Last updated: March 01, 2006
National Advisory Council for Human Genome Research - Summary of Meeting - March 2006
National Advisory Council for Human Genome Research
Summary of Meeting
Bethesda, Md.
September 10-11, 2001
The open session of the National Advisory Council for Human Genome Research (NACHGR) was convened for its thirty-third meeting at 8:50 a.m. on September 10, 2001, at the Natcher Conference Center, National Institutes of Health (NIH) Bethesda, Md. Francis Collins, director of the National Human Genome Research Institute (NHGRI), called the meeting to order.
The meeting was open to the public from 8:50 a.m. until 3:00 p.m. on September 10, 2001. In accordance with the provisions of Public Law 92-463, the meeting was closed to the public from 3:00 p.m. on September 10 until adjournment on September 11 for the review, discussion and evaluation of grant applications.
The closed session was forced to adjourn early on September 11 due to the attacks, but reconvened via teleconference on October 10, 2001 to complete remaining tasks.
Council members present:
Wylie Burke
Ronald Davis
William Gelbart
H. Robert Horvitz [Monday only]
Bronya Keats
Raju Kucherlapati
Kim Nickerson
Maynard Olson
Janet Rowley
Colleen Scanlon
Robert Waterston
Alan Williamson
Ex Officio member present:
Gerard Schellenberg
Council members absent:
Allen Buchanan
David Burgess
Richard Lifton
Staff from the National Human Genome Research Institute:
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Others present for all or a portion of the meeting:
Sally Amero, NIH, CSR
Diane Baker, University of Michigan
Robert Boyd, Knight-Ridder
Cheryl Corsaro, NIH, CSR
Dan Drell, U.S. Department of Energy
Lauren Hafner, The Blue Sheet
Steve Klein, NIH, NICHD
Edward Kloza, National Society of Genetic Counselors
Eliot Marshall, Science
Bernice Morrow, American Society of Human Genetics
Nancy Moy, SRI International
Sharon Olsen, International Society of Nurses in Genetics
Ari Patrinos, U.S. Department of Energy
Clif Poodry, NIGMS
Cheryl Scachen, National Society of Genetic Counselors
Michael Schaeffer, NIH, CSR
Katherine Schneider, National Society of Genetic Counselors
Angela Sharpe, COSSA
Maggie Snyder, NIH, OER, OS
Gerald Vovis, Genaissance Pharmaceuticals
Mike Watson, American College of Medical Genetics
Todd Zwillich, GenomeWeb
Introduction of Liaisons and New Staff
Dr. Jordan introduced new NHGRI employees. Peter Good is program director for Bioinformatics in the Division of Extramural Research. Maggie Bartlett is a visual information specialist in the Office of Communications.
Dr. Jordan welcomed liaisons to the council from the professional societies: Mike Watson, the representative from the American College of Medical Genetics, Edward Kloza the representative from the National Society of Genetic Counselors, Bernice Morrow, the representative from the American Society of Human Genetics and Sharon Olsen, the representative from the International Society of Nurses in Genetics. She also introduced Ari Patrinos and Dan Drell of the U.S. Department of Energy.
Dr. Jordan also extended welcome to members of the press: Lauren Hafner of The Blue Sheet and Todd Zwillich of GenomeWeb.
Approval of Minutes
The minutes from May 21, 2001 NACHGR meeting were approved as submitted.
Future Meeting Dates
The following dates were proposed for future meetings: February 11-12, 2002; May 20-21, 2002; September 9-10, 2002; February 10-11, 2003; May 19-20, 2003 and September 15-16, 2003.
Director's Report
General Announcements
Dr. Collins thanked those members leaving council including: Robert Horvitz, Colleen Scanlon, Alan Williamson and Allen Buchanan. He also congratulated Robert Horvitz and Patrick Brown who were both named to the list of "America's Best in Science" by Time magazine. The search for a new NIH director continues. Dr. Paul Sieving has been named the director of the National Eye Institute (NEI). Maria Freire is leaving her position as director of the NIH Office of Technology Transfer to become CEO of the Global Alliance for Tuberculosis Drug Testing.
The Secretary of the Department of Health and Human Services (DHHS), Tommy Thompson, conducted a visit to the NIH, including NHGRI, in August. Claude Allen, Deputy Secretary of DHHS also met with Dr. Collins in June. In connection with a meeting of the International Human Genome Sequencing Consortium in China, Chinese President Jiang Zemin held audience with Dr. Collins, Mark Guyer and members of the consortium on August 28 in Beijing to discuss the promise of genomics and the importance of data access. Dr. Collins congratulated the Beijing Genomics Institute, led by Yang Huanming, for their impressive contribution to the Human Genome Project (HGP).
