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Wednesday, February 12 (Afternoon)

11:00 a.m. – 8:00 p.m.
Meeting Registration
Islands Ballroom Registration Desk

Plenary Session: Genomic Studies I
Eric Green, NHGRI, Chair

Islands Ballroom

4:30 p.m. – 4:40 p.m.
Opening remarks

4:40 p.m. – 5:10 p.m.
Aviv Regev, Broad Institute of MIT and Harvard
"Harnessing Variation Between Single Cells to Decipher Intra and Intercellular Circuits in Immune Cells"

5:10 p.m. – 5:40 p.m.
Jeanne Lawrence, University of Massachusetts Medical School
“Silencing Trisomy 21 for Genome Balance in Down Syndrome Stem Cells”

5:40 p.m. – 6:10 p.m.
Wendy Winckler, Novartis Institutes for BioMedical Research
“Next Generation Diagnostics for Precision Cancer Medicine”

6:10 p.m. – 6:40 p.m.            
Valerie Schneider, National Center for Biotechnology Information
“Taking Advantage of GRCh38”

7:00 p.m. – 10:00 p.m.
Welcome Reception
Sunset Terrace
Sponsored by Roche




Thursday, February 13 (Morning)

7:30 a.m. – 9:00 a.m.
Breakfast
Capri Ballroom

8:00 a.m. – 3:00 p.m.
Meeting Registration
Islands Ballroom Registration Desk

Plenary Session: Genetic Studies I
Heidi Rehm, Partners Healthcare Center for Personalized Genetic Medicine, Chair

Islands Ballroom

9:00 a.m. – 9:30 a.m.
Evan Eichler, University of Washington
“Advances in Sequencing Technology Identify New Mutations, Genes and Pathways Related to Autism”

9:30 a.m. – 10:00 a.m.
Aravinda Chakravarti, Johns Hopkins University School of Medicine
“Hirschsprung Disease”

10:00 a.m. – 10:30 a.m.
Karen Mohlke, University of North Carolina School of Medicine
“Regulatory Variants at GWAS Loci for Complex Metabolic Traits”

10:30 a.m. – 11:00 a.m.
Coffee Break
Collier Hall
Sponsored by WaferGen Biosystems, Inc.
                                               
11:00 a.m. – 11:20 a.m.
* Nolan Kamitaki, Harvard Medical School
“Three Proliferative Disorders Arise Overwhelmingly From Somatic Mutations in the PIK3CA Gene”

11:20 a.m. – 11:40 a.m.          
* Angela Brooks-Wilson, BC Cancer Agency
“Identifying Genetic Risk Factors for Familial Lymphoid Cancer”

11:40 a.m. – 12:00 p.m.
* Mia Levy, Vanderbilt University
“Design and Validation of an Oncology NGS Laboratory-Developed Test Focused on Actionable Mutations”




Thursday, February 13 (Afternoon)

12:00 p.m. – 1:00 p.m.
Illumina, Inc. Workshop
Complimentary Lunch Provided
Palms Ballroom

12:00 p.m. – 1:00 p.m.
Lunch
Sunset Terrace

1:00 p.m. – 2:30 p.m.
Poster Session with Coffee & Dessert
Collier Hall

Plenary Session: Evolutionary Genomics
Len Pennacchio, Lawrence Berkeley National Laboratory, Chair

Islands Ballroom

2:35 p.m. – 3:05 p.m.
Thomas Gilbert, University of Copenhagen, Denmark
“Next-Gen eDNA in Biodiversity Monitoring – Potential and Problems”

3:05 p.m. – 3:35 p.m.
Beth Shapiro, University of California, Santa Cruz
“Paleogenomes, Ice-age Megafauna, and Rapid Warming: How Genomes From the Past Can Help Predict the Consequences of the Future Climate Change”

3:35 p.m. – 4:00 p.m.
Coffee Break
Sponsored by WaferGen Biosystems, Inc.
Collier Hall

4:00 p.m. – 4:30 p.m.
James Noonan, Yale University
“Epigenomic Analysis in the Developing Human Embryo”

4:30 p.m. – 5:00 p.m.
Julian Catchen, University of Oregon
“The Population Genomics of Rapid Evolution in the Wild”

