Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, March 1991; 2(6)
Informatics, ELSI, and Sequencing Working Groups Describe Progress
The DOE-NIH Joint Subcommittee on the Human Genome convened in Bethesda, Maryland, on December 3, 1990, with Sheldon Wolff and Norton Zinder presiding. Reports were heard from the joint working groups on DNA sequencing; informatics; and ethical, legal, and social issues. Representatives of international groups and other U.S. agencies were also present to describe the progress of their respective genome programs. [For a list of subcommittee members and their affiliations, see HGN 2(3), 7 (September 1990).]
[For a list of members, see HGN 2(2), 10 (July 1990).]
David Benton [National Center for Human Genome Research (NCHGR)] reported on the JITF meeting (November 30-December 1, 1990), which addressed the Human Genome Project need for public databases containing map and sequence data (see article JITF Discusses Map and Sequence Databases). Benton stated that JITF has developed a number of guidelines concerning the establishment of genome data resources.
The JITF report prompted a discussion of various informatics issues. Several participants noted that the complexity of currently available physical mapping data necessitates an experimental approach to database development and a period during which experience can be acquired. Mark Pearson (Du Pont) noted that three major database projects-the Genome Data Base at Johns Hopkins University, GenBank® at Los Alamos National Laboratory, and GenInfo at the NIH National Center for Biotechnology Information-are developing products that will be available this year and are attempting to integrate their operations and to facilitate access to these databases.
Maynard Olson (Washington University) noted at least three levels at which databases enter into the human genome program and cautioned against trying to develop a uniform technical standard that crosses these diverse settings:
Nancy Wexler (Columbia University and Hereditary Disease Foundation) discussed the September 10, 1990, ELSI meeting [see HGN 2(4), 6 (November 1990)]. Wexler noted that additional funding sources are needed because pilot testing programs will involve costly service components such as DNA analysis, as well as educational efforts to explain the importance of such programs to other agencies. She emphasized that the question of introducing new genetic screening tests will extend beyond cystic fibrosis (CF) as genetic linkages for other disorders are discovered.
Phillip Sharp (Massachusetts Institute of Technology) remarked that the national institutes having an interest in CF might help support pilot screening programs, and Robert Katz (NIH National Institute of Diabetes and Digestive and Kidney Diseases) suggested discussing the issue with the institutes involved in CF research.
The question of whether the Human Genome Project should fund pilot genetic-screening programs was discussed at length. While participants agreed that CF offers a paradigm for conducting and evaluating such programs, they expressed concern that the genome project might be expected to fund pilot programs for every genetically linked disease. Wexler predicted that although different pilot programs for individual diseases may be necessary at first, the need for research on these programs will decrease as experience is gained and standards of delivery are developed (see Subcommittee, PACHG Recommendation).
Mark Guyer (NCHGR) provided an update on efforts to establish the framework genetic linkage map of index markers that had been described by the mapping working group. He reported that applications received in response to the NCHGR July 1990 Request for Applications would be reviewed by the NIH National Advisory Council for Human Genome Research and awards made early in 1991.
Information on the developing framework map was provided in the subcommittee meeting notebooks. The information was based on presentations given at a meeting in Cincinnati, Ohio, on October 16, 1990. The number of markers, their identification, and their availability were summarized for each chromosome. Approximately 95% of the markers listed are in the public domain.
Guyer also mentioned two chromosome-specific workshops held since the June 1990 subcommittee and NIH Program Advisory Committee on the Human Genome (PACHG) meetings:
He added that a second round of workshops is planned for chromosomes 3, 11, 17, 21, 22, and X.
Director James B. Wyngaarden described the primary goals of HUGO:
HUGO has over 333 members representing more than 25 countries and is establishing offices in Bethesda, Maryland; Europe; and Japan. [For more information and a list of officers, see HGN 2(2), 6 (July 1990) and 2(4), 4 (November 1990).]
