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DOE Human Genome Program Contractor-Grantee Workshop III ORNL/M-2588 uman enome Program U.S. Department of Energy Contractor-Grantee Workshop III February 7-10, 1993 Santa Fe, New Mexico Date Published: January 1993 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-vii Poster Presentation Times viii Introduction To The Santa Fe Workshop ix Abstracts* U.S. Department of Energy Laboratories Human Genome Centers LANL-Los Alamos National Laboratory (1-20) LBL-Lawrence Berkeley Laboratory (21-48) LLNL-Lawrence Livermore National Laboratory (49-75) Ames Research Center (76) ANL-Argonne National Laboratory (77-80) BNL-Brookhaven National Laboratory (81) LANL-Los Alamos National Laboratory (82-90) LBL-Lawrence Berkeley Laboratory (91-96) ORNL-Oak Ridge National Laboratory (97-109) PNL-Pacific Northwest Laboratory (110-111) Other Institutions (112-198) Appendices A. Subject Index 199 B. Author Index 200 C. Anticipated Workshop Attendees 207 'Each section alphabetized by first author. iii Workshop Agenda DOE Human Genome Program Contractor-Grantee Workshop ill Santa Fe, NM February 7-10, 1993 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 thus a poster, associated with the talk. Schedule correct as of January 15, 1993. Agenda subject to change. Sunday, February 7, 1993 2:00-8:00 p.m. On-site Registration Eldorado Hotel 6:00-8:00 p.m. Reception Eldorado Hotel Monday, February 8, 1993 7:30a.m. On-site Registration continues 8:00 Welcome: David Galas 8:15 Opening Comments: Senator Pete Domenici 8:25 Report from HUGO: C. Thomas Caskey 8:40a.m. ELSI Chair-Michael Yesley 8:40 Michael Y esley (20) 8:55 Joe Mcinerney (197) 9:25 Troy Duster (117) 9:55 Phil Reilly ( 164) 10:25 Betsy Fader (131) 10:55 a.m. Break 11:25 a.m. Sequencing I Chair-Deborah Nickerson 11:25 Lloyd Smith 11:40 Current Efforts-prospects for scale-up and time frame for 300MB/yr 11:40 Chris Martin (37) 12:05 Robert Weiss (138) 12:30 p.m. Lunch 2:00p.m. Sequencing I (cont.) 2:00 Leroy Hood (149) 2:25 Ron Davis (128) v 2:50p.m. Sequencing Goals: Panel David Galas (chair), Lloyd Smith, Raymond Gesteland, Jasper Rine, Leroy Hood, Tom Caskey, Tony Carrano, Robert Moyzis 4:00-7:00 p.m. Poster Session I Hilton Ballroom Tuesday, February 9, 1993 8:00a.m. Sequencing II Chair-Deborah Nickerson 8:00a.m. Technology Developments for Large Scale Sequencing 8:00 Lloyd Smith (185) 8:25 Richard Mathies (150) 8:50 Klaus Schneider (179) 9:15 William Studier (81) 9:40 Steve Fodor (135) 10:05 a.m. Break 10:30 a.m. Informatics Chair-Diane C. Smith 10:30 Diane Smith: Informatics review and comment 10:45 Software Demonstration: Michael Cinkosky ( 4) 11:00 Ed Uberbacher (106, 108) 11:20 Jim Fickett (85-87) 11:40 Software Demonstration: Tom Marr (127) 12:00 noon Lunch 1:30 p.m. Informatics (cont.) 1:30 Ken Fasman (132) 1:50 Software Demonstration: Tom Slezak (72) 2:05 Software Demonstration: Richard Douthart (110) 2:20 Manfred Zorn ( 48) 2:40 Charles Lawrence (148) 3:00 Software Demonstration: Suzanna Lewis (32) 3:15 End of Session 4:00-7:00 p.m. Poster Session II Hilton Ballroom Wednesday, February 10, 1993 8:00a.m. Mapping Chair-Robert Moyzis 8:00 Bruce Birren (119, 154) 8:25 Pieter de Jong (63) 8:50 Natasha Kouprina (12) 9:20 Mary Kay McCormick (5, 13, 17) 9:45am. Break vi 10:15 a.m. Mapping (cont.) 10:15 Jasper Rine (42) 10:40 Glen Evans (186) 11:05 Daniel Pinkel (95) 11:30 Richard Woychik (109) 11:55 a.m. Lunch 1:30-4:30 p.m. Poster Session ill Hilton Ballroom 7:00p.m. eDNA 7:00p.m. 1. eDNA Update Chair-Mihael Polymeropoulos 7:00 M. Bento Soares (120) 7:15 Mark Adams (112) 7:30 James Sikela (184) 7:45 Joseph Gatewood (8, 18) 8:00 Chris Fields (133) 8:15p.m. 2. eDNA Technologies Chair-Greg Lennon 8:15 Jan-Fang Cheng (22) 8:27 Radoje Drrnanac (78, 79) 8:39 David L. Nelson (172) 8:51 Greg Lennon (65, 66) 9:03 Lisa Stubbs (107) 9:15p.m. Break 9:30p.m. Issues in eDNA Chair-Thomas Caskey Each speaker will have a short introduction (5 minutes), followed by an open dialog with panel and audience. The purpose is to stimulate discussion and seek input from the broader community. The session can accommodate ad hoc presentations (1-2 min.) from the audience. A series of questions will be provided to each speaker as a basis for the presentation. David Galas-Statement of DOE eDNA Goals and Opportunities M. Bento Soares-Library Needs Glen Evans-Full Length eDNA Sequencing Julie Korenberg-Faster eDNA Mapping Methods 11:00 p.m. Oose Additional funding has been provided by the Perkin Elmer Corporation. vii Poster Presentation