National Advisory Council for Human Genome Research
Summary of Meeting
May 21-22, 2001
The open session of the National Advisory Council for Human Genome Research (NHGRI) was convened for its thirty-second meeting at 8:30 a.m. on May 21, 2001, at the Natcher Conference Center, National Institutes of Health (NIH), Bethesda, MD. Dr. Francis Collins, director of the National Human Genome Research Institute (NHGRI), called the meeting to order.
The meeting was open to the public from 8:30 a.m. until 3:15 p.m. on May 21, 2001. In accordance with the provisions of Public Law 92-463, the meeting was closed to the public from 3:15 p.m. on May 21 until adjournment on May 22 for the review, discussion, and evaluation of grant applications. (1)
Council members present:
Ronald W. Davis
H. Robert Horvitz
Bronya J. Keats
Richard P. Lifton
Kim J. Nickerson
Janet D. Rowley
Robert H. Waterston
Alan R. Williamson
Council members absent:
Gerard Schellenberg (Ex-Officio Member)
Staff from the National Human Genome Research Institute:
Kate Berg, DIR
Joy Boyer, DER
Zena Breeden, OD
Lisa Brooks, DER
Jean Cahill, DER
Monika Christman, DER
Francis S. Collins, OD
Adam Felsenfeld, DER
Lynn Frampton, DER
Barbara Fuller, OD
Bettie Graham, DER
Karen Hajos, OD
Linda Hall, DER
Kathy Hudson, OD
Linda Jacobson, DER
Elke Jordan, OD
Ron King, DIR
Charles Leasure, OD
Monique Mansoura, OD
Jean McEwen, DER
Rodecia McKnight, DER
Susan Mix, OD
Kenji Nakamura, DER
Khang Nguyen, DER
Diane Patterson, DER
Jane Peterson, DER
Elizabeth Pledger, OD
Rudy Pozzatti, DER
Jerry Roberts, DER
Jeff Schloss, DER
Erin Shannon, DER
Larry Thompson, OD
Elizabeth Thomson, DER
Kris Wetterstrand, DER
Others present for all or a portion of the meeting:
Sally Amero, NIH/CSR
Richard Anderson, NIGMS
Sherri Calvo, Genome Web
Machi Dilworth, National Science Foundation
Irene Eckstrand, NIGMS
Marvin Frazier, U.S. Department of Energy
Lauren Hafner, FDC Reports
Rodney Howell, American College of Human Genetics
Jean Jenkins, International Society of Nurses in Genetics
Edward Kloza, National Society of Genetic Counselors
Tim Leshan, Capital Consulting
Ernest Marquez, NIGMS
Bernice Morrow, American Society of Human Genetics
Sharon Olsen, International Society of Nurses in Genetics
Liz Pennisi, Science Magazine
Chris Peterson, SRI
Cliff Poodry, NIGMS
Derrick Tabor, NIGMS
John Welch, Motorola
Introduction of Liaisons and New Staff
Dr. Jordan welcomed liaisons to the council from the professional societies: Rodney Howell, the representative from the American College of Human Genetics, Edward Kloza, the representative from the National Society of Genetic Counselors, Bernice Morrow from the American Society of Human Genetics, and Jean Jenkins from the International Society of Nurses in Genetics. She also introduced Machi Dilworth from the National Science Foundation (NSF), Cliff Poodry from the National Institute of General Medical Sciences, and Marvin Frazier from the Department of Energy (DOE).
Dr. Jordan also extended welcome to Members of the Press: Lauren Hafner of the Blue Sheet and Liz Pennisi from Science Magazine.
Elizabeth Pledger was introduced as Dr. Jordan's new assistant and Larry Thompson was introduced as the new Chief of Communications for NHGRI.
Approval of Minutes
The minutes from February 13, 2001 NACHGR meeting were approved as submitted
Future Meeting Dates
The following dates were proposed for future meetings: September 10-11, 2001; February 11-12, 2002; May 20-21, 2002; September 9-10, 2002; February 10-11, 2003; May 19-20, 2003. Dr. Jordan mentioned that those members going off council at the end of September 2001 may be asked to extend their appointment and attend the February 2002 council meeting.
