TCGC: Clinical Genome ConferenceTCGC: Clinical Genome ConferenceTCGC: Clinical Genome Conference
2014 Archived Content

TCGC: The Clinical Genome Conference

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Wednesday, June 11

8:00 am Morning Coffee


NGS Is Guiding Therapies 

8:30 Chairperson’s Opening Remarks

Jimmy Lin, M.D., Ph.D., President, Rare Genomics Institute

8:35 Next-Generation Sequencing Approaches for Identifying Patients Who May Benefit from PARP Inhibitor Therapy

Mitch RaponiMitch Raponi, Ph.D., Senior Director and Head, Molecular Diagnostics, Clovis Oncology

The following questions will be addressed: What biomarkers should we be focusing on to identify appropriate patients who will likely benefit from PARP inhibitors? How can we apply next-generation sequencing technologies to identify all patients who will respond to the PARP inhibitor rucaparib? What regulatory challenges are we faced with for approval of NGS companion diagnostics?

9:05 Whole-Genome and Whole-Transcriptome Sequencing to Guide Therapy for Patients with Advanced Cancer

Glen WeissGlen J. Weiss, M.D., MBA, Director, Clinical Research, Cancer Treatment Centers of America

Treating advanced cancer with agents that target a single-cell surface receptor, up-regulated or amplified gene product or mutated gene has met with some success; however, eventually the cancer progresses. We used next-generation sequencing technologies (NGS) including whole-genome sequencing (WGS), and where feasible, whole-transcriptome sequencing (WTS) to identify genomic events and associated expression changes in advanced cancer patients. While the initial effort was a slower process than anticipated due to a variety of issues, we demonstrated the feasibility of using NGS in advanced cancer patients so that treatments for patients with progressing tumors may be improved. This lecture will highlight some of these challenges and where we are today in bringing NGS to patients.

9:35 The Universal BRCAness Screening (UBS) Program

Akbari_MohammadMohammad Akbari, M.D., Ph.D., Assistant Professor, Dalla Lana School of Public Health, University of Toronto, Scientist, Women's College Research Institute

Currently, there are three major clinical gaps in using BRCA testing: 1) It is usually offered to patients after they have been diagnosed with cancer; 2) It is often offered to patients when their treatment has been completed and the test results cannot be used for their treatment; 3) It is not offered to all individuals who are at risk for hereditary cancer. The long term solution for addressing all these gaps is to have a universal population-based cancer genetic test for BRCAness screening. The WaferGen Seq-ReadyTM targeted sequencing solution shows excellent potential to become a reliable and cost effective solution for this type of high throughput population-based test.

10:05 Coffee Break in the Exhibit Hall with Poster Viewing

Data Mining 

Keynote Presentation

10:45 Translating a Trillion Points of Data into Therapies, Diagnostics and New Insights into Disease

Atal ButteAtul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children’s Hospital; Co-Founder, Personalis and Numedii

There is an urgent need to translate genome-era discoveries into clinical utility, but the difficulties in making bench-to-bedside translations have been well described. The nascent field of translational bioinformatics may help. Dr. Butte’s lab at Stanford builds and applies tools that convert more than a trillion points of molecular, clinical and epidemiological data—measured by researchers and clinicians over the past decade—into diagnostics, therapeutics and new insights into disease. Dr. Butte, a bioinformatician and pediatric endocrinologist, will highlight his lab’s work on using publicly available molecular measurements to find new uses for drugs, including drug repositioning for inflammatory bowel disease, discovering new treatable inflammatory mechanisms of disease in type 2 diabetes and the evaluation of patients presenting with whole genomes sequenced.

11:30 DGIdb – Mining the Druggable Genome

Malachi GriffithMalachi Griffith, Ph.D., Research Faculty, Genetics, The Genome Institute, Washington University School of Medicine

In the era of high-throughput genomics, investigators are frequently presented with lists of mutated or otherwise altered genes implicated in human disease. Numerous resources exist to generate hypotheses about how such genomic events might be targeted therapeutically or prioritized for drug development. The Drug-Gene Interaction database (DGIdb) mines these resources and provides an interface for searching lists of genes against a compendium of drug-gene interactions and potentially druggable genes. DGIdb can be accessed at
IN THE NEWS (Bio-IT World | Nov. 22, 2014) - Learn more>>>  

12:00 pm Analysis of Oncomine(R) Knowledgebase to Identify NFE2L2 Pathway as a Novel Therapeutic Opportunity in Multiple Cancer Types

Khazanov NickolayNickolay A. Khazanov, Ph.D., Bioinformatics Scientist, Life Sciences Solutions, Thermo Fisher Scientific

