Wednesday, February 24th
11:00 am-8:00 pm
Meeting Registration
Island Ballroom Registration Desk
(Sponsored by Life Technologies)
Utilization of New DNA Sequencing Technologies: An AGBT Tutorial Workshop
Island Ballroom
1:30-1:35 pm
Opening Remarks
Len Pennacchio, Joint Genome Institute
1:35–2:00 pm
Overview of New Sequencing Technologies
Richard Gibbs, Baylor College of Medicine
Technology Platforms Session
2:05-2:25 pm
Sequencing Center Experience I
Debbie Nickerson, University of Washington
2:30-2:50 pm
Sequencing Center Experience II
Susan Lucas, Joint Genome Institute
2:55-3:25 pm
Coffee break
(Sponsored by Roche Applied Science & 454 Sequencing)
Applications Session
3:30-3:50 pm
Genomic Enrichment
Kelly Frazer, University of California San Diego
3:55-4:15 pm
Paired Ends for Structural Variation and Genome Assembly
Mike Snyder, Stanford University
4:20-4:40 pm
Transcriptome/ RNA-seq
Joshua Levin, Broad Institute
4:45-5:05 pm
ChIP-seq
Barbara Wold, California Institute of Technology
5:10-5:15 pm
Closing Remarks
Len Pennacchio, Joint Genome Institute
Workshop Organizers: George Grills (Cornell University), Len Pennacchio (Joint Genome Institute), and Michael Zody (Broad Institute of MIT and Harvard).
7:00 pm-10:00 pm
Welcome Reception
Sunset Terrace
(Sponsored by Life Technologies)
Thursday, February 25th (Morning)
7:30 am-9:00 pm
Breakfast
Capri Ballroom
(Sponsored by Agilent Technologies)
8:00 am-3:00 pm
Meeting Registration
Island Ballroom Registration Desk
(Sponsored by Life Technologies)
Plenary Session: Genomic Applications I (Chad Nusbaum, Broad Institute of MIT and Harvard, Chair)
Island Ballroom
9:00 am-9:10 am
Opening Remarks
9:10 am-9:45 am
Keynote Speaker: Debbie Nickerson, University of Washington, “Exome Resequencing: Next Generation Mendelian Genetics and Beyond”
9:45 am-10:15 am
Stacey Gabriel, Broad Institute of MIT and Harvard, “Applications of New Sequencing Technology to Medical and Cancer Genetics”
10:15 am-10:45 am
Michael Zody, Broad Institute of MIT and Harvard, “Detecting Signatures of Selection in Domestic Chickens by Whole Genome Re-sequencing”
10:45 am-11:10 am
Coffee Break – Collier Hall
(Sponsored by Roche Applied Science & 454 Sequencing)
11:10 am-11:40 am
Arend Sidow, Stanford University School of Medicine, “Extremely High-Resolution Nucleosome Organization Maps and Gene Expression Analysis in Purified Human Cells”
11:40 am-12:10 pm
Carlos Bustamante, Stanford University School of Medicine, “Complete genome sequencing and analysis of a diploid African-American and Mexican-American genome: implications for personal ancestry reconstruction and multi-ethnic medical genomics”
Thursday, February 25th (Afternoon)
12:15 pm-1:00 pm
Lunch
Sunset Terrace
12:15 pm-2:15 pm
Workshop – Roche Applied Science
(Complimentary Lunch Provided)
1:00 pm-2:30 pm
Poster Session with Coffee & Dessert – Collier Hall
(Sponsored by Roche Applied Science & 454 Sequencing)
Plenary Session: Genomics of the Microbiome (Steve Jones, British Columbia Cancer Agency, Chair)
Island Ballroom
2:30 pm-3:00 pm
Julie Segre, NHGRI, “Human Skin Microbiome”
3:00 pm-3:30 pm
David Wang, Washington University School of Medicine, “Metagenomic Approaches to Pathogen Discovery”
3:30 pm-4:00 pm
Coffee Break – Collier Hall