Rick Lifton and Phil Green were elected to the National Academy of Sciences.
Shirley M. Caldwell Tilghman was elected Princeton's 19th President.
Donna J. Dean was appointed the Acting Director of the National Institute of Biomedical Imaging and Bioengineering (NIBIB).
Effective at the start of FY2002, NIGMS will assume oversight of the NIH's Biomedical Information Science and Technology Initiative (BISTI) through management of the BISTI Consortium.
Craig Higgins, former senior advisor on legislative affairs and director of the Education, Policy and Outreach Branch, left NHGRI/OD to become staff director for the Appropriations Subcommittee in the House responsible for NIH funding.
The search for a new NIH director is still ongoing. Various steps are being taken by Department of Health and Human Services (DHHS) Secretary Tommy Thompson and the White House to fill the position.
New NHGRI Initiatives in Genomics
A workshop to explore new ways of enhancing minority participation in genomics research was held April 16-17, 2001. The action plan from the meeting will be presented later in the open session of this council.
The Genome Center at Howard University was dedicated on May 1-2, 2001. Dr. Collins referred to this event as an example of the type of partnerships NHGRI would like to see developed in the future.
Dr. Collins visited NMSU and Diné College (on the Navajo Reservation in Tsaile, AZ) and interacted with faculty and students about their views of Native Americans and Genomics.
The first round of CEGS applications have been received and peer reviewed. These will be discussed in the closed session of this council. Awards will be made over the summer.
Recent Scientific Accomplishments
The publication of the draft sequence of the human genome, on February 15, 2001, has been acclaimed as a significant milestone and has stirred fascinating follow-up research. Currently, 40 percent of the human genome is in finished form. 95 percent is either finished or draft.
The Advisory Committee for Human Genome Sequencing met March 7-8, 2001.
The Ninth International Strategy meeting on Human Genome Sequencing was held May 9, 2001, Cold Spring Harbor, New York. The meeting involved the 16 centers who are responsible for finishing the genome. They are currently setting up a new tool to track the status of finishing and a more rigorous system to track gap closure. These 16 centers will meet again in late August in China. The goal is to have all the chromosomes in complete form no later than April 25, 2003, which is the 50th anniversary of the publication of the structure of the DNA double helix. Each chromosome will likely have a publication marking its completion. Dr. Collins thanked Team Sequence for their important role in facilitating the finishing process.
The Mouse Sequencing Consortium, a public-private consortium, was formed last October to accelerate sequencing of the mouse genome. The completion of 3X coverage of 95 percent of the genome was announced in early May. Over 16 million sequence traces have been deposited in the National Center for Biotechnology Information (NCBI) repository.
On February 28, 2001, the NIH expanded the sequencing program to include sequencing of the rat genome. Grants were awarded to Baylor College of Medicine and Celera Genomics. The scientific strategy is well planned out and these groups, in addition to Genome Therapeutics Corporation, which was previously funded, will work together to achieve full coverage of the rat.
The Mammalian Gene Collection (MGC) is an effort to obtain full length cDNA clones and sequence for as many mouse and human genes as possible. Currently there are 12 NIH institutes participating in the project. The goal is to deposit the sequence in GenBank and make clones available to the community. 75 percent of the clones sequenced so far do appear to be full length. A total of 7,500 clones have been completed.
There was a meeting last week in Boston to discuss the feasibility of taking full-length cDNA clones and putting them into expression vectors using the Gateway system. This project, called FlexGene, is being piloted by Josh LaBaer at Harvard University. It would be a natural follow-up to the MGC.
At last count, over 2.8 million SNPs are now in dbSNP. Dr. Collins noted that the presentations at the recent Cold Spring Harbor meeting first demonstrated that many investigators are utilizing these SNPs to do fascinating research previously impossible.
The first ELSI Research Advisory (ERA) meeting was held January 18-19, 2001. The next meeting is June 4-5, 2001.
The Hemochromatosis and Iron Overload study funded by NHGRI and National Heart, Lung and Blood Institute (NHLBI) is underway. This is a large scale effort to investigate the value of offering screening for hereditary hemochromatosis (HH). Recruitment of over 4,500 individuals has already begun.
