Cancer Sequencing Conference Header 

The paradigm for cancer diagnostics has shifted. Large scale genomic profiling of a tumor and then sending a patient down a treatment track has become commonplace and sequencing technology is no longer a main bottleneck. Cambridge Healthtech Institute's Inaugural Cancer Sequencing conference will focus on the newer pain point in cancer diagnostics - analyzing and making data actionable. At this event, the field's foremost experts will come together to discuss creative ways to distribute and explore next-generation sequencing (NGS) data. The disconnect between uncovering therapeutic targets and a lack of drugs will also be explored. This meeting will send attendees back to their organizations with ideas and solutions to move their cancer sequencing programs into the clinic.

Final Agenda


8:00 Registration and Morning Coffee

9:00 Chairperson’s Remarks

Andrew M. Hudson, MBChB BSc (Hons), MRCP, FRCR, Clinical Research Fellow, Cancer Research UK Manchester Institute, United Kingdom

9:05 KEYNOTE PRESENTATION: From NGS to a Truly Personalised Therapy

Hans LehrachHans Lehrach, Ph.D., Professor, Director Emeritus, Max Planck Institute for Molecular Genetics, Germany

We are in the middle of a revolution in Biology and Medicine, triggered primarily by the enormous increase in sequencing power (and concomitant decrease in sequencing cost) due to next generation sequencing techniques. While it took us in an international consortium more than ten years and between 1 and 3 billion US-Dollars to sequence the first human genome, we are now embarking on projects to sequence the genome of every cancer patients, as well as the genome and transcriptome of their tumors. To be able to use this flood of data we can generate on every patient to provide every patient with individually optimised medical care, we can use these data to model the patient and its tumour as interacting molecular models, which can be virtually ‘treated’ with ‘virtual drugs’ to be able to predict the effect and the side effects of ever possible therapy on the individual, to develop individually optimised therapies for every oncology patient. The development of such computer models of individual patients does however also offer new, revolutionary possibilities for virtualising drug development, increasing the number of drugs reaching the market, accelerating development, cutting costs, and cutting risk in the drug development, in turn, increasing the treatment options for patients.


9:35 Drivers, Passengers, and Biomarkers via Network Enrichment Analysis of Tumor Molecular Profiles

AndreyAlexeyenkoAndrey Alexeyenko, Ph.D., Research Scientist, Science for Life Laboratory, BILS, Karolinska Institute, SciLifeLab, Sweden

The characterization of molecular landscapes benefits from elevating analyses at the pathway level, i.e., quantifying alterations in functional modules (pathways) rather than those of individual genes. Our novel methods detect activation of such modules in a robust and unbiased way. Molecular features of cancer tumors are functionally interpreted via their network positions. This enables distinguishing driver mutations and discovering network-anchored biomarkers for specific phenotypes.

10:05 Inflammation Promotes Liver Cancer through Genomic Modifications Different from those Determined by Other Etiological Factors

FabioIannelliFabio Iannelli, Ph.D., Postdoc, IFOM Foundation – The FIRC Institute of Molecular Oncology, Italy

This presentation will illustrate how we used acquired genomic alterations, namely somatic point mutations and copy number variants (CNVs), to show that genetic heterogeneity of liver cancers correlates with their distinct pathogenesis and leads to different mechanisms of tumor progression. It will also provide evidence that solid tumors are not necessarily associated with mutational instability. Other key points like current challenges in CNV detection from exome sequencing data will be discussed.

10:35 Enriching Nucleic Acids for Next-Generation Sequencing Analyses of SNPs, CNVs, Gene Fusions and More

Heath_JoeJoe Don Heath, Ph.D., Vice President, Market Development-Diagnostics, NuGEN Technologies, Inc.

The novel Single Primer Enrichment Technology (SPET) and how it differs from existing target enrichment methods will be described. Sensitive variant detection from genomic DNA derived from fresh and FFPE tissues using 344 cancer-related genes will be demonstrated as well as utilization of SPET as a rapid, cost-effective screening tool for discovery of novel fusions and detection of known fusions with a panel of 500 cancer genes implicated in fusions events.