Late-stage drug attrition rates in oncology remain higher than in other therapeutic areas. To reduce attrition, it is critical to identify appropriate drug targets and preclinical models. NGS analysis of cancer exomes provides a comprehensive assessment of somatic mutations, genomic rearrangements and copy number alterations; however, discerning often rare driver events from abundant passenger aberrations remains a challenge. To maximize the value of NGS, it is imperative to develop data analysis/interpretation solutions that accurately assess genomic aberrations, delineate driver alterations from passengers, annotate alterations for clinical relevance and integrate alterations by gene and pathway. Here, we present our potential framework for the systematic analysis of thousands of NGS samples as well as expertly curated oncology data for the purpose of identifying potential drug targets, which was used to rank genes through an assessment of driver genomic aberrations, associations with patient survival and potential actionability. Using this framework, we found supporting evidence implicating NFE2L2 as an oncogene.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own


NGS Is Redefining Genomics 

2:00 Chairperson’s Remarks

Marc Salit, Ph.D., Group Leader, Biochemical Science and Multiplexed Biomolecular Science, National Institute of Standards and Technology (NIST)

Keynote Presentation

2:05 Extra-Cellular RNA: A Window into New Biological Phenomena

David GalasDavid Galas, Ph.D., Principal Scientist, Pacific Northwest Diabetes Research Institute

In recent years it has become clear that various body fluids, outside cells, contain a wide range of RNA molecules (exRNA). Included are microRNAs, but many others types are represented as well. Stable circulation of RNA is facilitated by binding to certain proteins and/or protection within microvesicles and exosomes. While the function of cell-to-cell communication for these molecules is implicated by new evidence, the roles of most of them remain ambiguous. Recent evidence that microbial RNA is included in the exRNA spectrum in plasma raises a number of intriguing questions and heightens awareness of the need to understand the origins, fates and functions of the wide range of circulating RNA.

2:50 Harnessing Single-Cell -Omics to Reveal Diversity and Mosaicism in the Brain

Jennifer ErwinJennifer Erwin, Ph.D., Research Scientist, Fred H. Gage Laboratory, Genetics, The Salk Institute for Biological Studies

It is now known that retrotransposition of LINE-1 mobile elements contributes genomic diversity to mouse and human neurons. The unique composition of genetic mosaicism present in the brain may contribute to disease and also the behavior differences observed between genetically identical organisms. Because each individual neuron has the potential to have a unique genome, single-cell approaches are essential to measure and observe this genomic diversity, which is obscured in bulk samples. We will present data using single-cell genome and transcriptome sequencing to characterize the nature and regulation of neuronal genome mosaicism.

3:20 Enabling DNA Sequencing for Routine Clinical Care
Roever_StefanStefan Roever, CEO & Founder, Genia Technologies
There is no debate that genetic information is needed to truly realize the promise of personalized medicine. The problem is that today’s DNA sequencers cost anywhere from $50K - $1M and utilize a complex workflow that does not lend itself to clinical utility. Genia is using standard semiconductor technology to enable massively parallel, single molecule DNA sequencing. The company has developed a versatile nanopore-based platform which allows for single molecule, electrical, real-time analysis. 

3:50 Refreshment Break in the Exhibit Hall with Poster Viewing

4:25 Analysis of Germline Genome Variation and Mosaic Variants in Somatic Tissues Using Integrated NGS- and PCR-Based Technology

Alexander UrbanAlexander Eckehart Urban, Ph.D., Assistant Professor, Department of Psychiatry and Behavioral Sciences and Department of Genetics (secondary), Center for Genomics and Personalized Medicine, Stanford University School of Medicine

We are investigating genome variants that affect brain development and function. We study germline variants that are associated with mental disorders and also the occurrence of genomic mosaicism in somatic tissue. We are using both tissue culture models and primary tissue samples in combination with next-generation sequencing-based approaches, targeted-capture and whole-genome, respectively, as well as PCR-based methods such as standard PCR, qPCR and digital droplet PCR.

Keynote Presentation

4:55 From Big Data to Network Medicine

John QuackenbushJohn Quackenbush, Ph.D., Professor, Dana-Farber Cancer Institute and Harvard School of Public Health; Co-Founder and CEO, GenoSpace

The sequencing of the human genome promised to open new ways of understanding human disease. New sequencing technologies, which have driven the cost of whole-genome sequencing to a few thousand dollars, have begun to make this vision a reality, allowing not only an integrated view of disease but also new ways of modeling the processes that drive it. We will describe methods that have begun to allow the creation of disease-specific network models and to extend these to modeling processes in individual patients.

5:40 Close of Day

5:30-6:00 Dinner Short Course Registration

6:00-9:00 Dinner Short Course (see Short Courses for details)


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