The recent Blue Ribbon Panel review of the NHGRI intramural program will be reported on by Raju Kucherlapati in the closed session.
Budget and Congressional Activities
The FY2002 HHS budget for NIH includes a 13.5 percent increase.
On April 4, 2001 the House Labor HHS Appropriations Subcommittee held the first in a series of "theme" hearings on the FY2002 budget, entitled Special Populations/ Health Disparities, at which NHGRI testified. Additional hearings are scheduled.
Currently several Congressional Bills regarding genetic non-discrimination are under consideration. Dr. Collins pointed out the recent genetic testing of employees for susceptibility to carpal tunnel syndrome by the Burlington-Northern Sante Fe Railroad Company as an example indicating the urgent need for legislation.
There was a conference on 3rd Party Rights and Risks at Virginia Commonwealth University on March 8-9, 2001. Under discussion was whether individuals in pedigree research can provide information about family members without getting informed consent from them. Dr. Collins pointed out that the oversight of human subject protection has moved from NIH to the Office of the Secretary. This office has a new advisory committee, the National Human Research Protection Advisory Committee. They plan to set up a Genetics Working Group to study the issue of informed consent for family members in pedigree studies.
Education and Outreach
Under Kathy Hudson's leadership, a multi-media kit to accompany the publication of the human sequence was officially released on February 12, 2001. So far, 40,000 kits have been sent out. NHGRI is currently working on a partnership with the American Society of Human Genetics where over 600 scientists have volunteered to serve as mentors to their local school systems in connection with use of the kit.
Plans are underway for the Third Annual Consumer Day to be held in Fall 2001.
The Genetic Alliance is sponsoring the People's Genome Celebration on June 8-10, 2001 in Washington, D.C.
Joseph McInerney has been appointed the Executive Director of the National Coalition for Health Professional Education in Genetics (NCHPEG). On February 14, 2000, NCHPEG endorsed recommendations for Core Competencies in Genetics Essential for All Health-Care Professionals.
The Assembly Comparison Workshop, co-sponsored by Celera and NHGRI will be held June 6, 2001 at HHMI headquarters. This is an effort to compare and evaluate the strategies for sequencing the mouse and rat genomes.
There will be a Proteomics workshop held jointly with NIGMS in the Fall of 2001. The purpose of the workshop will be to define the terms and identify the opportunities for research and needs for resources to stimulate this field of research.
Council Discussion of the Director's Report
Dr. Kucherlapati commented that any policies affecting pedigree research would have significant implications for human genetics research. It may be worthwhile for council to be informed about developments and promote an outcome that will encourage rather than hinder this type of research. Dr. Burgess pointed out that these decisions could have damaging implications, not just for pedigree studies, but for any type of genetic testing or study. Dr. Keats suggested that we ask that a member of council be on the genetics working group of NHRPAC currently reviewing informed consent policy for pedigree research. Dr. Collins agreed to find out the status of this committee and recommend council have a direct connection.
Report from the Department of Energy (DOE)
Dr. Frazier, Director of the Life Sciences Division at the DOE updated the council on genome-related activities at DOE. Dr. Frazier reported they have finished 39.1 Mb of Human Chromosome 19 and 29.7 Mb of Human Chromosome 16. They have had more difficulty finishing Human Chromosome 5, but are currently getting additional help from Washington University.
The DOE has finished 3 microbial genomes to 8X draft coverage. These organisms play roles as plant pathogens, as energy producers, or in bio-terrorism. They are also sequencing the White Rot Fungus which is an important organism for biomass conversion and hope this will be completed in the next year. In addition, DOE has completed 1X coverage of Ciona intestinalis and hope to have 6X coverage of Fugu by the end of the year.
Dr. Frazier outlined the DOE's future plans in the "Genomes to Life" advisory report. The program goals include (a) Using high throughput processes to identify molecular machines of life, (b) Characterizing gene regulatory networks, (c) Characterizing the functional repertoire of natural microbial communities, and (d) Developing the computational capabilities to advance understanding of complex biological systems and predict their behavior.
