The NHGRI Genome Sequencing Program (GSP)
Request for Comments:
Report: Future Opportunities for Genome Sequencing and Beyond: A Planning Workshop for the National Human Genome Research Institute
Submit your comments on the July 2014 NHGRI Genome sequencing workshop on the full report.
The Genome Sequencing Program of the National Human Genome Research Institute is an overarching program covering four areas - programs in their own right - that have been established to address current scientific opportunities within the context of the Strategic Plan for Genomics:
- Large-Scale Genome Sequencing and Analysis Centers (LSAC)
- Centers for Mendelian Genomics (CMG)
- Clinical Sequencing Exploratory Research (CSER)
- Genome Sequencing Informatics Tools (GS-IT)
In addition to pursuing fundamental questions in the genomics of biology and disease that can be addressed at large scale (LSAC), there is a focused program to elucidate the genomic basis for Mendelian diseases (CMG); one to uncover the significant issues that arise in applying genome sequencing in a clinical setting (CSER); and one to develop informatics tools that will enable the wider dispersion of the ability to analyze high-throughput genome sequence data (GS-IT).
Three of the programs (LSAC, CMG, CSER) have benefitted from collaborations and/or co-funding from the National Cancer Institute, the National Heart, Lung and Blood Institute, the National Institute on Aging, the National Institute for Diabetes, Digestive and Kidney Diseases, and the National Institute of Mental Health. Details about co-funding and collaborations can be found through the individual program page links above.
Because the scientific opportunities in genomics change rapidly, the scientific goals and organization of the GSP are revisited at four- to-five year intervals. The most recent full GSP evaluation was in 2010, resulting in the current areas of scientific focus and program structure. The next full evaluation will be in 2014.
For a summary of the process that led to the current program structure, see: NHGRI broadens sequencing program focus on inherited diseases, medical applications.
The solicitations for the current program elements are:
- RFA-HG-10-015: Genome Sequencing and Analysis Centers (U54)
- RFA-HG-10-016: Mendelian Disorders Genome Centers (U54)
- RFA-HG-10-017: Clinical Sequencing Exploratory Research (U01)
- RFA-HG-10-018: Informatics Tools for High-Throughput Sequence Data Analysis (U01)
- RFA-HG-10-019: Informatics Tools for High-Throughput Sequence Data Analysis (SBIR) (R43/R44)
A brief history of the sequencing program is available at: The NHGRI Genome Sequencing Program History
All four components of The NHGRI Genome Sequencing Program are under continuous programmatic evaluation. NHGRI Staff consults quarterly with a group of scientific advisors to the program about individual grantee and program performance. Program grantees submit quarterly reports that describe progress, including detailed production summaries for the more production-oriented programs. All major program decisions are vetted by the National Advisory Council for Human Genome Research.
In addition, the grantees are organized into a research network; within and between programs, these networks collaborate on matters such as best practices, standards, policies, methods development, data analysis, technology adaptation, and other common interests. All four programs meet with NHGRI Staff and the SAP at an annual meeting.
Data Release and Access Policies
NHGRI data release and access policies for genomic sequence are consistent with NIH policies: Genomic Data Sharing [nih.gov].
NHGRI data release policies for genome sequence data evolved from the original Bermuda and Ft. Lauderdale policies which were suited for the Human Genome Project data and organismal sequence data. With the advent of projects involving large numbers of samples from human subjects, this area is under continuous evaluation, much of it at the NIH, rather than the NHGRI level. See: http://grants.nih.gov/grants/guide/notice-files/NOT-OD-13-119.html for a discussion of the latest NIH policy proposals in this area.
Data Release Policies for the NHGRI GSP
NHGRI requires the LSAC, CMG, and CSER to release sequence and related data to appropriate databases, including GenBank/Short Read Archive and the assembly archive; dbGaP, and CGHub (for Cancer Genome Atlas data). NHGRI requires rapid pre-publication release of all organismal sequence data and assemblies, and also human data in a manner consistent with the terms of consent under which samples were collected.
Data Access Policies for the NHGRI GSP
The Large-Scale Sequencing Data Access and Release page contains information on policies and procedures for scientific researchers requiring access to NHGRI-sponsored large-scale sequencing data. In general, access to organismal sequence and assembly data follows the Ft. Lauderdale principles.
Human data access policies vary depending on the repository and consent terms; however, as above, NHGRI requires rapid deposition of data in repositories to which all members of the scientific community have equal access.
- Future Opportunities for Genome Sequencing and Beyond: A Planning Workshop for the National Human Genome Research Institute
July 28-29, 2014
Lu Wang, Ph.D.
(Centers for Mendelian Genomics)
(Clinical Sequencing Exploratory Research)
Heidi Sofia, Ph.D.
(Genome Sequencing Informatics Tools)
Kris Wetterstrand, M.S.
National Human Genome Research Institute
National Institutes of Health
5635 Fishers Lane
Suite 4076, MSC 9305
Bethesda, MD 20892-9305
Phone: (301) 496-7531
Fax: (301) 480-2770
Last Updated: October 27, 2014