2013 Archived Content
Genomics in Medicine
Individualized Care for Improved Outcomes
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Tuesday, February 12
8:00 am Morning Coffee
8:10 Chairperson’s Remarks
Daniel MacArthur, Ph.D., Group Leader, Analytic and Translational Genetics Unit, Massachusetts General Hospital
8:15 Under the Hood of the 1000 Genomes Project
Mark A. DePristo, Ph.D., Associate Director, Medical and Population Genetics Analysis, Broad Institute of MIT and Harvard (on behalf of The 1000 Genomes Project Consortium)
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. By combining low coverage whole genome sequencing, targeted exome capture, and array genotype data on over 1000 individuals with a worldwide geographic distribution, we have generated an integrated map of over 40 million SNPs, short indels and larger structural variants in the human genome. I discuss the evolution of the next-generation sequencing (NGS) data underlying the public 1000 Genomes Project resource, from some of the earliest technologies of 2009 to today’s state-of-the-art data from Illumina, Life Technologies, and Pacific Biosciences. I highlight key NGS analytic advances originating from the Project, including the BAM and VCF file formats, multi-sample variation discovery and genotyping algorithms, large-scale validation assays using multiple independent technologies, and the integration of disparate variant types, from SNPs to structural variants, using a unified likelihood-based imputation framework. Finally I outline lessons learned from the Pilot and Phase I freezes and outstanding challenges in variant calling and integration for population-scale sequencing that are driving the future directions of the 1000 Genomes Project.
8:45 Delivering Genomic Medicine: Challenges and Opportunities
Heidi L. Rehm, Ph.D., FACMG, Assistant Professor, Pathology, BWH and Harvard Medical School; Director, Laboratory for Molecular Medicine, Partners Healthcare Center for Personalized Genetic Medicine
This talk will cover the speaker’s experience in offering clinical sequencing to patients, from disease-targeted panels to whole genome analyses as well as supporting the interpretation and delivery of those results to physicians. The talk will also cover approaches to data sharing within the community to enhance our understanding of the clinical utility of human genetic variation.
9:15 From Sequence Files to Physicians Report and the Tools Needed to Get ThereMartin Seifert, Ph.D., CEO, Genomatix SoftwareProviding actionable biology from NGS data in a report useful to the practicing clinician is difficult. Ensuring the report is accurate, reproducible, and reflects the biology of the patient is an even larger task. We will show examples of Genomatix' approach to these issues and how we successfully ensure a secure, accurate, and reproducible report, bridging the gap from sequencer to clinician.
9:30 Rapid Identification of Disease Causative Mutations
Ali Torkamani, Ph.D., Co-Founder & CSO, Cypher GenomicsRecent successes in clinical genome sequencing have highlighted the potential for sequencing to greatly improve molecular diagnosis and clinical decision-making. However, these successes have relied upon large bioinformatics teams and in-depth literature surveys. We will demonstrate how the Cypher Genomics software service can quickly return a small set of well-annotated genetic variants most likely to contribute to a patient's disease.
10:00 Coffee Break with Exhibit and Poster Viewing
10:25 Chairperson's Remarks
David Dimmock, M.D., Assistant Professor, Pediatrics, Medical College of Wisconsin
10:30 Sequence Data on Demand: Access, Visualization and Communication of Genome Sequence Data between Physicians, Researchers, and Patients
Sitharthan Kamalakaran, Ph.D., Senior Member, Research Staff, Philips Research North America
Many tools exist that process sequencing data to extract meaningful information, but they are disparate and are usable by bioinformatics professionals or trained researchers. The results of the analysis are communicated to the oncologist through a summary report which highlights the major findings. Furthermore, the findings are limited by what is known at the time the report is generated and is static. The clinician needs to order a new report everytime the literature is updated. We present our research that focuses on development of a software platform for decision support using clinical sequencing data. The key contribution of our platform is bridging the output of genomic analyses and the clinical workflow, enabling oncologists to make clinical decisions through patient-specific, context-sensitive access to sequencing data. Our work addresses three clinical needs in oncology: (1) Visualize in-silico gene tests and signatures in the course of a diagnostic work-up (2) Update relevant findings as they are reported in literature and allow for longitudinal analysis of multiple samples and (3) Assist in open-ended analyses of individual patient sequencing data under sequencing tumor board supervision.
11:00 Targeted Next Generation Sequencing in FFPE Tumor Samples: Distilling High Quality Information from Low Quality SamplesDiane Ilsley, Ph.D., Marketing Manager, Asuragen, Inc.SuraSeq™ PCR-based enrichment procedures enable accurate and sensitive mutation detection from nanogram inputs of challenging FFPE tumor DNA. Case studies will be presented that highlight the use of complementary NGS platforms and novel bioinformatics for discovery and confirmation studies.
11:30 Transitioning New Technologies from the Bench to the Bedside: Direct Fetal Testing Using Circulating Cell-Free DNA
Allan T. Bombard, M.D., CMO, Sequenom
Bringing a new clinical test to market is challenging, but can be accomplished successfully if one understands the proper processes, follows well-established Regulator pathways, and relies on good science. This presentation will address clinical test implementation of new tests in the US, using circulating cell-free DNA for noninvasive prenatal testing (NIPT) of fetal aneuploidy from maternal plasma as an example.
12:00 Moving Genomic Screening to the Clinic: Next Steps
Bruce R. Korf, M.D., Ph.D., Wayne H. and Sara Crews Finley Chair in Medical Genetics; Professor and Chair, Department of Genetics; Director, Heflin Center for Genomic Sciences, University of Alabama at Birmingham
Since the sequencing of the human genome there has been an expectation that a flood of advances would find their way to the clinic, and, indeed, the pace of translation of genomics to clinical application is accelerating.It is likely that the future of medical care will evolve by the convergence of two disruptive technologies – that of information science and genomics, which, in a sense can be viewed as one and the same.
12:30 pm Close of Symposium
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