2016 Advances in Genome Biology and Technology Meeting

JW Marriott Orlando, Grande Lakes

Orlando, Florida

Scientific Program

Wednesday, February 10, 2016

11:00 a.m. – 8:00 p.m. Meeting Registration Mediterranean Ballroom Registration Desk
Plenary Session: Genomics I (Mike Zody, New York Genome Center, Chair) Mediterranean Ballroom
5:00 p.m. – 5:30 p.m. Sean Eddy, Harvard University “Genome evolution: the future of deciphering the past”
5:30 p.m. – 6:00 p.m. David Haussler, University of California, Santa Cruz “Global sharing of better and more genomes”
6:00 p.m. – 6:30 p.m. Pardis Sabeti, Harvard University “Genomic surveillance of microbial threats”
6:30 p.m. – 7:00 p.m. Matthew Sullivan, The Ohio State University “Unveiling viral ocean: towards a global map of ocean viruses”
7:00 p.m. – 10:00 p.m. Welcome Reception Valencia Terrace & Lawn


Thursday, February 11 (Morning)


7:30 a.m. – 9:00 a.m. Breakfast Coquina North
8:00 a.m. – 3:00 p.m. Meeting Registration Mediterranean Ballroom Registration Desk
Plenary Session: Clinical Genomics (Sharon Plon, Baylor College of Medicine, Chair) Mediterranean Ballroom
9:00 a.m. – 9:30 a.m. Sam Aparicio, British Columbia Cancer Research Centre “Clonal evolution and cancer medicine at single cell resolution”
9:30 a.m. – 10:00 a.m. Charles Chiu, University of California, San Francisco School of Medicine “Metagenomic deep sequencing for diagnosis of infectious diseases”
10:00 a.m. – 10:30 a.m. Luis Diaz, Johns Hopkins Hospital “Novel therapeutic and diagnostic applications of somatic mutations in solid tumor malignancies”
10:30 a.m. – 11:00 a.m. Coffee Break Coquina North* Denotes abstract selected talk
11:00 a.m. – 11:20 a.m. *Franck Rapaport, Memorial Sloan Kettering Cancer Center “Integrated DNA/RNA profiling for somatic alterations in adult B-cell ALL”
11:20 a.m. – 11:40 a.m. *John Martignetti, Icahn School of Medicine at Mount Sinai “A pre-operative, diagnostic gene panel for guiding primary treatment choices in endometrial cancer: advancing beyond the decades-old technology of dilation and curettage (D&C)”
11:40 a.m. – 12:00 p.m. *Katia Sol-Church, Nemours A.I. duPont Hospital for Children “Baratela Scott Syndrome is a rare recessive skeletal dysplasia caused by a new class of compound heterozygous defects”


Thursday, February 11 (Afternoon)

12:05 p.m. – 1:05 p.m. Qiagen Workshop (Complimentary Lunch Provided) Coquina North
12:00 p.m. – 2:00 p.m. AGBT Lunch Valencia Terrace & Lawn
1:10 p.m. – 2:10 p.m. Roche Workshop Coquina North
Plenary Session: Evolutionary Genomics (Ken Dewar, McGill University and Génome Québec Innovation Centre, Chair)Mediterranean Ballroom
2:15 p.m. – 2:45 p.m. Eske Willerslev, University of Copenhagen “How we developed our biological and cultural diversity”
2:45 p.m. – 3:15 p.m. Felicity Jones, Friedrich Miescher Laboratory of the Max Planck Society “Dissecting the genomic basis of adaption in natural stickleback populations”
3:15 p.m. – 3:45 p.m. Coffee Break Lower Level/Sponsor’s Promenade*Denotes abstract selected talk
3:50 p.m. – 4:10 p.m. *Beth Shapiro, University of California, Santa Cruz “Passenger pigeon paleogenomes reveal the genomic consequences of long-term extremely large effective population sizes”
4:10 p.m. – 4:30 p.m. *Daniel Rokhsar, DOE Joint Genome Institute “When genomes collide: the allotetraploid Xenopus laevis”
4:30 p.m. – 4:50 p.m. *Stephan Schuster, Nanyang Technological University “Why ethnicity matters for precision medicine”


Thursday, February 11 (Evening)


