Track 10 - April 5 – 7, 2016

Clinical Genomics

Determining Genomic Variation’s Contribution to Disease

Not all genetic variants are pathogenic. Data analysis from next-generation sequencing continues to improve researchers’ understanding of human health and disease. Track 10 addresses standards, methods, challenges and solutions that can maximize the utility of genome variant data in clinical settings.

Tuesday, April 5

7:00 am Workshop Registration and Morning Coffee

8:00 – 11:30 Recommended Morning Pre-Conference Workshops*
Intelligent Methods Optimization of Algorithms for NGS

12:30 – 4:00 pm Recommended Afternoon Pre-Conference Workshops*
Determining Genome Variation and Clinical Utility
DNA for Data Storage

* Separate registration required

2:00 – 6:00 Main Conference Registration


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Precision for Medicine5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, April 6

7:00 am Registration Open and Morning Coffee


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9:00 Benjamin Franklin Awards and Laureate Presentation

9:30 Best Practices Awards Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing


10:50 Chairperson’s Opening Remarks

David Heckerman, M.D., Ph. D., Distinguished Scientist, Microsoft Research, Microsoft

11:00 FEATURED PRESENTATION: Precision Medicine

Tim Harris, Ph.D., D.Sc., Venture Partner, SV Life Sciences

Before long, whole-genome sequencing will become routine and patients will have this information as part of their electronic medical record. The problem is how to associate changes in the genome with particular clinical phenotypes. This problem is starting to be tackled using information from GWAS. Examples of how this can help to find new drugs to treat patients with will be provided.
February 2016 Speaker Interview

11:30 FEATURED PRESENTATION: The Potential for IT to Enhance and Broaden the Use of Genetics in Clinical Care

Samuel (Sandy) Aronson, Executive Director, IT, Partners HealthCare Center for Personalized Genetic Medicine

Information technology can improve the effectiveness of genetic testing in clinical care, but such support is lacking in many environments. Efforts to address this issue will be discussed.

12:00 pm FEATURED PRESENTATION: Next-Generation Health Exploration and Analytics in Precision Healthcare

Yaron Turpaz, Ph.D., MBA, Chief Information Officer, Human Longevity, Inc.

Scott Skellenger, MBA, Vice President, Health Nucleus IT and Informatics, Human Longevity, Inc.

Human Longevity, Inc. (HLI) has built a cloud-based multifaceted genomic and phenotype knowledge management and application ecosystem that includes the HLI KnowledgebaseTM, the HLI Health NucleusTM client and clinician portals and the Health NucleusTM Avatar Application. The HLI KnowledgebaseTM currently includes over 10,000 integrated health records and the infrastructure to store, query and visualize genomic, metabolomic, microbiome and high-quality phenotype data in scientifically meaningful ways. As a key source to the KnowledgebaseTM, the Health NucleusTM suite of modalities and applications provides the broadest set of phenotype and medical data available, while the Integrated Avatar application puts the client in the center of their integrated genomic and phenotype results in a novel and engaging way new to the health exploration market. Together, these applications represent a state-of-the-art technology continuum supporting the comprehensive assembly and utility of the deepest and broadest genomics and phenotypic knowledge management solution available. This talk includes a brief introduction followed by an application demonstration of both the HLI KnowledgebaseTM and the Health NucleusTM Avatar Application.

12:30 Session Break

Paradigm 412:40 Luncheon Presentation I: Discovering Novel Structures in Large Cancer Data Sets from Both FMI and TCGA with SciDB

Eric Neumann, Ph.D, Vice President, Knowledge Discovery and Technology Innovations, Foundation Medicine, Inc.

Zachary Pitluk, Ph.D., Vice President, Life Sciences, Business Development, Paradigm4, Inc.

FMI has the largest genomics knowledge base of real-world clinical profiles. With such large data sets comes great analytic power. The SciDB platform enables FMI to integrate and align FMI proprietary data with TCGA data to enable deep analyses and comparisons for many different cancers. The combined results offer deeper insights into both tumor mechanisms and therapeutic responses of these cancers in patients.