Recent Scientific Accomplishments and Issues
Sequencing Update
The main focus of the human sequencing effort is finishing the genome. Over half of the genome is currently in finished form and an on-line gap-tracking system is being developed to assist the remaining finishing efforts. On September 7-9, there was a meeting at the Whitehead Institute to begin genome-wide analysis of the available mouse genome sequence. The Rat Genome Project recently issued a press release announcing the achievement of 1X sequence coverage of the rat genome. There are over ten million rat sequence reads available from the National Center for Bioinformatics (NCBI) and European Bioinformatics (EBI) trace repositories. The Whitehead Institute has sequenced Ciona savignyi to 10X coverage and is working on a genome assembly. The data is currently available on their Web site.
Extramural Program
Grants have been awarded for three Centers of Excellence in Genomic Science (CEGS). NHGRI has plans to establish about 10 centers over the next three years. Council will review the next set of applications at the February 2002 council session. The subsequent application receipt date is June 3, 2002.As part of the Mammalian Gene Collection (MGC), the identification of candidate full-length human and mouse cDNAs continues to progress well. To date, sequences from approximately 8,200 clones have been submitted to GenBank. The MGC advisory committee will meet in December and a manuscript describing the availability of this resource is being developed.
As of August 15, 2001, there were almost three million SNPs in dbSNP; 1.8 million are non-redundant, reference SNPs.
The Gene Ontology Consortium, founded to develop a common language to describe gene function, has recently published a paper in Genome Research describing their progress.
Ethical, Legal and Social Implications (ELSI)
The ELSI Research Advisors (ERA) held a meeting in June to discuss the NHGRI planning process.Recruitment for the Hemochromatosis and Iron Overload Study began in February 2001.
Minority Outreach Initiatives
NHGRI will partner with National Institute of General Medical Sciences (NIGMS) on the MARC Undergraduate Student Training in Academic Research Program to increase the number of under-represented minority students in the quantitative, behavioral and social sciences. NHGRI will also contribute to the NARCH Initiative, which supports partnerships between American Indian or Alaska Native tribes or tribal-based organizations and research-intensive institutions. NHGRI will support ELSI research as part of this initiative.The Division of Intramural Research (DIR) has implemented a summer student program in partnership with the National Human Genome Center at Howard University. Ten minority students participated in this program over the past summer.
Intramural Program
Dr. Collins highlighted three exceptional papers produced by researchers in DIR. Eric Green published a review entitled "Strategies for the systematic sequencing of complex genomes." A collaboration between Jeff Trent's group and researchers at the University of Michigan published a paper called "Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies." Paul Meltzer and researchers at Lund University in Sweden published "Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks."Policy
The NIH released a document regarding stem cell research that is a good source of information on this issue. A stem cell registry will be available from NIH in the next few weeks.The 2001 fiscal year ends September 30. The 2002 fiscal year budget is not yet available and NIH expects to operate under continuing resolutions.
The issue of genetic discrimination has been receiving considerable attention recently. The Genetic Non-discrimination in Health Insurance and Employment Act was introduced to the 107th Congress and there have been a number of Senate and House hearings on the subject.
Education and Outreach
Contents of the CD-ROM from the Human Genome Project Multimedia Education Kit, which was distributed to over 60,000 people starting in February 2001, will be made available by download from the Web. An additional video to appeal to minority communities and address their special issues is being designed.The People's Genome Celebration, sponsored by the Genetic Alliance, was held in Washington, D.C. on June 8-10 to celebrate the landmark mapping of the human genome. The Zeta Phi Beta Sorority National Education Foundation organized a "HGP Informational Conference for Minority Communities" in Atlanta on June 20, 2001. The conference was designed to inform individuals from minority communities about the challenges and impact of the HGP. Consumer Day will be held this year in collaboration with Howard University and Zeta Phi Beta.
The Current Topics in Genetic Research Short Course, hosted by the NHGRI Intramural Program was held August 6-9 and attended by 32 faculty members from universities with substantial minority enrollment.
Report from the Department of Energy (DOE)
Dr. Ari Patrinos provided a report on recent genome-related activities at the Department of Energy (DOE). The department continues its search for a leader in the Office of Science and is awaiting a budget for FY2002. He stressed the commitment of DOE and its Joint Genome Institute to finishing the human genome sequence. The Ciona intestinalis and Fugu projects will receive more sequencing capacity upon the completion of the finished human sequence. The data and genome assemblies for these two organisms will be made available as soon as possible. They are planning another "Microbe Month" for October/November and expect to sequence about twenty microbial genomes.
