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DOE Human Genome Program Contractor-Grantee Workshop IV Santa Fe, New Mexico November 13-17, 1994

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DOE Human Genome Program Contractor-Grantee Workshop IV Santa Fe, New Mexico November 13-17, 1994 Please address queries on this publication to: Human Genome Program U.S. Department of Energy Office of Health and Environmental Research ER-72 GTN Washington, DC 20585 301/903-6488, Fax: 301/903-8521 Internet: [email protected] This report has been reproduced directly from the best obtainable copy. Available to DOE and DOE contractors from the Office of Scientific and Technical Information; P. 0. Box 62; Oak Ridge, TN 37831. Price information: 615/576-8401. Available to the public from the National Technical Information Service; U.S. Department of Commerce; 5285 Port Royal Road; Springfield, VA 22161. CONF-9411116 Contractor-Grantee Workshop IV November 13-17, 1994 Santa Fe, New Mexico Date Published: October 1994 Prepared for the U.S. Department of Energy Office of Energy Research Office of Health and Environmental Research Washington, D.C. 20585 under budget and reporting code KP 0404000 Prepared by Human Genome Management Information System Oak Ridge National Laboratory Oak Ridge, TN 37831-6050 Managed by MARTIN MARIETTA ENERGY SYSTEMS, INC. for the U.S. DEPARTMENT OF ENERGY UNDER CONTRACT DE-AC05-840R21400 Contents Workshop Agenda v Poster Presentation Times viii Introduction To The Santa Fe Workshop ix Abstracts Mapping 1-75 Informatics 76-122 Sequencing 123-167 Instrumentation 168-183 Ethical, Legal, and Social Issues 184-201 Infrastructure 202-204 Appendices A. Author Index A1 B. National Laboratories Index B1 C. Anticipated Workshop Attendees C1 iii DOE Human Genome Program Contractor-Grantee Workshop IV Santa Fe, New Mexico November 13-17, 1994 Agenda Plenary sessions are in the Eldorado; poster sessions are in the Hilton. Each speaker and demonstration in the plenary sessions will have an abstract number and a poster associated with the talk. Abstract numbers indicated in parentheses. Schedule correct as of October 14, 1994. Agenda subject to change. Sunday, November 13, 1994 2:00-8:00p On-Site Registration Eldorado 6:00-8:30p Reception Eldorado Ballroom Monday, November 14, 1994 8:30a-3:30p On-Site Registration Continues Eldorado 8:30a Introductions Gene and Genome Mapping I RK. Moyzis, chair 9:00 Progress on Chromosomes 16 and 5 N.A Doggett, M. Altherr, D.L. Grady (1, 36-41) and (52-54) 10:25 Coffee Break 10:55 Progress on Chromosome 19 L.K. Ashworth, H.W. Mohrenweiser, B. Brandriff, T. Slezak (5, 29-31, 42-50) 12:20p National Laboratory Gene Library Project L.L. Deaven (25), J.C. Gingrich (26) 12:40 Lunch 2:00-3:00 Poster Session Setup Gene and Genome Mapping II A V. Carrano, chair 3:00 D.L. Nelson (56) 3:20 KH. Fasman (76) 3:40 A Gnirke (61) 4:00 M.D. Zorn (94) 4:20 L.J. Stubbs (31) 4:40 M.I. Simon (20) 5:15-7:30 Poster Session I & Computer Demonstrations Hilton v Tuesday, November 15, 1994 Gene and Genome Mapping ill C. T. Caskey, chair 8:30a J. Bashkin, D. Barker (130) 8:50 J.T. Petty (179) 9:10 R. Lipshutz (75) 9:30 P.M. Zweig (184) 9:50 M.C. Jefferson (186) 10:10 AF. Westin (197) 10:30 Coffee Break 11:00 AJ. Cuticchia (77) 11:25 J.-M.H. Vos (18) 11:45 R.P. Woychik (33) 12:05p J. Gray (66) 12:25 Lunch Sequencing I M. N aria, chair 3:00 R.S. Eisenberg (201) 3:30 L.E. Hood (147, 192) 4:10 M.J. Palazzolo (145) 4:35 R.K. Wilson (149) 5:00-7:30 Poster Session II & Computer Demonstrations Hilton Wednesday, November 16, 1994 Sequencing II D. Kingsbury, chair 8:30a C.A Fields (83) 8:55 D.J. States (105) 9:15 E.W. Myers (119) 9:35 M.J. Cinkosky (79) 10:00 E. C. Uberbacher ( 103) 10:30 Coffee Break 11:00 AD. Mirzabekov (124) 11:20 G.A Evans (125) 11:40 C.R. Cantor (34) 12:00 J.M. Jaklevic (174) 12:20p Lunch vi (VVednesday,conL) Sequencing m C. Cantor, chair 3:00 S. Tabor (157) 3:25 C.H.W. Chen (139) 3:45 C.M. Nelson (141) 4:05 P. Williams (140) 4:25 R.D. Smith (143) 5:00-7:30 Poster Session III & Computer Demonstrations Hilton Thursday, November 17, 1994 Sequencing IV LM. Smith, chair 8:30a N.J. Dovichi (131) 8:55 R.A Mathies, AN. Glazer (133} 9:20 B.L. Karger (132) 9:45 R.B. Weiss (148) 10:05 J. Balch (134) 10:25 Coffee Break 11:00 M.S. Westphall (135) 11:25 R.A Guilfoyle (156) 11:45 L. Ulanovsky ( 164) 12:05 J. Kieleczawa ( 161) 12:25 Summary 12:45 Lunch vii Poster Presentation Times· Hilton Ballroom The number assigned to the investigator's abstract determines when the poster will be presented. Divide abstract number by 3. Results with a remainder of 1 (Poster session I, Monday 5:15-7:30 p.m.) Results with a remainder of 2 (Poster session II, Tuesday 5:00-7:30 p.m.) Results with a remainder of 3 (Poster session III, Wednesday 5:00-7:30 p.m.) "Fosters should be mounted and ready for display before