Update on Workshop on Prioritization of Organisms for Genomic Sequencing
The goal of the July 9-10, 2001 workshop is to define criteria that will be used to decide sequencing priority among various organisms. The co-chairs of the meeting are Robert Horvitz and David Botstein.
The criteria will apply to organisms on which we currently have some genomic information and which we would like to sequence for comparative purposes. It will address the question that given genomes we know, what other genomes will make them more useful for solving problems in biology and medicine.
These guidelines will allow current large-scale sequencers, new sequencers and the scientific community to participate in the selection process. There has been some discussion of general ideas for the workshop and a list of individuals who will be invited to attend has been developed. The goal is to have 30 to 40 experts in comparative genomics, functional genomics, genome structure, evolution, population genetics, phylogeny and bioinformatics, as well as representatives from the sequencing centers.
Council discussion of Workshop on Prioritization of Organisms for Genomic Sequencing
Dr. Olson regretted he would not be able to attend the workshop but stressed his concern that comparative sequencing would be very resource intensive and increasingly difficult to justify outside of the scientific community. He felt the meeting organizers should give considerable thought to developing a vision for the project and gaining public interest. He suggested the "big picture" could focus on primate genomics, as the direct impact on medicine will underline the primary focus on health.
Dr. Gelbart agreed that NHGRI must continue to capture the imagination of both the public and Congress but we need to see what comes out of this workshop first.
Dr. Collins agreed that the study of primate genomes would interest the public. Dr. Guyer pointed out that this is just one of the many discussions that will take place at the workshop.
Report of Minority Training Workshop and Plan
NHGRI held a workshop April 16-17, 2001 to brainstorm creative ideas and models for increasing the number of underrepresented minorities pursuing research careers in genomics and related sciences. Dr. Collins thanked members of the planning committee: Kim Nickerson, David Burgess, Cliff Poodry, Elke Jordan, and Bettie Graham for their help with this initiative.
Dr. Graham gave a summary of the workshop to council. The workshop participants developed a list of factors they felt contributed to minority success in training for research careers. These include curriculum, research experience, mentoring, managing transitions, financial assistance, role models, early science education and partnerships. They also outlined initiatives that have been effective in recruiting and graduating underrepresented minority students. This led to a set of guiding principles for incorporating diversity into NHGRI programs. The workshop participants also suggested specific activities they felt would increase the number of underrepresented minorities in genomics research.
All of the above mentioned principles and recommendations can be found in the Workshop Summary, "Identifying New Paradigms for Increasing the Number of Minorities Pursuing Genomics Research."
Council Discussion of the Report on the Minority Training Workshop
Dr. Burgess remarked on the frank and open discussion generated by this workshop. He felt the meeting produced good advice from a diverse group of individuals. He stressed that there is an expectation from the community that something needs to be done and council should take this initiative very seriously.
Dr. Buchanan suggested adding more to the action plan that specifically relates to ELSI.
Dr. Horvitz wondered whether the situation with respect to underrepresented minorities was worse in genomics than in other fields of biomedicine. It does vary by field and genomics is particularly low in minority scientists.
There was concern as to how the list of effective programs was generated and to what extent they were known to be effective. Dr. Graham stated that the success of most existing minority programs is measured by self evaluation. Both the Myerhoff and UC Irvine programs are very successful in graduating students by giving them high level courses and significant mentoring. However, these programs are very difficult to replicate throughout the country as each situation is unique. The programs must have scientists involved and interested in the students for the program to be successful.
Based on the information and suggestions gathered at the workshop on minority training, NHGRI developed an action plan to present to council. Dr. Collins requested that council members look at the individual elements of the action plan and give feedback for feasibility and offer advice to fine tune the document. He also encouraged council members to give their views on what is not included in the action plan and should be.
Comments on the Proposed NHGRI Plan for Increasing the Number of Underrepresented Minorities Trained in Genomics and ELSI Research
Dr. Burgess suggested that those centers offering educational outreach activities have the capability to advertise these efforts on their Web pages. NHGRI could create a Web site template for these centers.
