The open session of the National Advisory Council for Human Genome Research was convened for its thirty-fifth meeting at 8:40 a.m. on May 20, 2002, at the Holiday Inn, Silver Spring, 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 8:40 a.m. until 11:45 a.m. on May 20, 2002. In accordance with the provisions of Public Law 92-463, the meeting was closed to the public from 11:45 a.m. on May 20 until adjournment on May 21 for the review, discussion, and evaluation of grant applications.
Vickie Yates Brown
David R. Burgess
Ronald W. Davis
William M. Gelbart
Bronya J. Keats
Maynard V. Olson
Janet D. Rowley
Robert H. Waterston
Wylie Burke (joined by phone for portions of the closed session)
Richard P. Lifton
Joy Boyer, DER
Lisa Brooks, DER
Jean Cahill, DER
Carol Carnahan, DER
Monika Christman, DER
Francis S. Collins, OD
Edith DeHaut, DER
Elise Feingold, DER
Adam Felsenfeld, DER
Lynn Frampton, DER
Barbara Fuller, OD
Peter Good, DER
Bettie Graham, DER
Mark Guyer, DER
Karen Hajos, OD
Linda Hall, DER
Belinda Jackson, DER
Linda Jacobson, OD
Elke Jordan, OD
Michael Lacy, OD
Tim Leshan, OD
Emily Linde, DER
Jean McEwen, DER
Rodecia McKnight, DER
Ken Nakamura, DER
Khang Nguyen, DER
Ken Ow, OD
Diane Patterson, DER
Jane Peterson, DER
Rudy Pozzatti, DER
Robin Prigal, OD
Jerry Roberts, DER
Jeff Schloss, DER
Erin Shannon, OD
Larry Thompson, OD
Elizabeth Thomson, DER
Kris Wetterstrand, DER
Joann A. Boughman, American Society of Human Genetics
Kirell Lakhman, GenomeWeb
Machi Dilworth, National Science Foundation
Scott Jenkins, The Blue Sheet
Edward Kloza, National Society of Genetic Counselors, Inc.
Sharon Olsen, International Society of Nurses in Genetics, Inc.
Ari Patrinos, U.S. Department of Energy
Gale Savage, Analytical Sciences, Inc.
Margaret Snyder, National Institutes of Health, OD/OER
Michael Watson, American College of Medical Genetics
Elke Jordan introduced new council member Eric Juengst. Russ Altman will join this afternoon's closed session as an ad hoc council member for the review of some applications.
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, Joann Boughman, 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 Machi Dilworth of the National Science Foundation.
Dr. Jordan extended welcome to Members of the Press: Scott Jenkins of the Blue Sheet and Kirell Lakhman of GenomeWeb.
The minutes from the February 11-12, 2002 Council meeting were approved with one change on page 7: 'Heterochromatic' was changed to 'heterogametic'.
The following dates were proposed for future meetings: September 9-10, 2002; February 10-11, 2003; May 19-20, 2003, September 15-16, 2003; February 9-10, 2004; May 10-11, 2004.
Dr. Jordan will retire July 1, 2002 after thirty years at NIH and fourteen years with NHGRI from its inception. She was presented with a collection of messages from present and former Council and advisory group members, expressing profound thanks, appreciation and admiration for her enormous contribution to the Institute and to the Human Genome Project.
Monique Mansoura has left her position as a policy analyst at NHGRI in order to take a position at the Office of Public Health Preparedness, where they examine issues of bio-terrorism. Kathy Hudson has left her position as NHGRI Director of the Office of Policy, Planning and Communications, and now directs the Genetics and Public Policy Center at the Phoebe R. Berman Bioethics Institute of the Johns Hopkins University, established through a grant from the Pew Charitable trusts.
Norman Davidson, chemical biologist at Caltech, passed away in February at age 85. He was one of the founding members of the advisory council for the Human Genome Project and earned the National Medal of Science for mapping properties of DNA. John Eisenberg, Director of the Agency for Health Care Research and Quality (AHRQ), passed away in March at age 55.
