Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, May 1992; 4(1)
At the January meeting of the NIH-DOE Joint Subcommittee on the Human Genome in Irvine, California, Paul Berg (Stanford University School of Medicine), Chair of the NIH Program Advisory Committee on the Human Genome (PACHG), and Leonard Lerman [Massachusetts Institute of Technology (MIT)] of the DOE Health and Environmental Research Advisory Committee presided as the subcommittee heard reports from several NIH-DOE working groups.
ELSI Working Group. Nancy Wexler (Hereditary Disease Foundation and Columbia University) spoke for the DOE-NIH Joint Working Group on Ethical, Legal, and Social Issues (ELSI) related to data generated by the Human Genome Project. She reviewed progress in five activities: (1) an NIH-funded consortium of eight clinical studies related to cystic fibrosis; (2) ELSI Insurance Task Force meetings to develop guidelines for using genetic information in underwriting; (3) a special ELSI initiative on guidelines for protecting the privacy of genetic information; (4) communication of concerns about exclusionary genetic testing by employers; and (5) NIH-DOE funding initiatives for public education on the impact of genetic data.
Mapping Working Group. Mark Guyer [National Center for Human Genome Research (NCHGR)] presented a list of quality index markers that have been identified, isolated, and mapped since the index marker project began in April 1991 [see HGN 3(2), 1-2 (July 1991)]; he reported that about half the needed 300 highly polymorphic markers have been assembled. Plans call for a full index marker map of the human genome to be constructed by January 1993, but interim information is being disseminated earlier [see HGN 3(6), 2 (March 1992) for information on an NCHGR catalog of index-quality markers and interim maps].
The subcommittee agreed that, in addition to index marker maps, a "baseline" map for each human chromosome should be constructed and published in a uniform format as soon as feasible. These maps eventually will contain the quality index markers as well as other useful markers. Helen Donis-Keller (Washington University) will coordinate the effort. Discussion followed about format and how best to distribute the baseline maps.
Committee members agreed that increasingly precise mapping goals may warrant supporting research through contracts or center grants with clearly delineated objectives rather than through regular research grants. A working group consisting of Mark Pearson (E. I. du Pont de Nemours & Company), Maynard Olson (Washington University School of Medicine), and Diane Smith (Xerox Corporation) was established to review this issue and make recommendations at the next meeting.
Olson submitted a proposal for measuring physical mapping progress. He commented on the difficulty of comparing "bottom up" and "top down" data and suggested a new "ordered marker" measure that would present information in much the same style as genetic mapping. The committee recommended that six to eight of the research groups involved in physical mapping convene to examine how this approach would affect them.
Mouse Genome Working Group. Verne Chapman (Roswell Park Cancer Institute) summarized the second meeting of the mouse working group and reported on the Mouse Genome Center at MIT [see HGN 3(6), 6-7 (March 1992)]. Information and materials are being distributed through a small business that makes marker kits commercially. The recently established Mouse Genome Society plans to sponsor workshops to review data and scrutinize information, chromosome by chromosome.
Sequencing Working Group. Pearson reported that several projects, including some involving bacterial, yeast, nematode, and human genomes, are ready to begin sequencing 1 Mb a year. The current cost of about $1.50 per base pair should be reduced to $0.50 within 5 years. Although technology has improved considerably, the truly novel technologies are still under development.
Intellectual Property Rights. William Smith and Thomas Kiley, California-based patent attorneys, were invited to discuss general issues raised by the recent NIH move to file patent applications for a large series of relatively short cDNA sequences called "expressed sequence tags." Because such patents could carry serious implications for human genome research, the committee agreed to develop an opinion letter about these applications and the rationale behind them. The letter will urge federal officials to obtain an authoritative ruling on the patentability of such material.
Smith described several recent patent rulings and expressed the opinion that rights to the composition of matter are the only issue that might cause problems in having a patent granted in the NIH case. In Kiley's view, the NIH case illustrates problems in the biotechnology industry, where the tendency is to try patenting at every stage of discovery. He outlined several potential remedies to weaknesses in the law, including the need for a clear research exemption and a stronger standard of utility. Kiley expressed concern that ambiguities in current law could lead to costly legal battles among biotechnology companies and recommended that basic sequence information should always be placed in the public domain.
Genome Informatics. Several investigators described substantial efforts to develop computer systems to handle the specialized and voluminous information being generated by gene mapping and sequencing research projects. Attention focused on very rapid analysis and dissemination of the newly developed data.
Nathan Goodman (Whitehead Institute for Biomedical Research) reviewed genetic mapping automation and reported an interactive program that helps plan and analyze experiments and automatically completes order forms for appropriate reagents. This program has enabled a small research group to rapidly accumulate and map 500 markers on the mouse genome.
Philip Green (Washington University) outlined an informatics approach that involves two complementary components: one statistical in which the "likelihood" of marker order is calculated by computer, and one combinatorial in which the program helps determine probable errors in the data set.
Elbert Branscomb [Lawrence Livermore National Laboratory (LLNL)] reported on a system that will enable research groups at different sites to exchange and analyze each other's data while maintaining the integrity of their own hardware and software. A prototype system involving Genome Data Base, IntelliGenetics, and LLNL is already functioning [see HGN 3(5), 5-7 (January 1992)].
James Fickett (Los Alamos National Laboratory) described Software for Integrated Genome Map Assembly, a system that eventually will automate mapmaking. Robert Waterston (Washington University) discussed data management for large-scale sequencing, especially of Caenorhabditus elegans. Dieter Soll (Yale University), Chair of the Joint Informatics Task Force, outlined the recently completed 2-year effort to describe the state of genome informatics and to specify needs in the field. This work has been summarized in a major draft report, which subcommittee members recommended should be edited professionally and distributed as soon as possible. The subcommittee also endorsed the report's main recommendations for increased support of interdisciplinary research and training in informatics.
At the NIH PACHG meeting, presided over by Berg, Elke Jordan (Deputy Director, NCHGR) reported that a delay in nominating new committee members may necessitate extending the terms of some members.
Budget. Several participants requested an explanation of the congressional appropriations process. Jordan explained that any significant shift of funds in future budgets from grants to contracts would necessitate considerable planning and a lead time of several years. The committee anticipated a need within a few years to conduct more of the overall program with contract rather than grant support. Participants noted that contracts will provide a more efficient means of support when large-scale sequencing projects begin. As an alternative to a complete switchover to contracts, members suggested that research grants be used more flexibly to achieve program goals.
Concept Clearance for Initiatives. Bettie Graham (NCHGR) summarized several NIH initiatives, including a request for applications for mouse genetics and a new program to support Russian and other East European scientists [see HGN 3(5), 5 (March 1992)]. A July meeting is planned in St. Petersburg to develop contacts between U.S. and Russian scientists.
David Benton (NCHGR) described an announcement of funding for a genome informatics program, and Berg recommended that NIH staff visit leading universities to recruit researchers into this field. Graham pointed out that NCHGR offers a new special-emphasis research career award (SERAC) that can provide computer scientists with support of up to $50,000 a year for 3 to 5 years.
The dates of the next Joint Subcommittee and PACHG meetings have not been set.
To receive minutes of Subcommittee and PACHG meetings, contact:
Reported by Leslie Fink, Office of Communications, NIH, NCHGR
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Human Genome Program, U.S. Department of Energy, Human Genome News (v4n1).
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.