Wednesday, February 15
11:00 am-8:00 pm
Meeting Registration - Island Ballroom Registration Desk
(Sponsored by Pacific Biosciences)
Utilization of New DNA Sequencing Technologies: An AGBT Tutorial Workshop
Island Ballroom
1:30-1:35 pm
Opening remarks
Ken Dewar, McGill University and Génome Québec Innovation Centre
Overview:
1:35-2:05 pm
Next-Generation Sequencing Technologies and Resources
Mark Adams, J. Craig Venter Institute
Applications:
2:10-2:30 pm
High Throughput Process Development in the Broad Institute Genome Sequencing Platform
Danielle Perrin, Broad Institute of MIT and Harvard
2:35-2:55 pm
Resequencing: Approaches & Challenges
Thomas Keane, The Wellcome Trust Sanger Institute
3:00-3:30 pm
Coffee break
3:30-3:50 pm
De Novo Assembly: From Single Cells to Metagenomes
Matt Blow, Joint Genome Institute
3:55-4:15 pm
Transcriptomics
Shawn Levy, HudsonAlpha Institute for Biotechnology
4:20-4:40 pm
Epigenomics
Olivier Elemento, Weill Cornell Medical College
4:45-5:05 pm
Sequencing as an Assay
Lisa White, Baylor College of Medicine
5:10-5:30 pm
Genotyping by Sequencing
Eric Johnson, University of Oregon
5:30-5:35 pm
Closing Remarks
Workshop Organizers:
Ken Dewar, (McGill University and Génome Québec Innovation Centre), George Grills (Cornell University), Len Pennacchio (Joint Genome Institute), and Michael Zody (Broad Institute of MIT and Harvard)
7:00-10:00 pm
Welcome Reception - Sunset Terrace
(Sponsored by Agilent Technologies)
Thursday, February 16 (Morning)
7:30-9:00 am
Breakfast - Capri Ballroom
(Sponsored by Agilent Technologies)
8:00 am-3:00 pm
Meeting Registration - Island Ballroom Registration Desk
(Sponsored by Pacific Biosciences)
Plenary Session: Clinical Translation of Genomics, (Chad Nusbaum, Broad Institute of MIT and Harvard, Chair)
Island Ballroom
9:00-9:10 am
Opening Remarks
9:10-9:45 am
Keynote Speaker: Lynn Jorde, University of Utah School of Medicine, “Whole-genome Sequencing, Mutation Rates, and Disease-gene Detection.”
9:45-10:15 am
Heidi Rehm, Partners Healthcare Center for Personalized Genetic Medicine, “Supporting Large Scale Sequencing in a Clinical Environment”
10:15-10:45 am
Lisa Shaffer, Perkin Elmer, Inc., “A Genotype First Approach to the Identification of New Chromosomal Syndromes”
10:45-11:10 am
Coffee Break – Collier Hall
(Sponsored by Illumina Inc.)
11:10-11:40 am
* Darrell Dinwiddie, Children's Mercy Hospital, “Initial Clinical Experience with Molecular Testing for >600 Severe Childhood Diseases by Target Enrichment and Next-Generation Sequencing”
11:40 am-12:10 pm
* Rong Chen, Personalis Inc., “Type 2 Diabetes Risk Alleles Demonstrate Extreme Directional Differentiation Among Human Populations, Compared to Other Diseases”
* ABSTRACT-SELECTED TALK
Thursday, February 16 (Afternoon)
12:10-1:10 pm
Agilent Technologies Workshop
(Complimentary Lunch Provided)
Palms Ballroom
12:10-1:10 pm
Lunch - Sunset Terrace
1:10-2:40 pm
Poster Session with Coffee & Dessert - Collier Hall
Plenary Session: Genomic Studies I (Len Pennacchio, Joint Genome Institute, Chair)
Island Ballroom
2:40-3:10 pm
Goncalo Abecasis, University of Michigan “Sequencing Thousands of Human Genomes”
3:10-3:40 pm
Ewan Birney, European Bioinformatics Institute, “ENCODE: Understanding Our Genome”
3:40-4:05 pm
Coffee Break - Collier Hall
4:05-4:35 pm
Charles Perou, The University of North Carolina at Chapel Hill, “Molecular Classification of Breast Tumors Using Gene Expression Profiling and Its Translation Into Clinical Practices”
4:35-5:05 pm
* Arend Sidow, Stanford University, “Breast Cancer Progression From Earliest Lesions to Clinically Relevant Carcinoma Revealed by Deep Whole Genome Sequencing”