Dr. Nickerson stressed the importance of having timely and concrete benchmarks. He pointed out that the action plan has no clear time table for the target goals. For example, how many minority conferences does NHGRI plan to attend? He added that NHGRI will need a plan for identifying success, which includes knowing which programs to continue and which ones to close.
Dr. Davis recalled from his experience that a more bottom up approach may be helpful. He suggested a system with direct support from one step to the next. Providing the time for mentoring and support is easier if individuals come to his lab with funding. He suggested that minorities may not know the minority supplement program exists.
Dr. Horvitz suggested that production centers have an opportunity for identifying people who are interested in genomics research. By offering a fellowship and scholarship program within the production centers, they could identify individuals with interest and talents in genomics.
Dr. Burgess suggested adding concrete and measurable goals to the plan. Each center or grant must have their own plan for success but NHGRI must equip the centers with the resources they need to succeed.
Dr. Buchanan noticed the action plan did not include partnering with industry or foundations. Dr. Nickerson pointed out that these groups attended the workshop and were enthusiastic but this was not highlighted in the report.
Dr. Gelbart pointed to the success of the National Institute of General Medical Sciences (NIGMS) MARC program. He suggested that NHGRI develop their own similar undergraduate programs. It was pointed out that the Action Plan calls for partnering with NIGMS in their minority programs.
Dr. Olson recalled a program in Seattle where they take genome sequencing into high school classrooms. This considerable contact with the public has made the genetics department more successful in graduating minority Ph.D. students.
Dr. Davis said he had a really tough time recruiting any students into genomics because the field requires them to be good at many aspects of science and it scares them. The last five graduate students he mentored have all started companies. Dr. Waterston agreed that it is difficult to get graduate students into this field but there is the opportunity to take advantage of the recent publicity about the genome. He has had opportunities to involve college and high school teachers in genome activities.
Dr. Burgess suggested using the recent report on health disparities in this country as a pitch to minority communities, as genomics may very well give new insights into the causes for health disparities.
Dr. Williamson wondered whether these were really economic and educational disparities. To what extent is it an under-representation of children from poorer backgrounds? Dr Nickerson referenced a WHO report on social factors and health. When you look at health outcomes both social and economic factors play a role but there are important covariates which include education, occupation, and social/ economic status.
Dr. Gelbart suggested that the CEGS may be better places to capture students at the graduate level and production centers may be better at capturing students at the undergraduate level.
Dr. Burgess referred to data about Myerhoff students, citing that students who were accepted to the program and then chose to go to other schools dropped out at an alarming rate where as those who entered the program did very well. Thus, apart from other factors, the nature of the program made a difference.
Dr. Burgess thought the Short Course for Faculty at Minority Institutions was a good way to start but he is not sure if it encourages curricular changes at the home institutions of the faculty.
Dr. King pointed out that 90 percent of items in the intramural action plan are current initiatives. Only 10 percent are new initiatives. This plan has been implemented for a number of years and has undergone an evolution and process of development. Each of these programs has taken a lot of time, patience, thought, and energy to succeed.
Dr. Nickerson wondered what the measurable goals for the intramural program were. He also asked about specific activities proposed to bring students in for summer internships.
Dr. Gelbart asked what ideas both DER and DIR had for mentoring. He felt that paying someone to mentor at the large centers would be a good investment.
Dr. King emphasized that evaluation must be folded into all of these activities. Keeping track of numbers and trainees will require additional staff effort.
NHGRI plans to reconvene some of the advisors to see where the program is going and to conduct an evaluation in five years.
Dr. Burgess cautioned about excessive emphasis on individual successes. Instead, programs should be evaluated for overall success. Dr. Jordan pointed out that tracking individuals provides an opportunity for intervention if there is a drop-out situation, but agreed that programs as a whole will be evaluated.
Dr. Collins thanked the Council for their comments. NHGRI will revise the Action Plan accordingly, incorporate suggestions and circulate a revised copy by e-mail to Council for quick turn around comments.
Dr. Burke suggested the minority training initiative be added to the agenda at the ERA meeting June 4-5, 2001. Comments from this meeting should be added to the draft.
