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Uman Enome News uman enome news ISSN:l050-6101 Vol. 3, No.1, May 1991 DOE Holds Contractor-Grantee Workshop Physical Mapping Efforts Going Well; Gels Increasing Sequencing Efficiency he DOE Human Genome Prograll1 held its second Contractor-Grantee Workshop Charles R. Cantor and HGMIS gratefully Tin Santa Fe, New Mexico, on February l7-W. More than 200 program-sponsored acknowledge contribu­ scientists attended the meeting, in addition to invited guests and industry represen­ tions to this article by tatives. DOE-supported human genome research projects are conducted at 7 DOE Elbert W. Branscomb, national laboratories (including its 3 human genome centers), 37 major universities, Anthony V. Carrano, and 32 companies through collaborations and awards. Projects were represented by Leroy E. Hood, oral presentations or posters. Robert K. Moyzis, and Robert J. Robbins. Six platform sessions focused on the more focus is needed on the immediate following: informatics needs of ongoing biology projects. • physical mapping progress, Many parallel efforts under way in cloning, • large DNA fragment cloning, informatics, mapping, and sequencing will • strategies for preparing samples for further improve the technologies required for efficient DNA sequencing, genomics. Program participants feel that this situation is healthy at present and that a few • new methods for a variety of genome efforts, • DNA sequencing instrumentation, and In This fssue .•. • database and computer algorithm needs for existing or projected genome Page Genome News research. 1 DOE Holds Contractor-Grantee Workshop David Galas, Associate Director, Office of 5 LANL, Life Technologies Approve CRADA Health and Environmental Research (OHER), 6 Conncil on Competitiveness Urges Action spoke about the relationship between the 7 Moore Calls Tech Transfer Critical to Fntnre' Human Genome Program and other OHER 8 NIH Discusses eDNA Role with Invited Group programs. Michael Yesley [Los Alamos 9 NCHGR Advisory Council Holds First Session National Laboratory (LANL)] presented ethi­ 9 NIH PACHG Appoints New Members, Chair cal,legal, and social issues pertaining to data produced in the genome project. 10 DOE·NIH Establish Mouse Working Group Meeting Reports The general impression conveyed by most 11 WorkshOp on Mouse Genome Mappiug presenters was that physical mapping efforts are going well; chromosomes 16, 19, and 13 Second X Chromosome Workshop portions of 11 are now well covered with Resources large numbers of assembled cOntigs. Fluo­ 14 Nouprofit Resource Centers Facilitate Mapping rescence in situ hybridization (FISH) is 18 Genome Literature Abstracts emerging as an extremely effective method for ordering cloned probes. For Your Information 19 U.S. Genome Research Funding Information Fractionating DNA fragments is becoming 20 Genome-Related Tutorials OlTered much faster with capillary or thin gel slab 21 Calendar of Genome Events electrophoresis. Informatics support for most 22 Training Calendar: Worksbops and Coursework physical mapping efforts and for large-scale DNA sequencing remains problematic, and 24 Acronym List, Subscription/Document Request 2 Human Genome News, May 1991 approaches will emerge as those most likely explained this method and showed the DOE Program Report to accelerate the project. usefulness of FISH in characterizing chro­ Update mosomal rearrangements. HGMIS is preparing One theme that recurred frequently during Glen Evans (Salk Institute) and collabora­ the 1991 revision of the the 3-day meeting was the rapid change in DOE Human Genome bottlenecks or rate-limiting steps, particu­ tors have used a combination of methods larly in DNA-sequencing efforts. Advances in mapping chromosome 11. In construct­ 1989~90 Program Report. in raw sequencing speed make automated ing several multimegabase contigs of To update the report production of DNA samples and melding of cloned DNA segments, Evans used a YAC and accurately reflect raw sequence reads increasingly important. as a hybridization probe against a filter DOE-funded genome array of cosmids to identify covered cos­ research projects, .. Physical Mapping mids. Given the appropriate libraries, a HGMIS asks investi­ Generally, impressive progress continues in gators to send abstracts, series of overlapping clones for 1- to 2-Mb photographs, and the construction of physical maps of selected regions apparently can be isolated in a fignres. Investigators human chromosomes. Yeast artificial chro­ matter of weeks. who have not already mosomes (yACs), though not without prob­ lems, are proving helpful in linking cosmid Both the chromosome 19 program at LLNL submitted this material and that of chromosome 16 at LANL have are reminded to forward contigs or providing rapid initial coverage of a region. collected