Wyngaarden stated that HUGO had established subcommittees, similar to the joint NIH-DOE working groups, to deal with ethical, legal, and social issues; informatics; intellectual property; mouse gene mapping; and genetic and physical mapping of the human genome. He noted that HUGO is currently involved in activities related to its initial mission of coordinating chromosome-specific workshops. Wyngaarden announced that a HUGO Council meeting in Oxford, England, on January 7 would explore the idea of identifying a conference center where these workshops might be conducted and where the computer facilities necessary for information exchange might reside. He reported that plans are proceeding smoothly for the 11th International Workshop on Human Gene Mapping to be held in London in August.
Bronwen Loder (CEC and HUGO) announced that the first phase of the CEC human genome program, whose objectives are similar to those of the U.S. project, began in June 1990 with a 2-year budget of approximately $20 million. She noted that this figure represents new money to be spent entirely on the human genome and that model organism research is being supported in other ways. She added that the second phase of the program, scheduled to begin in June 1992, is likely to receive considerably more funding than the first phase.
Loder reported that the following contracts for central facilities have been awarded:
Loder stated that cDNA sequencing is an important part of the European program, accounting for roughly 10% of the budget. She noted that contracts will be established this year with the data resource center at the German Cancer Center in Heidelberg and with five laboratories that will provide a yeast artificial chromosome screening service. The CEC program has requested proposals for projects in contig mapping, development of new mapping and sequencing technologies, and informatics.
Loder added that applications have also been requested for pilot studies on development and assessment of low-cost, efficient methods for specific diagnosis of severe genetic defects. The training component of the CEC program will soon be announced, and a committee on ethical, legal, and social issues will be established by formal action of the commission.
Diane McLaren (Medical Research Council, London) described the U.K. Human Genome Mapping Project and Michele Durand (Science Attache, French Embassy) presented information about the French human genome research program that began early this year [see HGN 2(5), 12 (January 1991)].
Reports from U.S. agencies were given by Stephen Heller [U.S. Department of Agriculture (USDA)] and Mary Clutter [National Science Foundation (NSF)]. Heller stated that the goal of the USDA plant genome research program is to facilitate the genetic improvement of plants by locating important genes and markers on chromosomes, determining gene structure, and transferring genes to improve performance. He referred to a Request for Proposals [Federal Register 55, 49380 (November 27, 1990)] calling for research in three areas: (1) generation of broad maps of agronomic and forest species with 25-cM gaps, (2) intense mapping and characterization of chromosomal trait regions, and (3) development of new technologies for mapping and sequencing.
Heller noted that the USDA program's FY 1991 budget allocation amounts to $14.674 million in new money, of which $11 million will be used for competitive grants and $3.674 million (a line item to the Agricultural Research Service) for the operational expenses of the Office of Plant Genome Mapping, initial mapping activities, database and electronic communications, prototype data analysis of two major crop species and one forest tree species, and laboratory robotics development. A portion of the Agricultural Research Service funds will also be used to help support the NSF Arabidopsis project [see HGN 2(3), 13 (September 1990)].
Clutter stated that the NSF FY 1991 budget includes $5 million in new money for the first year of the Arabidopsis genome project.
Following these presentations, James Watson (Director, NIH NCHGR) raised the question of establishing an NIH-DOE joint working group on mouse genome research. Guyer stated that participants in the Fifth International Mouse Workshop (November 4-8, 1990, Annapolis, Maryland) discussed a unified effort to develop mouse genetic and physical maps. He added that the mouse research community had requested that a working group be formed to help coordinate research and to develop a policy for mouse genomics in the United States.
To receive minutes of PACHG and Subcommittee Meetings, contact:
Next Scheduled DOE-NIH Joint Subcommittee and PACHG Meetings Set for June 25
Subcommittee, PACHG Recommendation Supports CF Pilot Testing
The subcommittee and PACHG formulated a draft message to NIH Acting Director William Raub. This message stated that the two groups recognize the importance of evaluating CF genetic testing as a precedent for intrducing new genetic tests that will result from the Human Genome Project and emphasized the immediate need for funding mechanisms to support CF researh-based pilot testing. The draft message contained the recommendation that NCHGR take a leadership role in developing these mechanisms.
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v2n6).
The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.