11:05 Coffee Break in the Exhibit Hall with Poster Viewing

11:45 Complete Pipeline for Clinical Reporting Of BRCA1/2 Massive Parallel Sequencing

Ettore Capoluongo, Ph.D., Professor, Clinical Biochemistry & Clinical Molecular Biology, Laboratory of Clinical Molecular Diagnostics, Laboratory Medicine, Policlinico Universitario “A. Gemelli”, Cattolica Del Sacro Cuore, Italy

12:15 FEATURED POSTER PRESENTATION: Incorporation of Breast Tumour Clinical Sequencing Supports Individualized Treatment in Oncology Practice

Armand Peeters, Ph.D., SHIP Project Manager, Breast Cancer Genomics, University of Stellenbosch

12:30 FEATURED POSTER PRESENTATION: COSMIC, the Catalogue of Somatic Mutations in Cancer

Minjie Ding, Senior Bioinformatican, Wellcome Trust Sanger Institute

SeraCare12:45 Luncheon Presentation: ACCUSEQ: Innovative Tools for Precision Cancer Diagnostics

Brown_TrevorTrevor W. Brown, Vice President, Precision Medicine, SeraCare

The promise of precision medicine depends upon accurate, precise and dependable use of next generation diagnostic techologies such as NGS and ddPCR. Adequate tools for assay development, validation and monitoring simply do not readily exist. SeraCare is developing new tools to help laboratories robustly characterize NGS assays and their analysis pipelines and to monitor routine performance, both within laboratories and between laboratories.

13:15 Session Break

14:15 Chairperson’s Remarks

Daniëlle A.M. Heideman, Ph.D., Clinical Scientist in Molecular Pathology; Associate Professor, Pathology, VU University Medical Center, The Netherlands

14:20 Performance of Amplicon-Based Next-Generation DNA Sequencing for Diagnostic Gene Mutation Profiling in Oncopathology

DanielleHeidemanDaniëlle A.M. Heideman, Ph.D., Clinical Scientist; Molecular Pathology; Associate Professor, Pathology, VU University Medical Center, The Netherlands

Next-generation sequencing (NGS) is an important technological advance which has helped in the identification of genetic determinants of cancer and the discovery of new diagnostic, prognostic and therapeutic biomarkers. NGS is now maturing to the point where it is being considered by many pathology laboratories for routine diagnostic use. I will present a comprehensive evaluation of amplicon-based NGS for diagnostic mutation profiling in oncopathology, with particular focus on FFPE specimens.


14:50 DNA Methylation in Human Variation, Disease Risk and Cancer

HeynHolgerHolger Heyn, Ph.D., Researcher, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), Spain

DNA methylation patterns are important to establish phenotypes, but little is known about their contribution to human variation and disease risk. We identified distinctly methylated genes with impact on susceptibility to certain diseases. DNA methylation differences could be traced back to genetic variation and we propose that interrogating the interplay between genetic and epigenetic code is providing new information about the biology of diseases.

15:20 Bioinformatics for Precision Medicine

Philippe Hupé, Ph.D., Deputy Director, Bioinformatics, Institut Curie, France

A seamless information system developed at Institut Curie which facilitates the data integration of genomics and clinical and tracks in real-time the processing of individual samples will be presented.

15:50 Refreshment Break in the Exhibit Hall with Poster Viewing

Considerations for Clinical Implementation

16:25 Chairperson’s Remarks

16:30 Whole Genome Sequencing from FFPE-Derived DNA Samples

Joanne Mason, Ph.D., Lead Scientist, BRC/NHS Oxford Molecular Diagnostics Centre, Oxford University Hospitals, United Kingdom

The easy availability of Formalin-Fixed Paraffin Embedded (FFPE) tissue makes it an ideal resource for molecular diagnostics. However, despite its stability and ability to preserve morphological information it is challenging to get high quality genetic material suitable for next-generation sequencing from FFPE samples. I will discuss how FFPE processing and extraction can be optimized to enable FFPE-derived DNA to be used for molecular diagnostics including for whole genome sequencing.