Dr. Collins requested that Council e-mail suggestions to himself, Elke Jordan, or Bettie Graham so these can be incorporated. NHGRI will aim to send out the new version in mid-June for a quick turn around. He hopes to have a working plan by mid-July.
Dr. Nickerson suggested that the action plan be sent to the workshop participants when it is final. Dr. Jordan assured him that was the plan.
Report on Protein Database Workshop
Lisa Brooks reported on the recent workshop sponsored by the National Library of Medicine (NLM), the NIGM S and NHGRI that was held to discuss the need for a central database to collect and curate protein related information. John Moult chaired the workshop, which included representatives from existing databases, users and funding agencies. In the face of increased availability of protein and proteomic data, attendees confirmed the need for a centralized database to provide standard formats and quality. The central database would need to interact with other protein databases, as well as ensure that the data is made freely available.
Concept Clearance - RFA for BAC Library Characterization
Jane Peterson presented a concept for an RFA for Bacterial Artificial Chromosome (BAC) Library Characterization that follows the BAC Library Construction RFA that was brought to council in February 2001. High resolution fingerprinting and BAC end sequencing are currently the technologies being utilized to characterize BAC libraries. This RFA would be used to encourage increased efficiency in these technologies and new, innovative approaches, as well as to increase the overall capacity for these types of activities. The RFA would fund at least two groups to characterize, in total, two large genomes in the first year, four large genomes in the second year and four or more large genomes in the third year.
In response to council inquiry, Staff explained that these activities would be intimately integrated into the process of organism selection for the next phase of genomic sequencing. Groups dedicated to working on a particular organism would not be turned away if a BAC library for their organism did not exist and if it was thought that they could offer particular technological innovation and/or process improvement that could be generally applied to the field. When setting throughput goals, Dr. Waterston encouraged NHGRI to take into account the number of clones in a library, which is related to the insert size and size of the genome. NHGRI staff will specify in the RFA the major goals of increasing the capacity for BAC library characterization through increasing the number of groups undertaking this activity, reducing costs, improving efficiencies and/or developing new technologies.
Concept Clearance - Developing Robust Components for Model Organism Databases
Dr. Brooks described a concept for developing components for model organism databases. NHGRI currently funds databases for four major model organism (fly, yeast, worm and mouse), but there are many more. There was a meeting about a year ago to address the desire not to fund the development of a new database for every model organism. At the meeting the concept of MODules (Model Organism Database) was developed, which are contained, exportable database components that can be used for a variety of organisms.
NHGRI and NIGMS have started a supplement program for the existing model organism databases to develop exportable MODules and would like to support other groups to develop MODules for new model organisms. All new MODules need to be integrated with the current major model organism databases and have common features (i.e. XML format, operable between groups, independent of each other). Four million dollars is allotted for the supplements to the existing databases and $4M additional for the competitive program to develop additional MODules. Dr. Olson advocated the inclusion of the human genome database as well as efforts for microbial genomes.
Announcements and Items of Interest
Dr. Jordan noted the items of interest in the Council folders, and referred Council to material in Tabs "N" through "S."
Dr. Collins suggested that at the next Council meeting NHGRI present the institute's strategy for developing the next five-year scientific plan. NHGRI needs to define its future role in genomics and other scientific areas.
Dr. Gelbart suggested a discussion of human annotation. NHGRI staff will try to arrange presentations of current human annotation efforts by the European Bioinformatics Institute (EBI), the NCBI and the University of California at Santa Cruz at a future meeting.
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 84 applications, totaling $76,248,885. The applications included 30 regular research grants, two pilot projects, one program project, 10 ELSI grants, three area grants, 19 center grants, one conference grant, three research career development awards, two training grants, five SBIR Phase I, four SBIR Phase II, two fellowship grants, and two others. A total of 54 applications requesting $58,396,173 were recommended.
I hereby certify that, to the best of my knowledge, the foregoing minutes are accurate and complete.
1 For the record, it is noted that to avoid a conflict of interest, Council members absent themselves from the meeting when the Council discusses applications from their respective institutions or in which a conflict of interest may occur. Members are asked to sign a statement to this effect. This does not apply to "en bloc."
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Last Reviewed: September 2005