Making Sense of the Sequence: Applications in Population Sciences


Overview

NCI's Epidemiology and Genomics Research Program (EGRP) sponsored the Making Sense of the Sequence: Applications in Population Sciences meeting on May 15-16, 2013 in Rockville, MD.

Despite the fact that over 20,000 cancer genomes will be sequenced by the end of 2013, germline whole exome or whole genome sequencing in epidemiologic studies of cancer risk are relatively nascent. This meeting aimed to advance the use of sequencing technologies in epidemiologic studies of cancer, and to enhance the integration of cancer genomics and somatic sequencing with population based germline sequencing studies. The collaborations stemming from this meeting will lead to improvements of our understanding of the genetic architecture of cancer, and of the biology and mechanisms underlying this complex disease.

The meeting brought together leading experts in the field to discuss key emerging themes including:

  1. establishment of best practices for applying germline and somatic sequencing in population based studies;
  2. integration of recent advances in cancer genomics, such as The Cancer Genome Atlas (TCGA), with sequencing studies in epidemiology;
  3. Identification of opportunities, challenges and resource needs for facilitating the interpretation and application of next generation sequencing in large-scale studies.

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Agenda

View agenda for Wednesday, May 15
Wednesday, May 15 Topic
8:30 a.m. Registration
9:00 a.m. - 9:30 a.m.
  • Overview and Welcome
    Elizabeth Gillanders, Ph.D.
    Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences (DCCPS), National Cancer Institute (NCI)
  • Goals of Workshop and Common Themes
    Carolyn Hutter, Ph.D.
    EGRP, DCCPS, NCI
Part 1: State of the Science
9:30 a.m. - 10:15 a.m. Germline Genetic Variation and Disease at the Population Level
  • Sequencing Studies of Complex Disease Risk (Exome Sequencing Project)
    Suzanne Leal, Ph.D.
    Baylor College of Medicine
  • Whole Exome/Genome Sequencing in Cancer
    Ulrike Peters, Ph.D., M.P.H.
    Fred Hutchinson Cancer Research Center
10:15 a.m. - 10:30 a.m. Break
10:30 a.m. - 11:15 a.m. The Cancer Genome
  • The Spectrum of Variation in the Cancer Genome
    Levi Garraway, M.D., Ph.D.
    Dana-Farber Cancer Institute/Brigham and Women's Hospital
  • The Cancer Genome Atlas: Insights into Cancer Biology
    Paul Spellman, Ph.D.
    Oregon Health and Science University
11:15 a.m. - 11:35 a.m. TCGA Piloting of FFPE Samples
Kenna Shaw, Ph.D.
The Cancer Genome Atlas Program Office, NCI
11:35 a.m. - 12:00 p.m. Discussion Session 1
Leah Mechanic, Ph.D., M.P.H.
EGRP, DCCPS, NCI
12:00 p.m. - 1:00 p.m. Lunch
Part 2: Contemporary Challenges and Lessons Learned
1:00 p.m. - 1:45 p.m. Lessons and Challenges for Sequencing Data
  • Is it Really "Whole" Genome and "Whole" Exome Sequencing?
    Deborah Nickerson, Ph.D.
    University of Washington School of Medicine
  • Lessons and Considerations for Sequencing Somatic Genomes
    Gaddy Getz, Ph.D.
    Broad Institute
1:45 p.m. - 2:45 p.m. Lessons and Challenges for Benchmarks and Reproducibility
  • Documentation, Reproducibility & Benchmarks in the Laboratory
    Elizabeth Pugh, Ph.D.
    Center for Inherited Disease Research
    Johns Hopkins University
  • Compression and Data Storage
    Stephen Sherry, Ph.D.
    National Center for Biotechnology Information
  • Quality Assured Analysis
    Paul Scheet, Ph.D.
    University of Texas MD Anderson Cancer Center
2:45 p.m. - 3:00 p.m. Break
3:00 p.m. - 3:45 p.m. Lessons and Challenges for Analysis
  • Analysis of Rare Variation: Exome and Whole Genome Data
    Peter Kraft, Ph.D.
    Harvard School of Public Health
  • Lessons and Considerations for Analysis in Diverse Populations
    Daniel Shriner, Ph.D.
    National Human Genome Research Institute
3:45 p.m. - 4:45 p.m. Discussion Session 2
Simon Gayther, Ph.D.
University of Southern California
Part 3: Integration of Somatic and Germline (continues on next day)
4:45 p.m. - 5:30 p.m. Integration of Genomic and Somatic Information I
  • Integrating Germline & Somatic Data for Clinically Relevant Outcomes
    John Maris, M.D.
    Children's Hospital of Philadelphia
  • Using Encode Data to Inform Interpretation and Integration
    Robert Klein, Ph.D.
    Memorial Sloan-Kettering Cancer Center