5:00 p.m. – 7:00 p.m. Poster & Software Demo – Wine & Cheese Reception Coquina North and South
5:00 p.m. – 7:30 p.m. Dinner on your own
Concurrent Session: Genome Technology(Ken Dewar, McGill University and Génome Québec Innovation Centre, Chair) Mediterranean Ballroom/General Session Room
7:30 p.m. – 7:50 p.m. Mariateresa de Cesare, University of Oxford “Unlocking the heterogeneity of the human transcriptome utilizing the ONT MinION TM”
7:50 p.m. – 8:10 p.m. Joel Malek, Weill Cornell Medical College in Qatar “AVA-Seq: a method for all-versus-all protein interaction mapping using next generation sequencing”
8:10 p.m. – 8:30 p.m. Israel Steinfeld, Agilent Technologies “Improved methods and analysis tools for efficient CRISPR/Cas genome editing”
8:30 p.m. – 8:50 p.m. James Hadfield, University of Cambridge “Progress in developing a nanopore rapid cancer MDX test”
8:50 p.m. – 9:10 p.m. GiWon Shin, Stanford University “STR-Seq: a massively parallel microsatellite sequencing and genotyping technology”
9:10 p.m. – 9:30 p.m. Jiabin Tang, Cedars-Sinai Medical Center “Non-invasive somatic mutation profiling of liquid biopsies using capture-based next generation”
Concurrent Session: Transcriptomics(Martin Hirst, University of British Columbia, Chair) Mediterranean Salons 6-8
7:30 p.m. – 7:50 p.m. Sten Linnarsson, Karolinska Institutet “Molecular anatomy of the mouse brain by single-cell RNA-seq”
7:50 p.m. – 8:10 p.m. Stefania Giacomello, SciLifeLab “Spatially resolved gene expression in the meristem of model angiosperm and gymnosperm species enabled by spatial transcriptomics”
8:10 p.m. – 8:30 p.m. Chia-Lin Wei, Lawrence Berkeley National Laboratory “Polycomb mediated 3-dimensional chromatin organization directs transcriptional silencing through extensive promoter looping and prevalent lncRNA association”
8:30 p.m. – 8:50 p.m. Max Seibold, National Jewish Health “Large-scale single cell transcriptome sequencing of the human airway epithelium”
8:50 p.m. – 9:10 p.m. Mohan Bolisetty, The Jackson Laboratory
 “Determining exon connectivity in complex mRNAs using the MinION sequencer”
9:10 p.m. – 9:30 p.m. Masako Suzuki, Albert Einstein College of Medicine “Metastable epialleles in mouse epialleles are defined by targeting of 5- hydroxymethylcytosine and increased DNA methylation entropy”
Concurrent Session: Genomic Medicine (Sharon Plon, Baylor College of Medicine, Chair) Palazzo Ballroom Salon E
7:30 p.m. – 7:50 p.m. Alexander Hoischen, Radboud University Medical Center “smMIP based BRCA1 and BRCA2 re-sequencing in a clinical setting”
7:50 p.m. – 8:10 p.m. Stephen Lincoln, Invitae “Clinically important variants are often technically challenging for NGS: implications for NGS methods, validation and confirmation”
8:10 p.m. – 8:30 p.m. Brendan Keating, University of Pennsylvania “Detection and validation of signatures of liver transplantation rejection diagnoses and successful minimization of immunosuppression from serum miRNA profiles”
8:30 p.m. – 8:50 p.m. Richard Moore, BC Cancer Agency Genome Sciences Centre “Whole genome and transcriptome sequencing for personalized cancer therapy: lessons learned from first 300 cases”
8:50 p.m. – 9:10 p.m. Matthew Bainbridge, Baylor College of Medicine “Neptune: an automated pipeline for clinical reporting of carrier-tests”
9:10 p.m. – 9:30 p.m. Lei Huang, Peking University “Live Births with monogenic diseases and chromosome abnormality simultaneously avoided by NGS-based PGD/PGS with linkage analyses”


Friday, February 12 (Morning)


