of biomar­

ker fingerprints by surface-enhanced Ra­ man scattering. According to the research­ ers, the current detection limit for sugars or proteins in fibroblasts was in the nanomolar range. Biosensors for selective detection of micro-organisms was another focus topic.

Researchers under Jürgen Popp from IPTH Jena presented an antibody-functionalised chip for the capture of pathogens that al­ lows their subsequent identification by Ra­ man spectroscopy. Till Bachmann (Edin­ burgh) presented a biosensor able to track the MRSA gene mecA down to concentra­ tions of just 10 pM using electrochemical impedance spectroscopy. According to his

Partners help overcome hurdles Whether simple test strips, lab-on-a-chip or multiplex sensors – biosensors can simul­ taneously detect several laboratory para­ meters at little expense, and only require small sample volumes. Since they often en­ able label-free detection, they can also re­ duce costs for consumables, and shorten the time needed to make a therapy decision. But despite their tremendous potential – espe­ cially in POC diagnostics – many biosensors never get past the development phase.

DiagnostikNet-BB includes renowned re­ search institutes and medium-sized diag­ nostic companies collaborating to engineer and manufacture marketable biosensors.

Network members include the TH Wildau, the Fraunhofer IBMT and Potsdam Universi­ ty, the Institute for High Performance Micro­ electronics (Frankfurt/O) and Berlin-based BST BioSensor Technology GmbH. In one project, the Biosystems Technology division at TH Wildau and Limetec Biotechnologies are aiming to replace the current Pandy test, which determines protein content in cere­ brospinal fluid, with a new rapid test for liq­ uor diagnostics. The Pandy test needs to be replaced because it requires toxic and mu­ tagenic phenol. The new approach provides a visual, easy-to-use, semi-quantitative test that utilises modified absorption properties of agglomerating nanoparticles. Such devel­ opment projects can be advanced rapidly in the network, and the Network Management team supports interested customers. D

© Jochen Zick

Contact

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Dr. Frauke Adams f.adams@diagnostiknet-bb.de www.diagnostiknet-bb.de

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Diagnostics & Genomic Medicine European OncoNetwork Consortium

Characterising colon and lung cancer Rosella Petraroli, Life Technologies Corp., Rome

Technology providers and users are increasingly collaborating in the development of new products or applications specifically tailored to customer needs. The Life Technologies Falcon team has been driving efforts like these since 2007, and in the process has successfully developed numerous applications and products.

Ever since Next-Gen sequencing platforms have become commercially available, the cancer research community has been pursuing opportunities to study cancer biomarkers with the new technology. “Semi­conductor sequencing in particular was a technological quantum leap compared with conventional Sanger sequencing methods,“ says Rosella Petraroli, a member of the Life Technologies Falcon team. “Researchers now believe that this is the right mo-

ment for cancer research to begin to really benefit from this technology, and want to find out how they could potentially use semiconductor sequencing for their studies”.

The project leader of the consortium adds that OncoNetwork’s task “was to bring the real experts from all over Europe together and let them work out the best solution. This resulted in a high quality of output that we were extremely excited about. It took just a one-day

Growth factors, e.g. EGF

Cell membrane

EGFR

meeting to decide on the concept for the panel, the first real team experience.

During the project, on every different level of collaboration, the tone was always honest and open – which was a key success factor for the community panel. The tremendous success and the quick turnaround were only possible because of the attitudes of those key opinion leaders.”

Most of the consortium members also appreciated the team spirit and productivity during the project. “We are sharing knowledge and technology, and that’s the main point,” said Aldo Scarpa, a professor of pathology at the University of Verona in describing his experience with the consortium. An associate professor and head of the laboratory for tumour genetics at Radboud University Nijmege Medical Centre in the Netherlands, Marjo­lijn J.L. Ligtenberg commented: “The big advantage is that you don’t have to test everything yourself, and you can learn from the experiences of others. For each single PCR reaction we’d probably need about 10 ng of DNA, and now we can do it in one reaction.”

Life Technologies’ OncoNetwork consor tium comprises eight cancer research groups from different translational research institutions in various European countries with many years of experience in adopting the latest DNA sequencing and genotyping technologies to pioneer colon and lung therapy research. The new panels enable the researchers to move from a single-mutation, multi-assay approach to a single-tube assay that covers 500 COSMIC mutations using just 10ng of DNA.