about two-thirds of their chromo­ it to: somes into cosmid contigs. A variety of HGMIS The powerful new FISH technique is providing very effective automated approaches are Oak Ridge National mapping data at several levels of resolution, being used to expand and link these con­ Laboratory extending from metaphase chromosomes. tigs. Existing maps are dense enough to be p.o. Box 2008 It offers a rapid and accurate method of useful to investigators wishing to locate Oak Ridge, TN regional clone assignment to a chromosome genes on these chromosomes; about 80% 37831-6050 band. Barbara Trask [Lawrence Livermore of randomly picked probes will fall on con­ National Laboratory (LLNL)] showed that tigs or clones already mapped. To aid such much higher resolution mapping can be studies, a series of anchor points has been achieved with interphase cells; once markers established between the current genetic are known to be close, their relative order and physical maps. No clone-order dis­ can be determined and distances estimated crepancies are evident between the two in the 50-kb to 1-Mb range. map types for either chromosome. The presence of a selectable marker near Excellent progress is being made wtth maps the long-arm telomere of chromosome 16 of X-chromosome regions. Thomas Caskey, made possible the construction of a set David Nelson, and their coworkers (Baylor of hybrid cell lines particularly convenient College of Medicine) are focusing on several for that chromosome. Grant Sutherland (Ade­ areas that contain genes of interest rather laide Children's Hospital, South Australia) than attempting to construct a complete DOE Human Genome Program staff (I. to r.) Charles Cantor Denan Wang (Lawrence Berkeley Laboratory Human (Principal Scientist), Robert Robbins (Informatics Detail .. Genome Center) explains her poster to DOE Human to DOE from tbe National Science Fonndation), and Genome Coordinating Committee (HGCC) member Benjamin Barnhart (Program Manager) view posters at tbe Anthony Carrano (Director, LLNL Human Genome Contractor-Grantee Workshop_ Center). Human Genome News, May 1991 3 map of this large chromosome. Caskey Berg (Washington University School of described the potency of using tandem Medicine) and his group have exploited the simple sequence repeats as genetic markers. bacterial Tn5supF transposon system by inserting a known 260-bp sequence into In the next few years, nearly complete contig lambda clones to serve as the priming site maps should be obtained on chromosomes for sequencing. This procedure eliminates 11,16,19, and X. the need to subclone large inserts, since III large-Insert Cloning Vectors sequencing could be accomplished directly from the lambda clone by primer walking Several groups reported new approaches from the inserted transposon. Claire Berg toward large-insert cloning vectors: (University of Connecticut) described the • Peter Hahn and his colleagues (State use of transposon yo (Tnl 000) to sequence Sylvia J. Spengler, University of New York, Syracuse) plasmid inserts. Robert Weiss and Raymond Executive Officer, employed double-minute chromo­ Gesteland (University of Utah) reported on HGCC, organized somes as megabase-cloning vehicles. applying this method to sequence p1asmids the DOE Contractor­ • Jean-Michel Vos (University of North containing 10-kb inserts. Their clone-pooling Grantee Workshop in Carolina, Chapel Hill) suggested the scheme is employed for rapid mapping of Santa Fe, New Mexico. Epstein-Barr virus as a cloning vehicle. the transposon integration sites; the mapped • Hiroshi Shizuya (Melvin Simon's transposons are then used as primer sites for multiplexed dideoxy sequencing. Reece Hart (Salk laboratory, Calffornia Institute of Tech­ Institnte) tries out the nology) described a new cloning sys­ William Studier (Brookhaven National lab­ online DOE Human tem using Escherichia coli and ITS oratory) reported on priming DNA sequenc­ Genome Information plasmid F factor. ing reactions by using sequences within the Database, assisted by • Philip Youderian (California Institute insert itself. George Church (Harvard Medi­ Beth Owens (HGMIS, of Biological Research) discussed a cal School) presented the status of his Oak Ridge National Laboratory). set of "stealth" vectors that carry an developments for computer-assisted mUlti­ S replicon, the Salmonella phage B-22 plexed sequencing. Arthur Riggs (Beckman early region, and a chloramphenicol Research Institute) described a ligation­ resistance determinant. The vectors mediated genomic sequencing strategy that can accept DNA inserts of several allows sequence information to be derived hundred kilobases, maintain them in from genomic DNA without subcloning. a single copy, and then amplify them III New Techniques for DNA Sequencing about 500-fold.
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