7:30 a.m. – 9:00 a.m. Breakfast Coquina North
Plenary Session: Technology I (John McPherson, University of California, Davis, Chair) Mediterranean Ballroom
9:00 a.m. – 9:30 a.m. Jay Flatley, Illumina “Beyond the $1000 Genome-What’s next for NGS?”
9:30 a.m. – 10:00 a.m. Anne Wojcicki, 23andMe “Making discoveries on the 23andMe platform”* Denotes abstract selected talk
10:00 a.m. – 10:20 a.m. *William Greenleaf, Stanford University “Single-cell chromatin accessibility reveals principles of regulatory variation”
10:25 a.m. – 10:55 a.m. Coffee Break Lower Level/Sponsor’s Promenade
11:00 a.m. – 11:20 a.m. *Jason Bielas, Fred Hutchinson Cancer Research Center “Deep profiling of complex cell populations using scalable single cell gene expression analysis”
11:20 a.m. – 11:40 a.m. *Paolo Piazza, University of Oxford “Linking epigenetics and gene expression at single cell levels using SMART-ATAC-seq”
11:40 a.m. – 12:00 p.m. *Andrea Kohn, University of Florida“Epitranscriptomic landscape of single neurons: insights in the memory mechanisms”


Friday, February 12 (Afternoon)


12:00 p.m. – 2:00 p.m Roche/PacBio SMRT® Sequencing Workshop (Complimentary Lunch Provided) Coquina North
12:00 p.m. – 2:00 p.m. AGBT Lunch Valencia Terrace & Lawn
Plenary Session: Genomics II (Eric Green, NHGRI, Chair) Mediterranean Ballroom
2:00 p.m. – 2:30 p.m. Harold Varmus, Weill Cornell Medicine and New York Genome Center “What genomics is teaching us about carcinogenesis”
2:30 p.m. – 3:00 p.m. Eddy Rubin, DOE Joint Genome Institute “Metagenomic diamond mining”
3:00 p.m. – 3:30 p.m. Debbie Nickerson, University of Washington “Scaling Mendelian genomics”
3:40 p.m. – 4:40 p.m. 10X Workshop (Complimentary coffee and snack provided) Coquina North
4:45 p.m. – 6:45 p.m. Poster Session and Break Coquina South


Friday, February 12 (Evening)


6:15 p.m. – 7:25 p.m. AGBT Dinner Valencia Terrace & Lawn
Concurrent Session: Biology (Robert Lyons, University of Michigan, Chair) Mediterranean Ballroom/General Session Room
7:30 p.m. – 7:50 p.m. Alexandre Melnikov, The Broad Institute of MIT & Harvard “Efficient sequencing of malaria parasite DNA from clinical samples to investigate genetic basis of drug resistance, demographic history and genomic diversity”
7:50 p.m. – 8:10 p.m. Valerie Schneider, National Center for Biotechnology Information “Evolving approaches to reference assembly improvement”
8:10 p.m. – 8:30 p.m. Christopher Mason, Weill Cornell Medical College “The NASA Twins Study as a systems biology model for long-term human spaceflight”
8:30 p.m. – 8:50 p.m. Gregory Buck, Virginia Commonwealth University “The impact of the vaginal microbiome on women’s reproductive health and pregnancy”
8:50 p.m. – 9:10 p.m. Richard Green, University of California, Santa Cruz “A fast, efficient metagenomic assembly method”
9:10 p.m. – 9:30 p.m. Ivan Liachko, University of Washington “Assembling whole genomes from mixed microbial communities using Hi-C”
Concurrent Session: Cancer (John McPherson University of California, Davis, Chair) Palazzo Ballroom Salon E
7:30 p.m. – 7:50 p.m. Somasekar Seshagiri, Genentech “Comprehensive analysis of tumors at whole tissue to single cell level”
7:50 p.m. – 8:10 p.m. Tyler Garvin, Cold Spring Harbor Laboratory “Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma”
8:10 p.m. – 8:30 p.m. Geoff Otto, Foundation Medicine “Assessment of the relative clinical utility of ctDNA and tissue biopsies for the detection of actionable genomic alterations in routine clinical oncology specimens”
8:30 p.m. – 8:50 p.m. Hiroyuki Aburatani, The University of Tokyo “Genomic assessment of chemotherapy sensitivity in High Grade Serous Ovarian Cancer”
8:50 p.m. – 9:10 p.m. Andrew Mungall, BC Cancer Agency Genome Sciences Centre “Detection of genomic rearrangements in archival lymphoma tissues using targeted capture sequencing”
9:10 p.m. – 9:30 p.m. Eric Zhao, BC Cancer Agency Genome Sciences Centre “A BRCA-Associated genomic signature predicts clinical improvement with cisplatin therapy”
Concurrent Session: Informatics (Paul Flicek, European Bioinformatics Institute, Chair) Mediterranean Salons 6-8
7:30 p.m. – 7:50 p.m. Geoffrey Nelson, MRC Laboratory of Molecular Biology “A high-throughput genomics approach to efficiently link genes to phenotype”
7:50 p.m. – 8:10 p.m. Maria Nattestad, Cold Spring Harbor Laboratory “SplitThreader: A graphical algorithm for the historical reconstruction of highly rearranged and amplified cancer genomes“
8:10 p.m. – 8:30 p.m. Robert Davey, The Genome Analysis Centre “Nanopore, PacBio and Illumina assemblies of antifungal bacterium Pseudomonas fluorescens”
8:30 p.m. – 8:50 p.m. David Jaffe, 10X Genomics “Low cost Linked-Reads yield long range haplotyped human assemblies from a nanogram of DNA”
8:50 p.m. – 9:10 p.m. Han Fang, Cold Spring Harbor Laboratory “Scikit-ribo: Accurate A-site prediction and robust modeling of translation control from Riboseq and RNAseq data”
9:10 p.m. – 9:30 p.m. Karen Meltz Steinberg, Washington University School of Medicine “The first African reference genome assembly”