1:10 Luncheon Presentation II (Sponsorship Opportunity Available) or Lunch on Your Own

1:40 Session Break


1:50 Chairperson’s Remarks

John E. Mattison, M.D., Chief Medical Information Officer, Assistant Medical Director, Southern California Medical Group, Kaiser Permanente; Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health GA4GH

1:55 Update of the Department of Veterans Affairs Precision Oncology (POP) Program

PodcastLouis Fiore, M.D., MPH, Executive Director, MAVERIC, Research, Veterans Affairs Boston Healthcare System

This presentation reviews the progress made to date on the VA Precision Oncology Program. The review includes progress on the informatics infrastructure and clinical success of the clinical trial matching, patient engagement, clinical prediction engine and sharing of genomic data components.

2:25 Connecting Rare Disease Patient Databases with the Matchmaker Exchange API

Orion Buske, Research Scientist, Department of Computer Science, University of Toronto; Genetics and Genome Biology Program, Hospital for Sick Children

Over 350 million people are affected by rare diseases, but many remain unsolved due to the challenge of finding additional families with the same disease. Using structured phenotype and genotype data, we are able to discover similar patients within patient databases such as PhenomeCentral. The Matchmaker Exchange API then enables patient matchmaking between such organizations, lowering the barrier for clinicians to finding similar patients.

2:55 An Ensemble Approach with Machine Learning to Detect Cancer Variants

Li Tai Fang, Senior Scientist, Bioinformatics, Research & Development, Bina Technologies

Accurately detecting somatic mutations in cancer is a challenging task due to tumor heterogeneity and sample contamination. To address this problem, Bina has developed SomaticSeq, a somatic mutation detection pipeline that integrates multiple cutting edge tools and machine learning. It has recently placed No. 1 and No. 2 in INDEL and SNV, respectively, during the last stage of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge.

3:10 Beyond the Cancer Genome - Computational Enablement of Holistic, Evidence-Driven Patient Care in Clinical Oncology

Laura Housman, Global Head, Therapeutics Business, SVP Corporate Development, Molecular Health, Inc.

In oncology, the molecular characterization of tumor genes as part of patient care is now synonymous with the concept of precision medicine. In this talk, I describe a computational platform that enables holistic clinical interpretation of multiple clinico-molecular parameters.

Microsoft Way3:25 Refreshment Break in the Exhibit Hall with Poster Viewing


4:00 The Next Phase for Healthcare Privacy and Security - Information Governance

Katherine Downing, Director, Practice Excellence, American Health Information Management Association

Security and privacy are of huge importance in business as our organizations continue to be the target of attack. Taking a holistic approach using Information Governance is the next generation for privacy and security. Information Governance is an organization-wide framework for managing information throughout its lifecycle and for supporting the organization’s strategy, operations, regulatory, legal, risk, and environmental requirements.

4:30 Securing Personal Genomic Data: The Potential of the Blockchain

Richard Shute, Ph.D., Consultant, Curlew Research

More people are having their genomes sequenced and letting sequencing companies use their data for research. What if people want to take back control of their own data? How would they confidently and securely manage their most highly personalized information? Blockchain technology (the global ledger behind Bitcoin) could be the answer to securely protecting genomic information and managing transactions associated with personal genomic data.

5:00 FEATURED PRESENTATION: The Role of Cybersecurity Leadership in This New World

Mansur Hasib, D.Sc., CISSP, PMP, CPHIMS, Cybersecurity Professor and Author, University System of Maryland

The world has changed. Technology drives the mission of the bio-IT world today. Yet this world has been the subject of some of the most sensational data breaches and even ransomware. What are we doing wrong? Technology certainly does not appear to be the answer. Yet, organizations appear prepared to dump money on the problem. In a highly interactive session, Dr. Hasib shares his views and analysis on the importance of people, leadership, and culture in cybersecurity.