5:15 p.m. – 7:15 p.m.
Software Demo Session
Light Dinner Provided
Marco Island Hilton

5:00 p.m. – 7:30 p.m.
Dinner on your own




Thursday, February 13 (Evening)

Concurrent Session: Genomic Technologies Applications
John McPherson, Ontario Institute for Cancer Research, Chair

Islands Ballroom

7:30 p.m. – 7:50 p.m.
* Ulf Gyllensten, Uppsala University
“High Throughput Full-Length Sequencing for Microbial Pathogen Screening in Human Clinical Samples Using the Ion Proton and Pacific Bioscience RSII Technologies”

7:50 p.m. – 8:10 p.m.
* Andrea Kohn, University of Florida
“Single-Neuron Semiconductor RNA-seq with Nanofluidic Capture: Toward Genomic Dissection of the Complex Brains and Memory Circuits”

8:10 p.m. – 8:30 p.m.
* Jason Ladner, USAMRIID
“Haplotype-Level Characterization and Direct Sequencing of Viral Populations: the Promise of Single-Molecule Sequencing Platforms for Advancing Our Understanding of Viral Evolution”

8:30 p.m. – 8:50 p.m.
* Jianhong Hu, Baylor College of Medicine
“Solution-Based Enrichment for Whole Exome Sequencing Using Low Input DNA”

8:50 p.m. – 9:10 p.m.
* Stephen Fodor, Cellular Research, Inc.
“Digital Encoding of Cellular mRNAs Enables Precise and Absolute Gene Expression Analysis by Single-Molecule Counting”

9:10 p.m. – 9:30 p.m.
* Chinnappa Kodira, GE Global Research Center
“Combining Next Generation Sequencing (NGS) with a Revolutionary Multiplexed Immunohistochemistry Technology for Interrogation of Tumor Heterogeneity in Cancers”




Thursday, February 13 (Evening)

Concurrent Session: Cancer and Transplant Genomics
Sharon Plon, Baylor College of Medicine, Chair

Salons E & F

7:30 p.m. – 7:50 p.m.
* Hoon Kim, The University of Texas MD Anderson Cancer Center
“The Intratumoral Heterogeneity of Glioblastoma Suggests a Pivotal Role for Clonal Evolution”

7:50 p.m. – 8:10 p.m.
* James Hadfield, Cancer Research, UK
“Monitoring Cancer Genome Evolution with Circulating Tumour DNA Exome Sequencing”

8:10 p.m. – 8:30 p.m.
* Rebecca Kusko, BU School of Medicine
“SEQing the Shared and Distinct Transcriptional Events Underlying Lung Adenocarcinoma in Ever Smokers and Never Smokers”

8:30 p.m. – 8:50 p.m.
* Doron Lipson, Foundation Medicine
“Clinical Next Generation Sequencing (NGS) of Advanced Non-Small Cell Lung Cancer (NSCLC) Reveals a High Frequency of Genomic Alterations Including Novel Targetable Kinase Fusions”  
       

8:50 p.m. – 9:10 p.m.
* Somasekar Seshagiri, Genentech, Inc.
“Exome Sequencing Identified Oncogenic ERBB3 Mutations”

9:10 p.m. – 9:30 p.m.
* Brendan Keating, University of Pennsylvania and Children’s Hospital of Philadelphia
“Accurate High-Resolution HLA Imputation Using Genotype Data and the Use of HLA Donor-Recipient Matching to Prognosticate Solid-Organ Transplantation Outcomes”




Thursday, February 13 (Evening)

Concurrent Session: Epigenomics & Transcriptomics
Deanna Church, Personalis, Inc., Chair
Salons G through J
                                   
7:30 p.m. – 7:50 p.m.
* Melissa Fullwood, Cancer Science Institute
“Analysis of Gastric Cancer Epigenomes Using ChIP-exo”

7:50 p.m. – 8:10 p.m.
* Martin Hirst, BC Cancer Agency
“Persistent and Transient Epigenomic States in Mammary Gland Development”