(Sponsored by Roche Applied Science & 454 Sequencing)
4:00 pm-4:30 pm
Thomas Briese, Columbia University, “New Frontiers in Molecular Diagnosis of Infectious Diseases”
4:30 pm-5:00 pm
Penny Chisholm, MIT, “From Single Cells to Global Metagenomics: What Prochlorococcus and its Phage Can Teach Us About Life”
5:00 pm-7:00 pm
Pacific Biosciences Roundtable Discussion
(Complimentary Dinner Provided)
Palm Ballroom
5:00 pm-7:00 pm
Dinner on your own
Thursday, February 25th (Evening)
Concurrent Session: Cancer Genomics (George Grills, Cornell University, Chair)
Island Ballroom
7:30 pm-7:50 pm
Elliott Margulies, NHGRI/NIH, “Sequencing and Analysis of Matched Tumor and Normal Genomes from a Melanoma Patient”
7:50 pm-8:10 pm
Andy Mungall, BC Cancer Agency, “Base-Pair Resolution of Somatic and Germline-Derived Genome Rearrangement Breakpoints in Follicular Lymphoma”
8:10 pm-8:30 pm
Timothy Triche, Childrens Hospital Los Angeles, “Unraveling the Complexity of Primary and Metastatic Ewing’s Sarcoma Using Helicos Single Molecule Sequencing”
8:30 pm-8:50 pm
Christopher Maher, University of Michigan Medical School, “Transcriptome Sequencing of ETS Rearrangement Negative Prostate Cancers Reveals Novel Class of Gene Fusions”
8:50 pm-9:10 pm
Ian Bosdet, BC Cancer Agency, “Mutational Profiling of Pre and Post-Treatment Lung Tumors Using Whole-Transcriptome Sequencing and Targeted Sequence Capture”
9:10 pm-9:30 pm
Ogan Abaan, NIH/NCI, “Identification of Novel Cancer Mutations in Sarcomas”
Concurrent Session: Genome Informatics (Michael Zody, Broad Institute of MIT and Harvard, Chair)
Salon E & F
7:30 pm-7:50 pm
Inanc Birol, BC Cancer Agency, “High-Throughput Analysis of Transcriptome Assemblies”
7:50 pm-8:10 pm
Kristian Cibulskis, Broad Institute of Harvard and MIT, “μTector: Accurate Somatic Mutation Detection in Whole Genome and Exome Capture”
8:10 pm-8:30 pm
David Gordon, University of Washington, “Consed and Next_phred for Next-Gen Sequencing”
8:30 pm-8:50 pm
Jeffrey Reid, Baylor College of Medicine, “miRNA Precursor Variants in Schizophrenia and Their Possible Effects on Expression and Function”
8:50 pm-9:10 pm
Samuel Payne, J. Craig Venter Institute, “Proteogenomics: Refining and Improving Genome Annotations”
9:10 pm-9:30 pm
Michael Stromberg, Boston College, “Novel Mobile Element Insertions Detected in Human Populations”
Concurrent Session: Genome Variation (Deanna Church, NIH/NLM/NCBI, Chair)
Salon G through J
7:30 pm-7:50 pm
Vanessa Hayes, Children’s Cancer Institute Australia for Medical Research, “Complete Bushmen and Bantu Genomes from Southern Africa”
7:50 pm-8:10 pm
Patrick Schnable, Iowa State University, “Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content”
8:10 pm-8:30 pm
M.R. Hoehe, Max Planck Institute for Molecular Genetics, “Molecular Haplotype Sequencing: MHC and Beyond”
8:30 pm-8:50 pm
Daniel MacArthur, Wellcome Trust Sanger Institute, “Loss-of-Function Mutations in Healthy Human Genomes: Implications for Clinical Genome Sequencing”
8:50 pm-9:10 pm
Jinkuk Kim, Whitehead Institute, “Allelic Imbalance Sequencing Reveals That Single-Nucleotide Polymorphisms Frequently Alter MicroRNA-Directed Repression”
9:10 pm-9:30 pm
Stephan Zuchner, University of Miami Miller School of Medicine, “Gene Identification Via Exome Sequencing In Hereditary Spastic Paraplegia Families”