Saturday, February 13 (Morning)


7:30 a.m. – 9:00 a.m. Breakfast Coquina North
Bronze Sponsor Workshops Mediterranean Ballroom
9:00 a.m. – 9:20 a.m. Fluidigm
9:20 a.m. – 9:40 a.m. Agilent “Beyond the Exome: Phasing and detection of structural variants for the elucidation of complex genotypes” Hakon Hakonarson, Children’s Hospital of Philadelphia
9:40 a.m. – 10:00 a.m. Thermo Fisher “Ion Torrent: leading innovations in targeted sequencing” Simon Cawley, Thermo Fisher Scientific
10:00 a.m. – 10:15 a.m. Lexogen “Spike-in RNA Variants (SIRVs): external transcript isoform controls in RNA-Sequencing”
10:15 a.m. – 10:40 a.m. Coffee Break Mediterranean Pre-Function Space
10:45 a.m. – 11:00 a.m. Illumina
11:00 a.m. – 11:15 a.m. New England BioLabs “A novel fully customizable hybridization-based enrichment technology integrating capture and library preparation.” Cynthia Hendrickson, Directed Genomics
11:15 a.m. – 11:30 a.m. NanoString “New optical barcode chemistries power 3D biology & sequencing-simultaneous DNA, RNA, & protein analysis and low error-rate targeted sequencing” Joseph Beechem, NanoString Technologies
11:30 a.m. – 11:45 p.m. Advanced Analytical “Ultrasensitive detection of nucleic acids and visualization of DNA through >165,000 bp with a new PFGE capillary electrophoresis system”
11:45 p.m. – 12:00 p.m. Kapa Biosystems “Hyper Drive: high performance, streamlined workflows for RNA-seq and target enrichment”


Saturday, February 13 (Afternoon)


12:00 p.m. – 1:15 p.m. AGBT Lunch Valencia Terrace & Lawn
Plenary Session: Technology II (Len Pennacchio, Lawrence Berkeley National Laboratory, Chair) Mediterranean Ballroom
1:30 p.m. – 2:00 p.m. Nick Loman, University of Birmingham “Real-time genome sequencing in the field”
2:00 p.m. – 2:30 p.m. Susan Rosenberg, Baylor College of Medicine “Freeze-frame synthetic proteins trap genome damage intermediates in living cells”* Denotes abstract selected talk
2:30 p.m. – 2:50 p.m. *Shawn Levy, HudsonAlpha Institute for Biotechnology “Unique run conditions allow multiplexed phased genomes on the HiSeq X to reveal”
2:50 p.m. – 3:10 p.m. Coffee Break Mediterranean Pre-Function Space
3:10 p.m. – 3:30 p.m. *Jonas Korlach, Pacific Biosciences “Addressing complex diseases and hidden heritability with the sequel system”
3:30 p.m. – 3:50 p.m. *Tamir Biezuner, Weizmann Institute of Science “A generic, cost-effective and scalable cell lineage analysis platform”
3:50 p.m. – 4:10 p.m. *Christopher Hill, University of Washington “Long-read sequence assembly of the gorilla genome”
4:10 p.m. – 4:40 p.m. Closing Comments and Meeting Feedback
7:00 p.m. – 12:00 a.m. Farewell Dinner Party Coquina Ballrooms