8:10 p.m. – 8:30 p.m.
* Hiroyuki Aburatani, The University of Tokyo
“Single Cell RNA Sequencing Reveals Transition of Cell Populations with Epigenomic Switch in Cell Fate Determination Along Cardiomyocyte Differentiation”

8:30 p.m. – 8:50 p.m.
* Andrew Mungall, BC Cancer Agency
“Detection of Pathogen Messenger RNA and MicroRNA Transcripts in Human Cancer Transcriptomes”

8:50 p.m. – 9:10 p.m.
* Brian Haas, Broad Institute of MIT and Harvard
“Single Cell Developmental Genomics: Trinity-Enabled Single Cell Transcriptome Study Identifies New Regulators of Salamander Limb Regeneration”

9:10 p.m. – 9:30 p.m.
* Anna Kiialainen, F. Hoffmann-La Roche AG
“Ribosomal Profiling for Understanding the Translational Landscape of mTOR Signaling in Autism”  




Friday, February 14 (Morning)

7:30 a.m. – 9:00 a.m.
Breakfast
Capri Ballroom

Plenary Session: Genomic Studies II
Elaine Mardis, Washington University School of Medicine, Chair

Islands Ballroom

9:00 a.m. – 9:30 a.m.
David Botstein, Princeton University
“Yeast, Evolution and Cancer”

9:30 a.m. – 10:00 a.m.
Joe DeRisi, University of California, San Francisco
“NGS in the Context of Critical Care:  A Case Example”

10:00 a.m. – 10:20 a.m.
* Yutaka Suzuki, University of Tokyo
“Interactive Transcriptome Analysis of Malaria Patients”

10:20 a.m. – 10:50 a.m.
Coffee Break
Collier Hall

10:50 a.m. – 11:10 a.m.
* Stephan Schuster, Penn State University
“California Condor: Population Genomics and Informed Breeding Aid Species Conservation”

11:10 a.m. – 11:30 a.m.
* David Jaffe, Broad Institute of MIT and Harvard
“Assembly of Bacterial Genomes Using Long Nanopore Reads”

11:30 a.m. – 11:45 a.m.
* W.R. McCombie, Cold Spring Harbor Laboratory
"A Near Perfect de novo Assembly of a Eukaryotic Genome Using Sequence Reads of Greater than 10 Kilobases Generated by the Pacific Biosciences RS II”

11:45 a.m. – 12:00 p.m.
* Gene Myers, Max Planck Institute for Molecular Cell Biology and Genetics
“A de novo Whole Genome Shotgun Assembler for Noisy Long Read Data”




Friday, February 14 (Afternoon)

12:00 p.m. – 2:00 p.m.
Workshop - Enzymatics, Inc.
“Targeted Next Generation Sequencing for Oncology”

Complimentary Lunch Provided
Palms Ballroom

12:00 p.m. – 1:00 p.m.
Lunch
Sunset Terrace

Bronze Sponsor Workshops
Islands Ballroom

2:00 p.m. – 2:20 p.m.
Nabsys, Inc., Barrett Bready
“Correcting Genome Assemblies Using Semiconductor-Based, Single Molecule Genomic Mapping”

2:20 p.m. – 2:40 p.m.
Agilent Technologies, Bob Ohgami, Stanford University Medical Center
“New Agilent NGS Products – Pioneering Advances in NGS Clinical Research”

2:40 p.m. – 3:00 p.m.
Pacific Biosciences, Jonas Korlach
“No Assembly Required: Extremely Long Reads for Full-length Transcript Isoform Sequencing”

3:00 p.m. – 3:20 p.m.
NuGen Technologies, Inc., Zora Modrusan, Genentech, Inc.
“Single Primer Enrichment Technology (SPET) Enables Fast and Reliable Detection of Cancer Associated Somatic Mutations”

3:20 p.m. – 3:40 p.m.
Coffee Break
Collier Hall

3:40 p.m. – 4:00 p.m.
KAPA Biosystems, Eric van der Walt
“Directed Evolution of Enzymes Improves Next-Generation Sequencing Sample Preparation”

4:00 p.m. – 4:20 p.m.
PerkinElmer, Patrick Descombes, Nestle Institute of Health Sciences SA
“Tuning Library Generation With Sequencing Throughtput”