5:05-7:00 pm
Pacific Biosciences Roundtable Discussion/Dinner
Palms Ballroom
5:05-7:30 pm
Dinner on your own
* ABSTRACT-SELECTED TALK
Thursday, February 16 (Evening)
Concurrent Session: Genomic Technology (George Grills, Cornell University, Chair)
Island Ballroom
7:30-7:50 pm
* Michael Ross, Broad Institute of MIT and Harvard, “Understanding Sequencing Bias Across Multiple Sequencing Technologies”
7:50-8:10 pm
* Jerrod Schwartz, University of Washington, “Infinipair: Capturing Native Long-range Contiguity by in situ Library Construction and Optical Sequencing Within an Illumina Flow Cell”
8:10-8:30 pm
* John Healy, GnuBio, Inc., “The GnuBIO Platforms: Desktop Sequencer for the Clinical and Applied Markets"
8:30-8:50 pm
* Megan Hersh, LaserGen, Inc., “Accurate Genome Sequencing of Pathogens Using Lightning Terminators™”
8:50-9:10 pm
* Andre Marziali, Boreal Genomics Inc/UBC, “Multiplexed Enrichment of Rare Alleles”
9:10-9:30 pm
* Sunney Xie, Harvard University, “Whole-Genome Amplification and Sequencing of Single Human Cells”
* ABSTRACT-SELECTED TALK
Concurrent Session: Medical Sequencing and Genetic Variation (Elaine Mardis, Washington University School of Medicine, Chair)
Salon E & F
7:30-7:50 pm
* Scott Devine, University of Maryland School of Medicine, “Natural Genetic Variation Associated with Exceptional Longevity in Humans”
7:50-8:10 pm
* Anthony Griswold, University of Miami, “Identification of Autism Risk Variants Through Targeted Next Generation Sequencing in a 1000 Case and 1000 Control Cohort”
8:10-8:30 pm
* Mait Metspalu, University of Tartu, “Shared and Unique Components of Human Population Structure and Genome-wide Signals of Positive Selection in South Asia”
8:30-8:50 pm
* Elliott Margulies, Illumina Cambridge Ltd., “Whole Genome Analysis of Monozygotic Twins and Their Parents: Accurate Detection of Rare Disease-Causing and De Novo Variants”
8:50-9:10 pm
* Wigard Kloosterman, University Medical Center Utrecht, “Mate-pair Sequencing Reveals Insight into the Mechanisms Driving Complex Genomic Rearrangements”
9:10-9:30 pm
* Shane McCarthy, Cold Spring Harbor Laboratory, “Family Based Whole Genome Sequencing of Schizophrenia”
* ABSTRACT-SELECTED TALK
Concurrent Session: Microbial Genomics (Ken Dewar, McGill University and Génome Québec Innovation Centre, Chair)
Salon G through J
7:30-7:50 pm
* Zhao Jin, Cornell University, “Using the Diversity within a Soil Metagenome to Infer Gene Sequence-Function Relationships”
7:50-8:10 pm
* Gregory Buck, Virginia Commonwealth University, “The Vaginal Microbiome: Disease, Genetics and the Environment”
8:10-8:30 pm
* Robert Edwards, San Diego State University, “Identification of Gene Repertoires Responsible for Persistence of a Global Pathogen Across Niche Dimensions by Ion Torrent Sequencing”
8:30-8:50 pm
* Chia-Lin Wei, Joint Genome Institute, “Metabolic RNA Labeling Coupled with Epigenetic Mapping Reveals the Dynamics of Transcriptome Control in Genetic Pathways of Algal Biodiesel Production”
8:50-9:10 pm
* Michael Zody, Broad Institute of MIT and Harvard, “Viral Genetics and Serotype-Specific Immunity Interact to Determine the Dynamics of Dengue Virus Disease Severity”
9:10-9:30 pm
* Seth Bordenstein, Vanderbilt University, “Targeted Genome Capture of Microbial Symbionts”
* ABSTRACT-SELECTED TALK
Friday, February 17 (Morning)
7:30-9:00 am
Breakfast - Capri Ballroom
Plenary Session: Genomic Studies and New Technologies, (Eric Green, NHGRI, Chair)
Island Ballroom
9:00-9:35 am
Keynote Speaker: Rick Myers, HudsonAlpha Institute for Biotechnology, “Genetics and Epigenetics of Human Gene Regulation”