The DOE's Genomes to Life Program continues to receive positive political support. There have been a number of workshops held recently to address various aspects of the Genomes to Life initiative, including one, chaired by Craig Venter, to examine the use of biotechnology in clean energy and carbon sequestration research towards addressing climate change. The "Computational and Systems Biology: Visions of the Future" workshop chaired by Eric Lander, was held September 6-7, 2001. Computational science will be very integral to the future of biological research. The DOE continues to be excited about potential collaborations in computational biology with other DOE offices, other funding agencies and the private sector.
Update on Mouse Sequencing
Dr. Bob Waterston presented an update on the mouse sequencing collaboration, which involves the Washington University Genome Sequencing Center, the Whitehead Institute for Genome Research, the Sanger Centre and an analysis effort called the "Homology Group." The goals of the project are to provide a robust physical map and a high quality, finished sequence of the mouse genome. The initial phase of whole genome shotgun sequencing has reached 2-3X coverage and will proceed to 5-6X coverage. This will be followed by a second phase of Bacterial Artificial Chromosome (BAC)-based sequencing, which is expected to begin in January 2002. The full shotgun of the BACs is expected to be done by early 2003. The genome will be finished by end of 2005.
To date, over 300,000 clones have been fingerprinted and assembled into less than 1,000 contigs. They are working to assign those contigs to mouse chromosomes using BAC- associated RH markers. Individual sequence reads are also being used to annotate the human sequence and preliminary sequence assemblies have been performed by a number of groups. About 3 percent of the genome seems to be conserved between the two species, only half of which can be attributed to known exons. Another effort anchors the mouse BAC map to the human sequence assembly using BAC end sequences and then, from that alignment, inferences regarding the order of both mouse and human contigs are made.
Concept Clearance - ELSI
Jean McEwen brought two ELSI initiatives to council for approval: "Dissertation Research Grants for Underrepresented Minorities in the Ethical, Legal and Social Implications (ELSI) of Genetics and Genomics Research" and "Studies of the Ethical, Legal and Social Implications of Genetic Variation Research for Individuals and Diverse Racial and Ethnic Groups." The first targets under-represented minority Ph.D. students in ELSI-related research at the dissertation-writing stage. NHGRI proposes to use the R03 small grant mechanism to award $25 K for 12 months, with the potential for a no cost extension for a second year. The second focuses on how information about genetic variation is understood and used by individuals and groups. NHGRI proposes to use the R01 and R03 mechanisms and commit $2M per year for up to three years. Support from other institutes will be sought.
Data Release Policies
Elise Feingold outlined the need for NHGRI to update its data release policies in order to accommodate new types of data, such as haplotype, two-hybrid and micro-array data, not appropriately covered with current policies. Council members discussed if the policies can be extended to cover hypothesis-driven research that may also be high-throughput, production data collection. Dr. Waterston pointed out that large-scale sequencing was a special case, since it was thought that it would take a long time to collect all the data and the data was a clear community resource. Rick Lifton recommended that this discussion include the NIH community, in order to develop a general set of guidelines applicable to all.
Many agreed that scientific credit and publication with concurrent, full data release is the optimal goal and that NHGRI should work to encourage it. Negotiation with individual investigators, to address what gets protected and what should be released, may be needed where more rapid release is appropriate. NHGRI should keep in mind that it is important to communicate what work is being done to the research community. It was agreed that this will be a topic of discussion at the February 2002 council.
Conclusions of the Protein Sequence Database Meeting & Concept Clearance for a Centralized Protein Sequence Database.
Peter Good described the conclusions of a workshop, held in early May 2001, to discuss the need for a centralized protein sequence database accessible and useful to a broad range of biological researchers. NHGRI, in collaboration with NIGMS and the National Library of Medicine (NLM), would like to establish a centralized protein sequence database that is highly curated, is coordinated with other databases and contains information on protein sequence, nomenclature, family classifications, alternative isoforms, function and regulation. An active advisory panel would be created to provide advice for management of the database. NHGRI proposes to use the P41 mechanism to support the database at a total of $4.5M per year for 3 years. This figure includes support from NHGRI, NIGMS, NLM and other NIH institutes.