Friday, February 26th (Morning)
7:30 am-9:00 am
Breakfast - Capri Ballroom
Plenary Session: Genomic Applications II (Eric Green, NHGRI, Chair)
Island Ballroom
9:00 am-9:35 am
Keynote Speaker: James Downing, St. Jude Children’s Hospital, "The Molecular Pathology of Acute Leukemia"
9:35 am-10:05 am
Elaine Mardis, Washington University School of Medicine, “Single Molecule Sequencing to Detect and Characterize Somatic Mutations in Cancer Genomes”
10:05 am-10:35 am
Levi Garraway, Harvard Medical School, “Applications of “Next-Generation” Sequencing in Translational Oncology”
10:35 am-11:00 am
Coffee Break – Collier Hall
(Sponsored by Roche Applied Science & 454 Sequencing)
11:00 am-11:30 am
Stan Nelson, UCLA, “Whole Human Cancer Genome Sequencing: Progress Towards Common Application”
11:30 am-12:00 pm
Vamsi Mootha, Harvard Medical School, “Defining the Genetic Basis of Human Mitochondrial Disorders”
Friday, February 26th (Afternoon & Evening)
12:00 pm-1:00 pm
Lunch - Sunset Terrace
(Sponsored by Complete Genomics, Inc.)
12:00 pm-2:00 pm
Workshop – Life Technologies
(Complimentary Lunch Provided)
2:00 pm-3:00 pm
Workshop – RainDance Technologies
3:00 pm-4:00 pm
Workshop – Pacific Biosciences
Concurrent Session: Genome Technology (Michael Metzker, Baylor College of Medicine, Chair)
Island Ballroom
4:30 pm-4:50 pm
Jonas Korlach, Pacific Biosciences, “Direct, Single-Molecule, Real-Time (SMRT™) RNA Sequencing”
4:50 pm-5:10 pm
Tanja Woyke, DOE Joint Genome Institute, “One Microbial Cell, One Complete Genome”
5:10 pm-5:30 pm
Alex Parker, Amgen, Inc., “A Nanoliter-Scale PCR Strategy for Efficient Preparation of Highly-Multiplexed 454 Sequencing Libraries from Sub-Nanogram Quantities of Template DNA”
5:30 pm-5:50 pm
Yaniv Erlich, Cold Spring Harbor Laboratory, “DNA Sudoku”
5:50 pm-6:10 pm
Han Cao, BioNanomatrix, Inc. “Development of Dynamic Single Molecule Analysis Platform Using Nanochannel Array”
6:10 pm-6:30 pm
Stephen Jackson, NanoString Technologies, Inc. “The nCounter™ System: Digital Gene Expression Analysis Downstream of Next Generation Sequencing Results”
Concurrent Session: Transcriptome Genomics (Gina Costa, Life Technologies, Chair)
Salon E & F
4:30 pm-4:50 pm
Joshua Levin, Broad Institute of MIT and Harvard, “Strand-Specific RNA-Seq Methods: Development, Evaluation, and Application to Yeast Antisense Transcription Discovery”
4:50 pm-5:10 pm
Brian Haas, Broad Institute of MIT and Harvard, “Application of mRNA-seq to Genome Annotation and Differential Expression Within Three Schizosaccharomyces Species”
5:10 pm-5:30 pm
N. Cloonan, The University of Queensland, “Translation-State RNAseq of Human Embryonic Stem Cells Using Paired-End Sequencing”
5:30 pm-5:50 pm
Manuel Garber, Broad Institute of MIT and Harvard, “Annotating LincRNA Transcripts Using Targeted Sequencing”
5:50 pm-6:10 pm
Christopher Mason, Weill Cornell Medical College, “Developmental Changes in Human Neocortical Transcriptome Revealed by RNA-Seq”
6:10 pm-6:30 pm
Shurjo Sen, NHGRI/NIH, “Transcriptome Profiling of ClinSeq Participants by Massively Parallel Short-Read DNA Sequencing”
Concurrent Session: Genome Biology (Lisa Stubbs, University of Illinois, Chair)
Salon G through J
4:30 pm-4:50 pm