An overview of the project Kinase

Kinase

Cell proliferation

EGFR-triggered signalling in cancer proliferation

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Current methods used to study and screen cancer include Sanger sequencing (which is still regarded as the gold standard), quantitative PCR methods, (Strip)–hybridization, high-resolution melting and a few other molecular bio­ logy techniques. The challenges with these traditional methods are that laboratories usually have to run a high

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PATENT ATTORNEYS · ATTORNEYS-AT-LAW Munich · Basel · Berlin

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Diagnostics & Genomic Medicine

The Life Technologies Falcon team (left to right): Frank Opdam, Astrid Ferlinz, Alexander Sartori; Rosella Petraroli, Simone Günther, Alain Rico, Annelore Meissner-Müller, Nathalie Bernard. number of tests (lab flow), while relatively high amounts of DNA sample are also required in order to obtain comprehensive results. Sensitivity and speed of these current methods need to be improved to ensure quick results from a small amount of sample. “Sometimes it takes several days – or even weeks – to do sequencing and maybe real-time PCR or other techniques that allow us to identify single molecule alterations,” says Dr. Nicola Normanno. “And that only gives you indications of one anomaly,” adds Scarpa.“But now we know that a tumour is a hetero­geneous cell population, not only in morphological terms, but also molecular ones. So we need some overview of this phenomenon – this can be done using panels”.

“The big advantage is that you can detect mutations in a lot of genes at once, not just the particular ones you are looking for,” comments Dr. Ian Cree, a professor of pathology from the University of Warwick in the UK.

Panel content designed for high utility The OncoNetwork consortium has collaborated to select genomic content for the panel based on universal interest and clinical research relevance. The entire panel is contained in a single pool of primers, and is designed to cover the regions of interest with performance of at least 500x average base read depths for eight sam-

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ples on a single Ion 316™ Chip. The primer pool was designed and assembled using Life Technologies Ion AmpliSeq™ Designer, and requires only 10 ng of input DNA, accommodating the scarcity that is typical of FFPE starting material.

The OncoNetwork panel targets hotspots in the following genes: KRAS, EGFR, BRAF, PIK3CA, AKT1, ERBB2, PTEN, NRAS, STK11, MAP2K1, ALK, DDR2, CTNNB1, MET, TP53, SMAD4, FBXW7, FGFR3, NOTCH1, ERBB4, FGFR1, FGFR2.

Consortium-tested and verified panel using 155 unique samples “Lung and colon cancer are the most studied cancer types. Many biomarkers are identifiers in those cancers. Right now, biomarkers are only used for clinical decisions when the sample is meta­ static, which can often be too late for the patients. Based on the new sequencing platforms, the tendency in the future will probably be that molecular profiles will be run in parallel with the histological profiles, which will be far more specific,” comments head of the Life Technologies Falcon team Dr. Simone Günther.

During development and optimisation of this panel, the consortium member labs carried out thorough testing and verification using 155 unique samples that included FFPE lung and colon cancer control samples and previously characterised samples. To evaluate the quality of the panel, the consortium

labs performed three testing phases. In the first, all the labs tested the same five control samples. In phase two, each lab selected 10 samples previously characterised using orthog­onal platforms, and these were blindly tested by another lab from the consortium. In the third phase, each lab tested and selected 15 of their own samples. Based on the results, Life Technologies further optimised the panel, which was then re-tested by the consortium on a selected set of samples.

All the resulting sequences were analysed using Ion Reporter™ Software.

This dataset is available for download in the dataset section of the Ion Community at ioncommunity.lifetechnologies.com. The panel, combined with the Ion PGM™ System, enables easy, rapid and economic multi-gene screening of colon and lung cancer mutations using just 10 ng of DNA per sample. Dr. Pierre Laurent Puig comments: “To have these types of kits in our hands will accelerate the throughput of the characterisation of tumours and make personalised medicine a reality.“ With this comprehensive verification process, the consortium members demonstrated that detection accuracy of sequence variants using the Ion AmpliSeq™ Colon and Lung Cancer Panel was equal to or better than that obtained using existing methodologies. Dr. Orla Shields, a professor at Trinity College’s Institute of Molecular Medicine in Dublin, remarked on the relevance for the broader community: “To have a worked-out panel available for tapping into is tremendously beneficial.”

And the next project is already in the pipeline: “The great success of this project encouraged us to take similar approaches to other targets. The current consortium, now with global participation, is developing a fusion transcript panel that is based on our RNA-sequencing chemistry,” confirmed Rosella Petraroli.

D Contact Anke Werse Manager Marketing Communications Europe anke.werse@lifetech.com

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