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Please click here to download the following podcasts: 

In the Wake of the Flood 

Using VAAST to Identify Causative Mutations 

Taking NGS into the Clinic 

1000 Genomes Project: Cancer, Genetic Variation, and Drug Response 

Mapping Genomes in 3D 

The Human Microbiome Project: Next-Generation Sequencing and Analysis of the Indigenous Microbiota 

Building a Genome Sequencing Center: Managing and Mining Two Years of NGS Data 

Next-Generation Sequencing Data Management - Day 1

Day One  |  Day Two  |  Day Three  |  Short Courses 

NGS platforms now generate terabytes of genomic data, calling into question: What is the best way to benefit from this data bonanza? CHI’s Next-Generation Sequencing Data Management combines unique perspectives from a variety of researchers, engineers, biostatisticians, and software developers involved with NGS data management. This team of scientists will present case studies creating a common ground on which to explore how best to store, transfer, and analyze NGS data sets with the common goal of turning data into knowledge.

Monday, September 26

7:30 am Registration and Morning Coffee

» Plenary Keynote Session 

8:30 Chairperson’s Opening Remarks

Richard Resnick, CEO, GenomeQuest


8:40 The Catalog of Human Microbial Reference Genomes: Are We (Almost) There Yet?Sarah Highlander Sarah K. Highlander, Ph.D., Associate Professor, Molecular Virology and Microbiology, Human Genome Sequencing Center, Baylor College of MedicineA key resource for the NIH RoadMap Human Microbiome Project (HMP), and for metagenomics projects in general, is a representative “catalog” of annotated microbial genome sequences to serve as a reference for classification and functional annotation of a microbiome. The “JumpStart” phase of the HMP set a goal of creating a collection of 200 sequenced genomes from cultured microbes that represent various human body sites. The RFA, entitled “Construction of a Reference Sequence Data Set for the Human Microbiome Project”, solicited an additional 400 microbial sequences, including those from uncultured microbes, eukaryotes and reference viruses. Shortly after the HMP began, the target was reset to 900. Advancements in sequencing technologies and methods to capture uncultured organisms have now raised the number to 3000. Cooperative international projects are also adding to the data set. Current HMP metrics and analyses will be presented and perspectives on future reference genome sequencing goals and requirements will be discussed.

Podcast9:20 In the Wake of the Flood

Toby BloomToby Bloom, Ph.D., Director, Informatics, Genome Sequencing Platform, Broad Institute of MIT and Harvard

With storage issues largely under control, we are now seeing the second phase challenges associated with the scale-up of massively-parallel sequencing. How do we handle the computational load, the network overload, and the challenges of managing the sequencing of hundreds or even thousands of samples concurrently? This talk explores new strategies and new technologies for the next phase of next-gen informatics.


10:00 Networking Coffee Break

10:30 What Does Clinical Grade Whole Genome Sequencing Mean?

Isaac KohaneIsaac Kohane, Ph.D., Director, Children’s Hospital Informatics Program, Harvard Medical School






Co-Sponsored by

Genome Quest - Sponsored by logo 

NGS Leaders

11:10 Genomics in Clinical Trials: Has the Time Come?Genomics applied to clinical trials has long promised immense rewards. The advanced stratification of patients into responders, non-responders, and adverse responders could fundamentally lower the overall cost of trials and accelerate time-to-market for target groups. Now with plummeting costs of next-generation sequencing, increasingly affordable data storage solutions, a proliferation of analysis and inference tools that bridge the research and clinical settings, and a growing volume of validated biomarkers, has the time come to realize those rewards?


Kevin DaviesKevin Davies, Ph.D., Author, The $1,000 Genome & Editor-in-Chief, Bio-IT World


KhalilIya Khalil, Ph.D., Senior Vice President & Co-founder, GNS Healthcare

ResnickRichard Resnick, CEO, GenomeQuest

Brad SmithBradley L. Smith, Ph.D., Vice President, Translational Medicine, Quintiles

Toby BloomToby Bloom, Ph.D., Director, Informatics, Genome Sequencing Platform, Broad Institute of MIT and Harvard

Questions for the Panel: 

* Can these methods really lead to benefits such as streamlined recruitment, improved decision-making during trials, and lower overall costs for trials?
* What can be done to accelerate adoption and success?  
* What types of trials are the best candidates for these methods?
* What success stories can you share?
* Who is/should be leading the charge: pharma or their CROs?
* At what sequencing price point will genomics become mainstream in clinical trials?

12:15 pm Close of Morning Session 

Sponsored by
Agilent Technologies
12:30 Luncheon Presentation

Part 1: Exome Sequencing Identifies Mendelian Disease Genes and Provides Insight to Tumorigenic MechanismsEmilie Lalonde, Ph.D. Candidate, Medical Biophysics, University of Toronto and Ontario Institute for Cancer ResearchWithin the last two years, exome sequencing has rapidly become an invaluable tool in medical genetics. I will discuss the concepts and procedures of exome sequencing, including a brief overview of the exome sequencing pipeline used in more than 160 samples analyzed by our group. The successful implementation of this pipeline to answer various medical questions will be illustrated with examples in both Mendelian diseases and cancers.

Part 2: The Agilent Technologies SureSelect Platform for Target Enrichment: Focus your Next-Gen Sequencing on DNA that MattersSpeaker to be Announced, Agilent TechnologiesDuring this presentation you will learn how the SureSelect Target Enrichment technology works and its main applications. We will also present the current SureSelect product portfolio, which expands from All Exon kits to small capture customizable assays, including updates on new recently launched products that expand your opportunities for scientific discovery. 


Afternoon Plenary Sequencing Selects Session 

2:15 Chairperson's RemarksKevin Davies, Ph.D., Author, The $1,000 Genome & Editor-in-Chief, Bio-IT World

Hosted byComplete Genomics 2:20 Identification of Candidate Disease Genes Using Whole-Genome Sequencing to Solve Complex Structural Rearrangements in HumansEric Morrow, Ph.D., M.D., Assistant Professor, Brown UniversityChildren who present with neurodevelopmental disorders such as autism will often have chromosomal rearrangements.  These rearrangements may be detectable with current medical diagnostic testing such as a karyotype or array comparative genomic hybridization.  These tests are considered standard of care for first presentation of these disorders in the clinic; yet, many structural rearrangements have complex breakpoints.  Data from whole genome sequencing allows researcher, and perhaps soon, the clinical laboratory to resolve these complex rearrangements. 

Hosted by
2:55 Human Whole Genome Analysis…for Humans
Nathan Pearson, Director, Research, Knome, Inc.Whole genome and exome interpretation are key – but dauntingly hard – new ways to understand disease and drug response.  To spark insights for research clients, we've built a fast cloud-based pipeline that parses, richly annotates, and thoroughly compares many genomes at once, delivering results with handy query tools to quickly find candidate variants, genes, and pathways.  

3:30 Networking Refreshment Break (West Pre-Function, 5th Level)

4:00 Hosted by
Partek New 
Integrative Biomedical Informatics: A Multidisciplinary Approach for Translational Research
Yate-Ching Yuan, Ph.D., Director, Bioinformatics Core Facility, Beckman Research Institute, City of Hope Medical CenterThis presentation will share our experiences in establishing flexible and scalable translational research platform using an integrated cyber-infrastructure with cloud computing to support high-throughput data analysis pipeline, management, and integration of multidisciplinary genomics data with disease phonotype in order to enable the exploitation of disease understanding and patient outcomes in biomarker and move towards personalized medicine.

4:35 Speaker to be Announced 

5:15 Welcome Reception and Grand Opening of Exhibit Hall

6:30 Close of Day

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