5:30 – 6:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

Thursday, April 7

7:00 am Registration and Morning Coffee


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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced


10:30 Chairperson’s Opening Remarks

Zachary Pitluk, Ph.D., Vice President, Life Sciences, Business Development, Paradigm4, Inc.

10:40 Predicting Variants Likely to Cause Glanzmann Thrombasthenia

Yupu Liang, Ph.D., Director, Bioinformatics Program, Center for Clinical and Translational Science, Rockefeller University

As genetic testing becomes increasingly popular, patients and physicians are faced with tough questions: Does a particular genetic variation translate into a predisposition to an illness, or is it simply a benign rearrangement? This talk describes our experience on evaluating clinical impact of novel mutations on Integrin aggregation receptor from NGS data.

11:10 When Exomes Fail: Whole-Genome and Transcriptome Sequencing for Rare Disease Diagnosis

Monkol Lek, Ph.D., Senior Research Fellow, Analytic and Translational Genetics Unit, Massachusetts General Hospital

The current diagnosis rate from exome sequencing in our cohort of over 1,200 muscle disease samples is approximately 30-40%. This presentation focuses on how whole-genome sequencing and RNA sequencing can be applied to identify pathogenic variants.

11:40 Genomic Variants in Context and at Scale - Integrative Approaches to Predict Pathogenicity and Stratify Patient Cohorts

Janusz Dutkowski, Ph.D., Founder and CEO, Data4Cure, Inc.

Improved understanding of individual genomic variants may be possible if we study them at a systems level rather than in isolation. New integrative methods allow us to analyze many genomes together in the context of molecular networks and pathways to detect aberrations clustering in key cellular machinery. We use these approaches to develop multiscale maps of disease biology that span individual variants, genes, pathways and processes, and inform the identification of disease subtypes and biomarkers, as well as characterization of individual variants.

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing


1:55 Chairperson’s Remarks

Samantha A. Schrier Vergano, M.D., FAAP, FACMG, Division Director, Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters

2:00 What If Your Biology Holds the Key that Protects Others from Disease? Changing the Discourse around Sharing Health Data

Jason Bobe, Associate Professor, Director, Sharing Lab, Icahn Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine; Executive Director,

The protection of personal health and medical data has been recognized as an important goal for decades. The societal value of sharing data is immense, but to date paid much less attention. Designing a biomedical research enterprise that provides individuals access to their own data and improved options for sharing is paramount for addressing critical social concerns like better health, new therapies and disease prevention strategies.

2:30 Community-Driven Approaches to Support Variant Interpretation

Steven Harrison, Ph.D., Variant Scientist, Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine; Harvard Medical School

Improving our knowledge of genomic variation requires a massive effort in data sharing. Community-driven groups are working to incorporate shared data into variant assessment processes by guiding gene and disease specifications to the ACMG Interpreting Sequence Variant Guidelines, developing variant curation applications, aggregating shared data to inform the community of discrepancies and concordance in variant interpretations, and developing resources to facilitate data sharing.

3:00 Military Health Care Dilemmas and Genetic Discrimination: A Cautionary Tale of One Family’s Experience with Whole-Exome Sequencing

Samantha A. Schrier Vergano, M.D., FAAP, FACMG, Division Director, Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters

Whole-exome sequencing (WES) has increased our ability to analyze large parts of the human genome, bringing with it complicated ethical considerations. Secondary findings, results that convey genetic risk in asymptomatic individuals outside the initial indication for testing, can have significant social or legal implications. We discuss these issues in the experience with a family with careers in the U.S military, potentially jeopardizing their employment and privacy.

3:30 Development and Validation of an SNP Panel for Sample Identity Quality Control for Use in a High-Throughput Clinical Genetics Laboratory

Thomas B. Freeman, Senior Data Scientist, Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai

In clinical genetic testing, it is absolutely imperative that each patient receives the proper test results. We describe the development, implementation and validation of a sample identity SNP panel run in parallel with the DNA-Seq pipeline for sample identity verification. This workflow is integrated with LIMS and data analysis pipeline to provided automated sample identity quality control.

4:00 Conference Adjourns

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