9:35-10:05 am
Tom Gingeras, Cold Spring Harbor Laboratory, “Important Lessons from Complex Genomes”
10:05-10:25 am
* Geoffrey Smith, Illumina Cambridge Ltd., “The Miseq DNA Sequencing Platform and Application in Clinical Microbiology”
10:25-11:00 am
Coffee Break – Collier Hall
11:00-11:20 am
* Joseph Boland, National Cancer Institute, “Exome Sequencing on the PGM: Exome in a Day”
11:20-11:40 am
* Richard Roberts, New England Biolabs, “Characterization of DNA Methyltransferase Specificities Using Single-Molecule, Real-Time DNA Sequencing”
11:40 am-12:00 pm
* Clive Brown, Oxford Nanopore Technologies, “Single Molecule ‘Strand’ Sequencing Using Protein Nanopores and Scalable Electronic Devices”
* ABSTRACT-SELECTED TALK
Friday, February 17 (Afternoon & Evening)
12:00-1:00 pm
Lunch - Sunset Terrace
12:15-2:15 pm
Pacific Biosciences Workshop
(Complimentary Lunch Provided)
Palms Ballroom
Bronze Sponsor Workshops (Andre Marziali, University of British Columbia, Chair)
Island Ballroom
2:15-2:35 pm
Illumina, Inc., Elliott Margulies, “From Sample to Answer: Fast and Accurate Genome Sequencing for the Clinic”
2:35-2:55 pm
Caliper a Perkin Elmer Company, Kevin Hrusovsky, “Next Generation Technologies Enabling a Revolution in Medicine”
2:55-3:15 pm
Complete Genomics, Carlos Bustamante, Stanford University, “Population Genetic Inference in the Personal Era”
3:15-3:35 pm
RainDance Technologies, Andy Watson, “Recent Publication Successes: The Power of RainDance Targeted Sequencing”
3:35-3:55 pm
Advanced Analytical, Steve Siembieda, “Fragment Analyzer™- Streamlining Quality and Quantity Analysis of Nucleic Acids”
3:55-4:15 pm
NuGen Technologies, Inc., Elaine Mardis, Washington University School of Medicine, “Simplifying Genomic Sample Preparation with Digital Microfluidics”
4:30-6:00 pm
Poster Session with Wine Reception
(Sponsored by Agilent Technologies)
Collier Hall
6:00-7:00 pm
Dinner - Sunset Terrace
Concurrent Session: Cancer and Transcriptomes (Michael Metzker, Baylor College of Medicine, Chair)
Island Ballroom
7:30-7:50 pm
* Sean Grimmond, University of Queensland, “Cohort Based Genome Analyses of Primary Pancreatic Adenocarcinoma”
7:50-8:10 pm
* David Smith, Mayo Clinic, “Exome, Transcriptome and Methylome Analysis of Oropharygneal Cancers”
8:10-8:30 pm
* John McPherson, Ontario Institute for Cancer Research & Univ. of Toronto, “Evaluating Targeted Resequencing as a Diagnostic Tool: a Prospective Clinical Trial”
8:30-8:50 pm
* Samuel Levy, Scripps Translational Science Institute, “Somatic Detection in Tumor Genomes Facilitated by de-novo Assembly and Genome-to-Genome Mapping Employing Illumina and Ion Torrent Sequence Data”
8:50-9:10 pm
* Rebecca Kusko, Boston University School of Medicine, “Comprehensive Profiling of the Lung Transcriptome in Emphysema and IPF Using RNA-Seq”
9:10-9:30 pm
* Maria Mendez-Lago, British Columbia Cancer Agency, “Integrative Genomic Analysis of Diffuse Large B-cell Lymphoma”
* ABSTRACT-SELECTED TALK
Concurrent Session: Genome Biology (Steven Jones, British Columbia Cancer Agency, Chair)
Salon E & F
7:30-7:50 pm
* Chris Gunter, HudsonAlpha Institute for Biotechnology, “Measurement of T Cell Repertoire Diversity in the Peripheral Blood by Novel Multiplex PCR and Next-Generation Sequencing Methods”
7:50-8:10 pm
* Joanna Kelley, Stanford University, “Multi-Platform De Novo Assembly and Population Genomic Analysis of a Self-Fertilizing Hermaphroditic Fish, Kryptolebias Marmoratus”
8:10-8:30 pm
* Martin Hirst, BC Cancer Agency, “Epigenetic Contributions to Cell Identity in Human Breast”
8:30-8:50 pm