Harold Varmus has been named recipient of a 2001 National Medal of Science recognizing his service as the NIH Director from 1993 to 1999 and his significant scientific accomplishments. The General Motors Cancer Research Foundation Annual Scientific Conference will be held June 4 and 5, 2002 at the NIH campus. The 2002 Alfred P. Sloan Jr. Prize co-recipients are John Sulston and Robert Waterston. The Gairdner Foundation 2002 International Awards in Genomic Research were awarded to: Phillip P. Green, Eric S. Lander, Maynard V. Olson, John E. Sulston, Craig Venter, Michael S. Waterman, Robert Waterston, Jean Weissenbach. The Gairdner International Award of Merit was given to James D. Watson and Francis S. Collins.
The Senate has confirmed Elias Zerhouni's appointment as NIH Director. Dr. Zerhouni currently serves as the Executive Vice Dean at the School of Medicine at Johns Hopkins. President Bush has nominated Richard Carmona as Surgeon General. The Senate has not yet approved his nomination. Eve Slater was confirmed as the Department of Health and Human Services Assistant Secretary for Health on January 25, 2002, and officially sworn in on February 8, 2002.
By April 2003 and coincident with the completion of the finished human genome sequence, NHGRI intends to publish a genomics research plan encompassing the Institute's research activities from 2003 onward. The plan will be formally brought to the Council in February 2003. Eleven workshops will be held by November 2002, building on the December 2001 Airlie House meeting and leading to another meeting at Airlie House in November 2002. One such planning meeting already took place in April 2002 to address the future of proteomics research. Emphasis was placed on developing better technology, reagents needed for protein analysis, affinity reagents for all human proteins, comprehensive sets of RNAi reagents, common tissue banks, additional informatics resources, training opportunities and extensive access to proteomic resources. NHGRI will need to determine how best to contribute to research in this area.
In April 2003, a number of public outreach events are planned to mark the release of the new research plan, the 50th anniversary of the publication of the structure of DNA, and the completion of the finished human genome sequence. These activities are anticipated to include a day-long scientific symposium at NIH, a gala event at the Library of Congress, a public symposium at the Smithsonian, national 'DNA day' educational activity, museum events across the country, events at sequencing centers, an ecumenical religious observance at the National Cathedral and possibly a U.S. postage stamp.
The second round of review has taken place for the prioritization of organisms from which to make BAC libraries. The Genome Resource and Sequencing Priority Panel (GRASPP) reviewed four proposals covering 26 organisms and recommended thirteen (high or moderate priority) of these for library construction. The first review of genomic sequencing proposals was also conducted in March. Fourteen white papers were submitted covering 27 organisms, the results of which will be discussed in the closed session. The review assessed the biological and medical relevance of the species proposed, not sequencing strategies. Organisms were placed into priority categories. NHGRI staff, the sequencing centers and the Sequencing Advisory Panel will work together to address matching center interest with the approved organisms and determining the sequencing strategy to be employed.
The euchromatic portion of the human genome will be finished by April 2003. Currently, 78.2% is in finished form, up from 66.3% as reported at the February 2002 Council session. As recently reported at the Eleventh International Strategy Meeting on Human Genome Sequencing in May 2002, major gaps are already proportionally fewer per Megabase than were reported for the first two published human chromosomes, 21 and 22. All human chromosomes will be published by the end of 2003, along with a summary publication describing what has been learned since the publication describing the draft sequence in February 2001. The International Human Genome Sequencing Consortium (IHGSC) continues to be committed to meeting these goals and has recently organized collaborative efforts between centers to centrally close gaps. These efforts aim to leverage off the centers' areas of expertise and specific resource capabilities. The next IHGSC meeting will take place in Yokohama, Japan in late August 2002.
The first meeting of the International Sequencing Consortium, a forum for large-scale sequencing groups, was recently held at Cold Spring Harbor Laboratory. The consortium discussed topics such as current and future sequencing projects, data release policies, and potential collaborative interactions. Also at Cold Spring Harbor, a group of centers interested in sequencing the chimpanzee genome gathered to coordinate their efforts.