Report of Comparative Genomics Workshop and a Process for Choosing Additional Organisms for Large-Scale Sequencing
Mark Guyer reported on the July 9-10 workshop entitled "Developing Guidelines for Choosing New Genomic Sequencing Targets." The purposes of the workshop were to discuss the opportunities available from comparative genome analysis using whole genome data sets and to develop a set of guidelines that should be addressed by investigators, particular research communities and/or large-scale sequencing centers proposing to use NHGRI funds for sequencing a genome.
Dr. Guyer pointed out that most projects will be done by single groups or very small collaborations and will be shorter in duration than the typical NHGRI center grant. Many sequences will be done to answer specific biological questions. NHGRI aims to create a system where sequencing targets will be prioritized on the basis of peer review and scientific competition through the submission of a white paper. The white paper will go through a formal review process and be matched with capacity available from the large-scale sequencing centers by NHGRI staff and the advisors. The workshop generated specific rationales and strategic recommendations that are outlined in the report. Based on these, NHGRI staff has developed a set of issues that applicants will need to address in the white papers. It is expected that the review committee, once established, will have five members including at least two council members.
Council agreed that this is a good step forward in formalizing this process, allowing for public input, matching capacity with demand, keeping a steady production state and judging different types of projects (e.g. many small genomes versus one large genome, draft sequence versus finished sequence) against each other. One concern was raised that the expected turnaround time of one year will work well for large genomes, but not for small genomes, which may require a faster response to fit into unexpected sequence capacity. NHGRI staff will work on options for projects that may need to be moved through the system quickly. Council agreed that applications should be accepted three times a year and brought to council each time. This process should closely integrate into the strategic planning process that is now getting underway, during which staff should consider the proportion of the NHGRI budget that will be devoted to large-scale sequencing in the future.
Proposal For Construction of New BAC Libraries
Dr. Guyer presented a proposal for selecting targets for BAC library construction, which is similar to that proposed for selecting sequencing targets. The current funding level from NHGRI and other NIH institutes will support the construction of over fifteen BAC libraries per year. Applicants will submit a written request, accepted three times a year, assigned as high or standard priority by a review committee and reported to council once a year. Those libraries requested by collaborating ICs will automatically be rated high priority. A BAC Resource Steering Panel will be formed to monitor library production and provide guidance to the library producers.
Report of Haplotype Map Workshop and Developing a Haplotype Map of the Human Genome for Finding Genes Related to Health and Disease
Lisa Brooks reported on the July 18-19 workshop entitled: "Developing a Haplotype Map of the Human Genome for Finding Genes Related to Health and Disease." The purposes of the workshop were to discuss how haplotype maps could be used for finding genes contributing to disease; the methods for constructing such maps; the data about haplotype structure in populations; the types of populations and samples that might be considered for a map; the ethical issues, including those related to studying genetic variation in identified populations; and how such a project could be organized.
The workshop attendees stressed that this international effort should be very open and well coordinated and that data should be released publicly and rapidly. Two working groups were established. The population and ELSI Group will identify potential benefits and risks to populations, how to minimize those risks, and the methods for population consultation. The methods group will determine methods for determining genotypes and haplotypes, the number and types of samples needed, the types and density of markers and a hierarchical testing scheme.
Strategic Planning Process
Dr. Collins presented NHGRI's strategy for developing the next five-year scientific plan and vision for the future, which will integrate all branches (DIR, DER and Policy/ELSI programs) of the institute.
A number of workshops have happened or are being planned, to bring together members of the scientific community to help NHGRI articulate its goals in genomic science. Those goals will need to be integrated with medical applications, technology development, cost reduction, ELSI, informatics and training. The planning process will be officially inaugurated with the first "Book End Meeting" to be held December 12-14, 2001.
Council members stressed that NHGRI should direct the planning process and the development of NHGRI's vision to capture how progress in genomic science has and will influence society through enabling biomedical research, improving public health, revolutionizing drug development and transforming the practice of medicine.
Announcements and Items of Interest
Dr. Jordan noted the items of interest in the council folders, and referred council to material in Tab "S."
Council-Initiated Discussion
None.
Budget Table
Dr. Jordan referred to the budget table found under Tab "U."
Conflict of Interest
Dr. Jordan read the Conflict of Interest policy to council and asked them to sign the forms provided.
Review of Applications
In closed session, the council reviewed 89 applications, totaling $25,186,128. The applications included 17 regular research grants, seven pilot projects, 18 ELSI grants, nine requests for application, one center grant, three conference grants, one research career development award, one training grant, 21 SBIR Phase I, three SBIR Phase II, two fellowship grants, and six others. A total of 55 applications requesting $21,734,236 were recommended.
I hereby certify that, to the best of my knowledge, the foregoing minutes are accurate and complete.
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