Brian Weiner, Broad Institute of MIT and Harvard, “Comparative Analysis of Mycobacterium Tuberculosis”
4:50 pm-5:10 pm
Geoff Smith, Illumina, Inc., “Genomic Diversity Among Drug Sensitive and Multidrug Resistant Isolates of Mycobacterium Tuberculosis with Identical DNA Fingerprints”
5:10 pm-5:30 pm
Francois Vigneault, Harvard Medical School, “Tracking Human Immune Response Dynamics Through VDJ Sequencing”
5:30 pm-5:50 pm
Rupali Patwardhan, University of Washington, “Massively Parallel, High-Resolution Functional Dissection of Regulatory Elements with Next Generation DNA Synthesis and Sequencing”
5:50 pm-6:10 pm
Lauren McNew, Battelle Memorial Institute, “Detecting Signatures of Deliberate Selection in the Biological Warfare Simulant Bacillus Atrophaeus”
6:10 pm-6:30 pm
Chia-Lin Wei, Genome Institute of Singapore, “Dynamic Changes in the Human Methylome During Differentiation”
6:30 pm-7:30 pm
Poster Session with Wine Tasting
(Sponsored by Illumina, Inc.)
9:15 pm
(Fireworks sponsored by Pacific Biosciences)
Saturday, February 27th (Morning)
7:30 am-9:00 am
Breakfast
Capri Ballroom
Plenary Session: Genomic Applications III (Andre Marziali, University of British Columbia, Chair)
Island Ballroom
9:00 am-9:35 am
Keynote: Henry Erlich, Roche Molecular System, "Applications of Next Generation Sequencing: HLA typing with the GSFLX system."
9:35 am-10:05 am
Jesse Gray, Harvard Medical School, “Widespread RNA Polymerase II Recruitment and Transcription at Enhancers During Stimulus-Dependent Gene Expression”
10:05 am-10:35 am
Bing Ren, UCSD, “Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells”
10:35 am-11:00 am
Coffee Break – Capri Ballroom
(Sponsored by Roche Applied Science & 454 Sequencing)
11:00 am-11:30 am
Joseph Puglisi, Stanford University School of Medicine, “The Molecular Choreography of Translation”
11:30 am-12:00 pm
Yardena Samuels, NHGRI, “Mutational Analysis of the Melanoma Genome”
Saturday, February 27th (Afternoon)
12:00 pm-1:15 pm
Lunch
Sunset Terrace
12:00 pm-1:00 pm
Workshop – Illumina, Inc.
(Complimentary Lunch Provided)
1:00 pm-2:00 pm
Workshop – Complete Genomics Inc.
“Complete Genome Sequencing for Human Disease Studies”
Plenary Session: New Genomic Frontiers (Elaine Mardis, Washington University School of Medicine, Chair)
Island Ballroom
2:00 pm-2:30 pm
Rade Drmanac, Complete Genomics, Inc., “Technology and Infrastructure Development for Sequencing Thousands of High Quality, Complete Human Genomes for Large-Scale Disease Studies”
2:30 pm-3:00 pm
Patrice Milos, Helicos BioSciences Corp., “A True Unbiased View of Genome Biology: Helicos Single Molecule Sequencing”
3:00 pm-3:30 pm
Eric Schadt, Pacific Biosciences Inc., “Integrating DNA and RNA Variation Data to Elucidate Molecular Networks Underlying Biological Hydrogen Production by Bacteria”
3:30 pm-4:00 pm
Joseph Beechem, Life Technologies, “Single Molecule Real-Time Nucleic Acid Sequencing-by-Synthesis Using Quantum-dot (Qdot™) Nanocrystal and Dye-Labeled DNA Polymerases with FRET-Based Detection”
4:00 pm-4:30 pm
Jonathan Rothberg, ION Torrent Systems, “Post-Light Sequencing with Semiconductor Chips”
7:00 pm-12:00 am
Farewell Dinner Party
(Sponsored by Illumina, Inc.)
Island Ballroom
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