The Mouse Genome Sequencing Consortium (MGSC) has released an assembly of the whole genome shotgun dataset. They are now turning their efforts to a BAC-based finishing strategy. The Rat Genome Sequencing Consortium (RGSC), led by Richard Gibbs at Baylor and including Celera Genomics and Genome Therapeutics, has achieved four-fold coverage of the rat genome. The RGSC ultimately aims to produce an assembly of seven-fold coverage of the genome in whole genome shotgun reads and light shotgun coverage of a set of BAC clones.
Fourteen-fold coverage of the Ciona savignyi genome has been generated and an assembly is underway at the Whitehead Institute Center for Genome Research. The DOE Joint Genome Institute's Ciona intestinalis genome sequencing effort has achieved six-fold coverage and has produced an assembly consisting of 700 contigs and 300 scaffolds.
Genoscope and the Whitehead Institute have produced an assembly of the puffer fish, Tetraodon nigroviridis, from 5.6-fold genome coverage layered onto a physical map consisting of 23,000 fingerprinted BAC clones. The assembly can be downloaded from the Genoscope web site. A second puffer fish, Fugu rubripes, has been sequenced to six-fold coverage and assembled by the Fugu rubripes Sequencing and Analysis Consortium, led by Sydney Brenner.
A Request for Applications (RFA) for Large-scale Genotyping for the Haplotype Map of the Human Genome has been issued. Applications are due May 29, 2002 and will come to the September Council session for consideration. Large-scale data collection is planned for four populations from Africa, China, Europe and Japan, to accompany smaller-scale, pilot projects using samples from additional populations. This effort is an international collaboration between laboratories in a number of countries and will be supported by multiple NIH institutes, federal agencies and private organizations, potentially including The SNPs Consortium.
The second set of applications for Centers of Excellence in Genomic Science (CEGS) was considered at the February 2002 Council meeting and awards are currently being negotiated. The next application receipt date is June 3, 2002.
The Mammalian Gene Collection currently has approximately 13,100 non-redundant full open reading frame cDNA clones (7,900 human and 5,200 mouse).
Responses to the NHGRI Action Plan to increase the number of under-represented minorities in genome and ELSI research have been submitted and were recently assessed. NHGRI staff will work with grantees to maximize the success of the proposed activities towards meeting the Action Plan goals. A meeting to discuss "Increased Participation of Underrepresented Minority Groups in Doctoral Degree Programs in Genomics-relevant Science" was held April 15th on the NIH campus involving NIH staff and representatives from eighteen professional and scientific societies.
NHGRI and NIH/OD are organizing a conference with the National Medical Association, representatives of historically Black colleges and the Black Graduate Student Association on June 24 and 25, 2002 in order to expand collaborations between these organizations and to benefit minority populations.
Elizabeth Thomson has developed, and has been delivering to various audiences, a three part grant writing workshop for minority researchers.
William Gahl has verbally accepted the position as Clinical Director in the NHGRI intramural research program. Dr. Gahl is currently a Medical Officer and Chief, Section on Human Biochemical Genetics, Heritable Disorders Branch at NICHD.
A Vitamin C transporter knockout study, recently published in the May 2002 issue of Nature Medicine, shows a possible link between reduced vitamin C availability during pregnancy. The authors include Robert Nussbaum of the NHGRI Intramural Research Program.
The Senate Labor Health and Human Services and Education Appropriations Sub-committee held a hearing on March 21, 2002 to review the NIH budget. The House Labor Health and Human Services and Education Appropriations Sub-committee held an overview hearing regarding the NIH budget on March 13, 2002 and a 'theme hearing' entitled "Disease Prevention and Health Promotion", in which NHGRI participated, on April 16, 2002. The President's budget provided $27.3 billion for the NIH and $466,695,000 for the NHGRI in FY 2003. The hope is that Congress will provide this level of increase in the final appropriation to complete the five-year doubling of the NIH budget. Some in Congress are already beginning to ask about NIH funding levels for FY 2004.
Ralph Regula (R-OH) and David Obey (D-WI) asked NIH representatives to come to their districts and participate in Public Health Forums, "From Bench to Bedside and Beyond - How Research is Changing the Public's Health". Dr. Collins traveled with other NIH officials to the Marshfield Clinic in Wisconsin on May 4, 2002 and to Kent State University, Stark Campus in Ohio on May 11, 2002.