4:20 p.m. – 4:40 p.m.
NanoString Technologies, Inc., Joseph Beechem
“A Proven Technology for the Rapid Translation of Genomic Discovery to a Clinically Validated Assay: Multiplexed, Amplification-Free, Single-Molecule Digital Counting of DNAs, RNAs and Proteins”

4:40 p.m. – 5:00 p.m.
Fluidigm Corp., Marc Unger
“New Insight in System Biology Through Single-Cell Sequencing”

5:00 p.m. – 6:25 p.m.
Poster Session with Wine Reception
Sponsored by Illumina, Inc.
Collier Hall




Friday, February 14 (Evening)

6:25 p.m. – 7:25 p.m.
Dinner
Sunset Terrace

Concurrent Session: Genomic Technologies Development
Robert Lyons, University of Michigan, Chair

Islands Ballroom

7:30 p.m. – 7:50 p.m.
* David Wheeler, Baylor College of Medicine
“Patterns of Structural Rearrangement in Human Cancer Revealed by Ultra-Long Read Sequencing”

7:50 p.m. – 8:10 p.m.
* Hesaam Esfandyarpour, Genapsys, Inc.
“The GENIUS™ Platform: A Next Generation Sequencing Platform That Exceeds Quality and Cost Goals for Universal Deployment In and Out of Core Laboratory Environments”

8:10 p.m. – 8:30 p.m.
* Patrik Ståhl, CMB, Karolinska Institute
“Digital Pathological Analysis Through Spatially Resolved Gene Panels”

8:30 p.m. – 8:50 p.m.
* Sean McGrath, The Genome Institute at Washington University
“Pacific Bioscience Long-Read RNA-Seq for Gene Isoform Identification and de novo Gene Prediction”

8:50 p.m. – 9:10 p.m.
* John Havens, Integrated DNA Technologies
“Enhanced Molecular Inversion Probes for NGS Target Enrichment”

9:10 p.m. – 9:30 p.m.
* Zak Wescoe, University of California, Santa Cruz
“Error Rates for Nanopore Discrimination Among Cytosine and Four Epigenetic Variants Along Individual DNA Strands”




Friday, February 14 (Evening)

Concurrent Session: Computational Biology
Mike Zody, Broad Institute of MIT and Harvard, Chair

Salons E & F

7:30 p.m. – 7:50 p.m.
* Yaniv Erlich, Whitehead Institute for Biomedical Research
“Genome-Wide Analysis of Expression Short Tandem Repeats”

7:50 p.m. – 8:10 p.m.
* Sven Bilke, National Cancer Institute
“A Chromatin Structure Based Model Accurately Predicts DNA Replication Timing in Human Cells”

8:10 p.m. – 8:30 p.m.
* Ryan Layer, University of Virginia
“A 24-Hour, Open-Source Variant Calling Pipeline For Clinical Genome Interpretation”

8:30 p.m. – 8:50 p.m.
* Jason Chin, Pacific Biosciences, Inc.
“String Graph Assembly For Diploid Genomes With Long Reads”

8:50 p.m. – 9:10 p.m.
* Michael Lawrence, Broad Institute of MIT and Harvard
“Patterns of Mutation Across Cancer”

9:10 p.m. – 9:30 p.m.
* Neda Zamani, Uppsala University
“New Algorithms for de novo Metatranscriptome Assembly”




Friday, February 14 (Evening)

Concurrent Session: Medical, Animal and Microbial Genomics
Deanna Church, Personalis, Inc., Chair
Salons G through J

7:30 p.m. – 7:50 p.m.
* Petri Auvinen, University of Helsinki
“Taxonomically and Functionally Diverse Microbial Communities in Deep Crystalline Rocks of the Fennoscandian Shield”

7:50 p.m. – 8:10 p.m.
* Jim Mullikin, National Human Genome Research Institute
“Sequence Analysis of Plasmid Diversity Amongst Hospital-Associated Carbapenem-Resistant Enterobactericeae”