Session I begins. All posters will remain up throughout the meeting. viii Introduction to the Santa Fe Workshop Welcome to the fourth Contractor-Grantee Workshop sponsored by the Department of Energy (DOE) Human Genome Program. As all funded projects are represented here, this gathering offers valuable opportunities for scientists, program managers, and invited guests to review the program's content and progress and to assess its direction. We also encourage investigators to take this opportunity to discuss their successes and challenges and initiate new collaborations. DOE program management strongly encourages collaborations among investigators and genome centers. Much progress has been achieved since the last workshop held in February 1993. High-resolution physical mapping of chromosomes 16 and 19 is now virtually complete, with results soon to be published. Cosmid, PAC, and BAC libraries produced by the program are having a major impact on genome activities around the world. The National Laboratory Gene Library Project has achieved its Phase Two goals of producing cosmid libraries for each human chromosome. As technology improves and more groups become involved, DNA sequencing is starting to pick up; a stretch of about 685 kb from the human T-cell receptor is now the longest contiguous sequence entered in the databases. I believe we can expect rapid progress in sequencing technology in the near future. We have also made considerable progress in the rapid analysis of newly developed sequence data. Of particular note is the online implementation of Smith-Waterman analysis at the GRAIL-genQUEST server at Oak Ridge National Laboratory. Managing and increasing access to the rising tide of genome data and independently maintained databases that contain crucial mapping, structural, and other biological data are critical challenges. Late last year, after an extensive review of the program's informatics activities, DOE expanded its mission by establishing the Genome Sequence Data Base (GSDB), which now functions both as a service facility and research resource. GSDB is housed at the newly established National Center for Genome Resources in Santa Fe. A major current goal is to facilitate close cooperation between GSDB and the Genome Data Base located at John Hopkins University. Thus, the program is moving closer to its vision of a system of interlocking community databases that will allow easy access to independently maintained databases containing relevant biological data. Of the 204 abstracts in this book, some 200 describe the genome research of DOE-funded grantees and contractors located at the multidisciplinary centers at Lawrence Berkeley Laboratory, Lawrence Livermore National Laboratory, and Los Alamos National Laboratory; other DOE-supported laboratories; and more than 54 universities, research organizations, and companies in the United States and abroad. Included are 16 abstracts from ongoing projects in the Ethical, Legal, and Social Issues (ELSI) component, an area that continues to attract considerable attention from a wide variety of interested parties. Three abstracts summarize work in the new Microbial Genome Initiative launched this year by the Office of Health and Environmental Research (OHER) to provide genome sequence and mapping data on industrially important microorganisms and those that live under extreme conditions. Many of the projects will be discussed at plenary sessions held throughout the workshop, and all are represented in the poster sessions. Following up the successful debut at the last workshop, two informatics resource rooms will again be set up and maintained to allow researchers to exhibit new resources and software capabilities. OHER would like to extend thanks to all contributors for their efforts in moving the Human Genome Program toward its goals. We anticipate that this will again be a very interesting and productive meeting, and special thanks go to all who have contributed to its organization. David A Smith, Director Health Effects and Life Sciences Research Division Office of Health and Environmental Research ix I I I I I I I I I I Mapping This page intentionally left blank. Efforts Toward the Development of a Transcription Map of Human Chromosome 16 The Los Alamos Genomics Group. Presented by Amanda Ford and Cleo Naranjo. Life Sciences Division and Center for Human Genome Studies, Los Alamos National Laboratory, Los Alamos, NM 87545. Individual chromosomes provide the skeletal framework on which genomic data is organized. As the physical map and an ordered assemblage of molecular clones for chromosome 16 nears completion, we have embarked on the construction of an 'expressed sequence map' of the chromosome. To this end we have chosen the strategy of exon amplification to identify expressed sequences on chromosome 16.
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