On March 13, 2002, Representatives Lynn Rivers (D-MI) and David Weldon (R-FL) introduced two bills addressing gene-patenting issues. HR 3967 would create a research exemption in the patent law and require public disclosure of information in patent applications filed by researchers. HR 3966 directs the Director of the Office of Science and Technology Policy to conduct a study of the impact of Federal policies on the innovation process for genomic technologies, and for other purposes.
On March 6, 2002, Senator Olympia Snowe (R-ME) introduced a new genetic nondiscrimination bill, S. 1995, the "Genetic Information Non-discrimination Act of 2002." This bill includes a section on employment discrimination and is similar to Senator Daschle's bill, S. 318, the "Genetic Non-discrimination in Health Insurance and Employment Act".
The 13th meeting of the Secretary's Advisory Committee on Genetic Testing, led by Ed McCabe, was held May 14 and 15, 2002 in Baltimore, MD. The agenda included highlights from the education conference, reports from the 'Informed Consent' and 'Internal Review Board' working groups and presentations of case studies from the 'Data' working group regarding the development and clinical applications of a genetic test.
The President's Bioethics Council, chaired by Leon Kass, has met three times this year. The primary focus of the Council's deliberations has been on the issue of cloning. The Council is currently developing advice to give to the President regarding this topic.
NHGRI and the Office of Rare Disease established a Genetic and Rare Disease Information Center to facilitate and enhance knowledge and understanding of genetic and rare disorders through effective dissemination of information. Since the Center opened on January 11, 2002, it has received over 1,500 inquires.
In February 2002, NHGRI launched the web version of "The Human Genome Project: Exploring Our Molecular Selves" multimedia education kit. Last week, the American Society of Human Genetics/Human Genome Project mentorship network program was launched on the website. Over 600 volunteers have signed up to participate in this program to help local high school teachers effectively use the education kit in the classroom.
Ari Patrinos provided a report on activities at the U.S. Department of Energy (DOE). The DOE's Joint Genome Institute (JGI) is involved in finishing human chromosomes 5, 9 and 16, which remain the highest priority within the biology program. The next major venture for the DOE is its "Bringing the Genome to Life" program. The first major round of reviews for this program is now underway and awards will be made this summer. Another DOE focus will be to support research resources that serve the broader scientific community by providing facilities for activities such as mass spectrometry, imaging, mouse genetics and genomic production sequencing. JGI has a similar system to NHGRI's process for choosing organisms for genomic sequencing.
Trevor Hawkins has left his position as Director of JGI and Eddy Rubin has been appointed the interim Director. The DOE production sequencing effort is currently sequencing a billion base pairs a month, with read lengths of over 600 bases and pass rates of over 90%. The sea squirt, Ciona intestinalis, will shortly reach eight-fold sequence coverage. The C. intestinalis assembly has been done and an annotation jamboree was held in April 2002. Some other DOE-supported sequencing projects are: the blue-green algae Chlamydomonas, an ocean diatom Thalassiosira pseudonana, the Black Cottonwood, a number of microbes and Xenopus tropicalis.
Bettie Graham outlined activities that have been initiated regarding the NHGRI Minority Action Plan that was approved by Council in May 2001. The overall goal of the Action Plan is to increase the number of under-represented minorities participating in genome and ELSI science research through community outreach, increased opportunities at all career levels and active participation by all three branches (Extramural, Intramural, and the Office of the Director) of NHGRI. Extramural grants required to respond to the Plan are: production sequencing centers, Centers of Excellence in Genomic Science, databases and other large grants.
A six member ad hoc group was convened in April 2002 to assess the responses received from NHGRI grantees and to provide advice for improving the proposed plans. Proposals often included multiple activities, each of which was assessed individually while keeping in mind particular strengths of the applicant institutions, milestones and evaluation components. Monitoring of these programs and tracking of progress will be handled through NHGRI staff efforts and a sub-committee of Council who will continue to provide advice to NHGRI grantees, evaluate how well activities are meeting NHGRI goals, and report periodically to Council.