Times The number assigned to the investigator's abstract determines when his or her poster will be presented: • Numbers with a remainder of 1 (Poster Session I) • Numbers with a remainder of 2 (Poster Session II) • Numbers evenly divisible by 3 (Poster Session III) Poster Sessions Hilton Ballroom Session I Monday (4-7 p.m.) Session II Tuesday ( 4-7 p.m.) Session III Wednesday (1:30-4:30 p.m.) All posters should be mounted and ready for display before Session I begins. viii Introduction to the Santa Fe Workshop Welcome to the Third Contractor-Grantee Workshop sponsored by the Department of Energy (DOE) Human Genome Program. This meeting, designed to foster interaction among investigators and facilitate project coordination, offers DOE-supported genome researchers, program managers, and invited guests the opportunity to become familiar with current research, assess progress, and initiate collaborations. The DOE Human Genome Program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last such workshop, held in 1991. The 115 abstracts and 208 attendees of 1991 have grown to almost 200 abstracts and 400 attendees in 1993. Numerous collaborations resulting from the previous workshop have already borne fruit, and we expect that this meeting will prove equally successful. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions in the Eldorado Hotel's Anasazi Ballroom on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques; informatics support; and chromosome and eDNA mapping and sequencing. All poster exhibits in the Hilton Mesa Ballroom will be open in the evenings throughout the meeting to maximize their availability to all attendees. New material resources and software are also on exhibit in a separate area of the Hilton. With its multidisciplinary capacities, DOE is uniquely positioned to exploit the exciting opportunities presented by the Human Genome Project and ultimately to provide some measure of understanding of the genomic effects of radiation and chemicals. Serving as research sites for a multitude of interdisciplinary mapping and sequencing efforts are the three DOE human genome centers at Lawrence Berkeley, Lawrence Livermore, and Los Alamos national laboratories, as well as other DOE-supported laboratories and more than 40 different universities and research organizations. The Office of Health and Environmental Research appreciates the hard work and commitment of all contributors who, by their efforts, are advancing genome research toward the goals established over 2 years ago. David A Smith, Director Health Effects and Life Sciences Research Division ix LANL Los Alamos National Laboratory Center for Human Genome Studies Strategies for the Development of a Gene Map of Human Chromosome 4 Michael R. Altherr 1&2 , James F. Gusella 3 and Alan J. Buckler 3_ 1 Genomics and Structural Biology Group, LANL, 2 Department of Biological Chemistry, University of California Irvine. 3 Neurogenetics Laboratory, Massachusetts General Hospital. Individual chromosomes provide the skeletal framework on which genomic data is organized. The genetic map provides the sinew for each chromosome and a contiguous array of molecular clones represents the dermis. Recently, this level of resolution was achieved for two human chromosomes and is near completion for several others. With these tools in hand investigators are positioned to begin more detailed analysis of chromosome structure and gene organization. One interesting piece of data in which to dress these developing bodies would be the localization of chromosome specific expressed sequences. To this end we have initiated two strategies to identify expressed sequences on human chromosome 4. Our first strategy employs 96-well plate pools of DNA from the flow sorted and arrayed chromosome 4 cosmid library as substrate for exon trapping. This technique has proved extremely efficient at identifying expressed sequences in the Huntington disease region and in the vicinity of several disease loci. The second strategy employs the hybridization of degenerate oligonucleotides capable of recognizing specific functional domains (eg. homeobox domain) to grided arrays of the chromosom be sub-localized rapidly using a somatic cell hybrid mapping panel with an average bin size representing 8% of chromosome 4. In addition, we have constructed a collection of chromosome 4 radiation hybrids and we are currently in the process of constructing a radiation hybrid map using the chromosome 4 genetic marker reference map.
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