View agenda for Thursday, May 16
Thursday, May 16 Topic
Part 3: Integration of Somatic and Germline (continued)
8:30 a.m. - 9:15 a.m. Integration of Genomic and Somatic Information II
  • Using Somatic Data to Aid Interpretation of Germline Variation
    Matthew Freedman, M.D.
    Dana-Farber Cancer Institute
    Harvard Medical School
    Broad Institute
  • Interactions Between Germline Variants and the Somatic Mutation Landscape
    Li Ding, Ph.D.
    Washington University in St. Louis
9:15 a.m. - 10:15 a.m. Discussion Session 3
Funmi Olopade, M.D., F.A.C.P.
University of Chicago Medicine
10:15 a.m. - 10:30 a.m. Break
Part 4: Interpretation and Big Data Frameworks
10:30 a.m. - 11:15 a.m. Interpretation and Application
  • Bioinformatic Tools for Next-Generation Sequence Analysis
    Rachel Karchin, Ph.D.
    Johns Hopkins University
  • Network-based Approaches to Cancer Genome Analysis
    Hannah Carter, M.Eng., Oh.D.
    University of California San Diego School of Medicine
11:15 a.m. - 12:30 p.m. Resources for Big Data
  • Big Data to Knowledge (BD2K)
    Jennifer Couch, Ph.D.
    Division of Cancer Biology (DCB), NCI
  • Clouds/Federated Databases
    University of Chicago
  • Software and Other Sequence Based Community Resources
    William FitzHugh, M.S.
    5AM Solutions
12:30 p.m. - 1:00 p.m. Pick up lunch to bring back to room
1:00 p.m. - 2:00 p.m. Discussion Session 4
Stephen Sherry, Ph.D.
National Center for Biotechnology Information
2:00 p.m. - 2:15 p.m. Break
Wrap-up Session
2:15 p.m. - 2:45 p.m. Meeting Wrap-up and Summary
Carolyn Hutter, Ph.D.
EGRP, DCCPS, NCI
2:45 p.m. - 3:30 p.m. Future Directions and Concluding Remarks
Stephen Chanock, M.D.
Division of Cancer Epidemiology and Genetics (DCEG), NCI
3:30 p.m. Adjourn Meeting

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Workshop Summary

A meeting summary is currently in development and will be included here when completed.

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Planning Committee

  • Stephen Chanock, M.D., DCEG, NCI
  • Nilanjan Chatterjee, Ph.D., DCEG, NCI
  • Huann-Sheng Chen, Ph.D., Surveillance Research Program, DCCPS, NCI
  • Elizabeth Gillanders, Ph.D., EGRP, DCCPS, NCI
  • Tiffany Green, M.H.S., M.P.H, EGRP, DCCPS, NCI
  • Emily Harris, Ph.D., M.P.H., National Institute of Dental and Craniofacial Research
  • Carolyn Hutter, Ph.D., EGRP, DCCPS, NCI
  • Leah Mechanic, Ph.D., M.P.H., EGRP, DCCPS, NCI
  • Stefanie Nelson, Ph.D., EGRP, DCCPS, NCI
  • Dina Paltoo, Ph.D., Office of the Director, National Institutes of Health
  • George Papanicolaou, Ph.D., National Heart Lung and Blood Institute
  • Erin Ramos, Ph.D., National Human Genome Research Institute
  • Kenna Shaw, Ph.D., TCGA, NCI

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Related Resources

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Contact

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