Council noted that institutions are often competing for a very small pool of under-represented minority applicants interested in genomics, and that it is critical to broaden the pool through outreach. Recent statistics show that under-represented minorities do make up 15% of university graduates in the natural sciences, but that under-represented minority students do not enter or drop out of graduate programs at a higher rate than others.
Bob Waterston reported on the status of the mouse genome assembly and its analysis. The project to sequence and assemble the C57BL/6J mouse genome is a collaboration between Washington University Genome Sequencing Center, the Whitehead Institute Center for Genome Research, the Sanger Institute and Ensembl. The main components of this effort are a physical map of fingerprinted BAC clones (47.8X clone coverage), six-fold (6.3X) sequence coverage of the genome in whole genome shotgun reads, and a BAC-based finishing strategy.
Of 41.4 million whole genome shotgun sequence reads produced, 33.6 million were used in a whole genome assembly. Two assemblies were performed, one by David Jaffe at MIT using the Arachne assembler and one by Jim Mullikin at the Sanger Institute using the PHUSION assembler. Deanna Church at NCBI evaluated the two assemblies in order to choose one for submission to GenBank. As a result, the Arachne assembly was submitted to GenBank in early May 2002. The assembly consists of 224,713 contigs, 44,543 super-contigs and 98 ultra-contigs (super-contigs layered on to the physical map). A total of 2.383 gigabases of high quality sequence was anchored to the physical map. The assembly exhibits very good agreement with other genetic and physical maps. The Mouse Genome Sequencing Consortium has begun the BAC-based finishing component of the project.
A large group of collaborators are working on the initial analysis of the mouse genome assembly. The mouse genome has been aligned to the human genome to locate syntenic regions and identify putative functional elements. The estimation of neutral evolution rates has been done using four-fold degenerate sites in coding sequence and aligned ancient repeats. The level of conservation between the two species has been found to be variable across the genome. Using ESTs, full-length cDNAs (from RefSeq, the Mammalian Gene Collection and the RIKEN Institute), homologies, improved gene finders and mouse/human conservation, approximately 28,000 genes have been predicted.
Peter Good provided a status report on Model Organism Database (MOD) activities. There are four MODs currently supported by NHGRI: Saccharomyces Genome Database, WormBase, FlyBase and Mouse Genome Database. In addition, a 'Request for Applications' (RFA) was recently issued for a central protein database. Applications have been submitted and will come to the September 2002 Council session. Another RFA was also issued for developing generic components of MODs. Applications have just been received and will also come to the September 2002 Council session for consideration.
Recently, there was a Model Organism Database meeting co-chaired by Lincoln Stein and Steve Oliver. Six main topics were addressed by the group: the essential nature of MODs, good practices for MODs, benefits of MOD reuse, high priority needs, moving towards generic components and intellectual property issues. In order to promote interoperability between MOD components, regular workshops were recommended. There was strong support for open source software.
Dr. Jordan noted the items of interest in the Council-folders, and referred Council to material in Tab N.
Dr. Collins noted that applications responsive to the Haplotype Map Project RFA will be discussed at the September 2002 Council session, along with a substantial discussion of the NHGRI planning process. Other items for presentations were suggested: comparative genomics of the rat genome made by a member of the Rat Genome Sequencing Consortium, presentation by Eric Green of his lab's multi-species comparative sequencing project, comparative genomics of Caenorhabditis elegans and C. briggsae.
Dr. Jordan referred to the budget table found under Tab P.
Dr. Jordan read the Conflict of Interest policy to Council and asked them to sign the forms provided.
In closed session, the Council reviewed 90 applications, totaling $21,990,478. The applications included 25 regular research grants, one response to a program announcement, six pilot projects, one program project, 23 ELSI grants, one area grant, two conference grants, one training grant, one continuing education training program grant, 15 SBIR Phase I, 2 SBIR Phase II, five fellowship grants, two STTR Phase I and five others. A total of 45 applications requesting $13,389,514 were recommended.
I hereby certify that, to the best of my knowledge, the foregoing minutes are accurate and complete.
|Top of page|
Last Reviewed: March 2006