17:00 Evolution of Colorectal Cancer inferred from Deep-Sequencing Data

FrancescaCiccarelliFrancesca Ciccarelli, Ph.D., Associate Professor, Division of Cancer Studies, King’s College London, United Kingdom

In my talk I will present our method to rebuild the evolutionary history of cancer clones based on DNA deep sequencing data. I will then show its application to the reconstruction of the history of a set of colorectal cancers. Finally, I will highlight how this analysis can help in interpreting the biology of the single lesion and to help in the choice of the therapeutic intervention.

17:30 Discrepancies in Cancer Genomic Sequencing Highlight Opportunities for Driver Mutation Discovery

Andrew M. Hudson, MBChB BSc (Hons), MRCP, FRCR, Clinical Research Fellow, Cancer Research UK Manchester Institute, United Kingdom

Comparing genomics data from CCLE and COSMIC revealed marked discrepancies in the detection of missense mutations in identical cell lines (57.38% conformity). Reasons for this discrepancy include difficult sequencing of GC-rich regions (sequencing cold-spots), passaging effects and variation of dbSNP filtering. These data highlight that significant opportunities in discovering oncogenic mutations exist by optimizing the sequencing of GC-rich regions.

18:00 Welcome Reception in the Exhibit Hall with Poster Viewing

19:00 Close of Day Two


8:00 Registration and Morning Coffee

Considerations for Clinical Implementation (cont’d)

8:40 Chairperson’s Remarks

Kristin Pothier, Partner, Ernst & Young LLP, United States

8:45 Characterization of Pathways Involved in Colorectal Cancer Resistance to Neoadjuvant Chemoradiotherapy

Fernanda Koyama, Ph.D., Research Scientist, Molecular Oncology Center, Ludwig Institute for Cancer Research at Hospital Sirio-Libanes, Brazil

A number of works trying to classify patients have failed when approaching differential gene expression data as the only source of biological information. As the gene signatures rely on the sample set, there is an increasing need for a biological understanding to produce a signature in terms of pathways and biological processes. In this regard we promote a change in the way we look for sequencing data, specifically RNA-Seq, in an attempt to identify rectal cancer patients that are refractory to neoadjuvance treatment by identifying biological pathways involved in tumor resistance.

Natera9:15 A SNP-Based Massively-Multiplexed PCR Approach for Detection of SNAs and CNAs in Plasma, Tumor Tissues, and Single Cells

Hill_MatthewMatthew Hill, Ph.D., Vice President, Research and Development, Natera Inc.

Sensitive detection of large numbers of single nucleotide and copy number alterations (SNAs and CNAs) in cancer tissues and plasma has proven challenging. Leveraging methods proven in noninvasive prental testing, we demonstrate the ability to detect multiple SNAs with sensitivities to 0.01% and CNAs to 0.45% on multiple chromosome segments. In addition to plasma, this technology can be applied to fresh-frozen and FFPE tissue, as well as single cells.

9:45 PANEL INTRODUCTION: Global Innovation and Advancement of NGS

Kristin Pothier, Partner, Ernst & Young LLP, United States

As NGS transitions from the research bench to the clinic, NGS companies will need to develop new strategies while pharmaceutical companies will need to proactively develop partnerships in order to fully maximize the potential of personalized medicine. Lastly, established and emerging companies will need to innovate rapidly as next-next generation sequencing comes to fruition.

10:15 Coffee Break in the Exhibit Hall with Poster Viewing

10:45 PANEL DISCUSSION: Implementing NGS: Commercial and Clinical Laboratory Challenges

Moderator: Kristin Pothier, Partner, Ernst & Young LLP, United States

The NGS space is evolving rapidly, with new tests and new technologies coming online at an ever-accelerating pace. According to Richard Klausner, Chief Medical Officer of Illumina, we are moving out of the era of companion diagnostics and into the era of companion therapeutics. This panel will address:

• Getting started with NGS: from cost to assays
• Technological limitations
• Integration into routine workflow
• Developing the infrastructure needed to sustain an NGS program
• Partnerships


Sarah T. Bobulsky, Vice President, Life Sciences, Parthenon-EY
Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity (an MPLN company)

Joe Don Heath, Ph.D., Vice President, Market Development-Diagnostics, NuGEN Technologies, Inc.

11:45 Close of Conference