8:10 p.m. – 8:30 p.m.
* Shurjo Sen, National Human Genome Research Institute
“Increased TREML4 Expression and rs2803496 Genotypes are Associated with Coronary Artery Calcification”

8:30 p.m. – 8:50 p.m.
* Alexander Hoischen, Radboud University Medical Center
“Molecular Inversion Probe Based Resequencing Identifies Recurrently Mutated Genes in Intellectual Disability”

8:50 p.m. – 9:10 p.m.
* Ira Hall, University of Virginia
“The Landscape of Somatic Genome Variation in Single Neurons”

9:10 p.m. – 9:30 p.m.
* Jun Zhu, National Heart, Lung, and Blood Institute
“Global Intron Retention: A Novel Gene Regulatory Mechanism During T Cell Activation”




Saturday, February 15 (Morning)

7:30 a.m. – 9:00 a.m.
Breakfast
Capri Ballroom

Plenary Session: Technologies
Andre Marziali, University of British Columbia, Chair
                           
Islands Ballroom

9:00 a.m. – 9:05 a.m.
Opening Remarks

9:05 a.m. – 9:25 a.m.
* Jeffery Schloss, National Human Genome Research Institute
“Ambitious Goals, Concerted Efforts, Conscientious Collaborations – 10 Years Hence”

9:25 a.m. – 9:55 a.m.
Paul Blainey, Broad Institute of MIT and Harvard
“Highly Integrated Microfluidic Shotgun Library Construction”

9:55 a.m. – 10:25 a.m.
Mathias Ehrich, Sequenom, Inc., Sequenom, Inc.
“Non Invasive Prenatal Testing: A Showcase of High Volume Next Generation”

10:25 a.m. – 10:55 a.m.
Coffee Break
Capri Ballroom

10:55 a.m. – 11:15 a.m.
* Carlos Bustamante, Stanford University
“Any Way You Want It: Applications of Whole Genome Capture to Ancient DNA, Metagenomics, and Orthogonal Validation”

11:15 a.m. – 11:35 a.m.
* Joshua Burton, University of Washington
“Chromosome-Scale Scaffolding of de novo Genome Assemblies Based on Chromatin Interactions”

11:35 a.m. – 11:55 a.m.
* Fuchou Tang, Peking University
“Dissecting the Transcriptome and DNA Methylome Landscapes of Human Preimplantation Embryos and Embryonic Stem Cells”




Saturday, February 15 (Afternoon)

12:00 p.m. – 1:00 p.m.
Lunch
Sunset Terrace

12:00 p.m. – 1:00 p.m.
Ion Torrent by Life Technologies Workshop
“Ion Torrent Innovations Update”

Palms Ballroom

1:00 p.m. – 2:00 p.m.
QIAGEN GmbH Workshop
Islands Ballroom

Plenary Session: Genetic Studies II
Ken Dewar, McGill University and Genome Quebec Innovation Centre, Chair

Islands Ballroom

2:30 p.m. – 3:00 p.m.
Daniel MacArthur, Massachusetts General Hospital
“Functional Annotation at Scale:  Analysis of Genetic Variation From Over 50,000 Human Exomes”

3:00 p.m. – 3:30 p.m.
Greg Porreca, Good Start Genetics
“Applying Next-Generation DNA Sequencing to Carrier Screening in the Clinical Laboratory”

3:30 p.m. – 3:50 p.m.
* Anthony Griswold, University of Miami
“Integrated Analyses of Genome Wide Association and Targeted Sequencing Data Identify Loss of Function and Noncoding Regulatory Rare Variants Contributing to Autism Spectrum Disorder”

3:50 p.m. – 4:10 p.m.
* Obi Griffith, Washington University School of Medicine
“The Mutational Landscape of Hepatocellular Carcinoma in Non-Cirrhotic Livers”

4:10 p.m. – 4:30 p.m.
* William Greenleaf, Stanford University
“Transposition of Native Chromatin for Mulitmodal Regulatory Analysis and Personal Epigenomics”

           
4:30 p.m. – 5:00 p.m.
Closing Comments and Meeting Feedback

7:00 p.m. – 12:00 a.m.
Farewell Dinner Party
Sponsored by QIAGEN GmbH
Islands Ballroom




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