* R. Alan Harris, Baylor College of Medicine, “Evolutionary Genetics of Small Body Size and Dizygotic Twinning in Callitrichid Primates”
8:50-9:10 pm
* Michael Talkowski, MGH/Harvard Medical School/Broad Institute, “The Complex Genetic Architecture of Balanced Chromosomal Rearrangements Contributing to Autism and Other Neurodevelopmental Abnormalities”
9:10-9:30 pm
* Eric Schadt, Pacific Biosciences, “Integrating Kinetic Variation Events Identified From SMRT Sequencing Data with Other High-Dimension Molecular Profiling Data Uncovers Novel Regulatory Mechanisms”
* ABSTRACT-SELECTED TALK
Concurrent Session: Computational Biology (Mike Zody, Broad Institute of MIT and Harvard, Chair)
Salon G through J
7:30-7:50 pm
* Inanc Birol, Canada’s Michael Smith Genome Sciences Centre, “Establishing Correlation Networks Between Gene and miRNA Expression in Acute Myeloid Leukemia”
7:50-8:10 pm
* Yaniv Erlich, Whitehead Institute for Biomedical Research, “Surname Leakage From Whole Genome Sequencing Datasets”
8:10-8:30 pm
* Michael Schatz, Cold Spring Harbor Laboratory, “Metassembler: Improving de novo Genome Assembly”
8:30-8:50 pm
* David Jaffe, Broad Institute of MIT and Harvard, “Near-Finished Prokaryotic Genome Assemblies From a Low-Cost Combination of Short and Long Reads”
8:50-9:10 pm
* Joanna Racynska, UT Southwestern Medical Center, “Novel Method for Removal of Sequence Biases in ChIP-seq Data”
9:10-9:30 pm
* Eugene Yaschenko, NCBI/NLM/NIH, “Compression Strategies for NGS Data”
* ABSTRACT-SELECTED TALK
Saturday, February 18 (Morning)
7:30-9:00 am
Breakfast - Capri Ballroom
Plenary Session: Genomic Studies II (Deanna Church, NCBI, Chair)
Island Ballroom
9:00-9:35 am
Keynote Speaker: Michel Georges, University of Liege
9:35-10:05 am
* Jesse Gray, Harvard Medical School, “An RNA-Seq Snapshot Reveals Genome-Wide, in vivo mRNA Dynamics From Unperturbed Cells at Steady-State”
10:05-10:35 am
* Patrick Schnable, Iowa State University, “Gene Loss During a Domestication Bottleneck: Identification, Characterization and Genetic Mapping of Teosinte Genes That are Absent From the Maize Genome”
10:35-11:10 am
Coffee Break – Capri Ballroom
11:10-11:40 am
* Emily Hodges, Howard Hughes Medical Institute & Cold Spring Harbor Laboratory, “Directional Changes and Poised DNA Methylation Characterize Epigenetic Patterns That Underlie Lineage Identity of Human Blood Cell Methylomes”
11:40 am-12:10 pm
* James Galagan, Boston University, “Discovering the Regulatory Network of TB: Dissecting the Regulation of the Hypoxic Response”
* ABSTRACT-SELECTED TALK
Saturday, February 18 (Afternoon & Evening)
12:10-1:10 pm
Lunch - Sunset Terrace
12:10-1:10 pm
Roche Applied Science Workshop
(Complimentary Lunch Provided)
Palms Ballroom
Plenary Session: Genomic Studies III (Elaine Mardis, Washington University School of Medicine, Chair)
Island Ballroom
2:30-3:00 pm
Vivian Cheung, University of Pennsylvania, “RNA and DNA Sequence Differences in the Human Genome”
3:00-3:30 pm
Lior Pachter, University of California, Berkeley, “Streaming Algorithms for Analyzing and Maintaining RNA-Seq Data”
3:30-4:00 pm
Gerald Tuskan, Oak Ridge National Laboratory “Integrating Population-Scale Resequencing and Shotgun Proteomics Within the Populus Common Garden Experiment”
4:00-4:30 pm
Steve Benner, Foundation for Applied Molecular Evolution, “Reagent Innovations for Sensitive, Clean, and Highly Multiplexed Analysis of DNA”
4:30-5:00 pm
Closing Comments and Meeting Feedback
7:00-12:00 am
Farewell Dinner Party – Island Ballroom
(Sponsored by Roche Applied Science)
Island Ballroom
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