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Uman Enome News uman enome news ISSN: 10~101 Vol. 4, No.4, November 1992 Researchers Report Mapping Progress Data Published on Chromosomes Yand 21, Leukemia Gene, Genetic Linkage Map nternational progress in physical and genetic mapping has recently been Mapping Ireported as the U.S. Human Genome Project moves into its third year: Techniques • Physical maps covering the entire func­ National Center for Human Genome Put 5-Year tional portions of human chromosomes Research (NCHGR) to further the interim Goals in Sight Y and 21 have been completed. Yeast (5-year) Human Genome Project goal of artificial chromosome (Y AC) clones constructing physical maps of all human now cover 98% of the Y chromosome chromosomes with markers spaced at euchromatic region. The YAC contig 100-kb intervals (see box, p. 4). for chromosome 21 spans the pericen­ tromeric through subtelomeric loci of The euchromatic region includes the short arm, centromere, and proximal long 21 q and is estimated to contain 42 Mb. arm. It contains all known genes on the • A gene that appears to be associated with some forms of childhood leukemia has been identified during construction of a physical map of human chromo­ In This Issue... some 11. Findings suggest that chro­ Page Genome News mosomal breakage during transloca­ 1 Researchers Report Mapping Progress tion disrupts the function of the gene, 3 Ninth NIH Genome Center Established at University onowa whose product may be involved in 5 NIH-DOE Joint Working Gronp on the Monse regulating other genes active in white 5 High School Teachers Attend San Francisco Forum blood cells. 5 DOE Sponsoring Workshop for Science Teachers • The most comprehensive and up-to­ 5 University of Utah Plans Mapping, Sequencing Workshop date genetic linkage map of the human 7 GenBank Transition Provides Continuity genome has been published. The new 8 DOE Announcements: R&D 100 Award, Activities, Resources map contains 1676 markers spaced an GOB Forum average of about 5 cM apart, covering 10 GDB Version 5.0 Highlights 90% of the genome. 10 Data Conversion Aids for Software Developers • Y CHROMOSOME 11 GDB User Support, Registration In two articles appearing in the October 2 11 Training Course Schedule issue of Science, David Page and his col­ 11 Standard Reports Available via FTP leagues at the Whitehead Institute and Mas­ Meeting Reports sachusetts Institute of Technology presented 12 Conference on Ethics and Technology their physical map of the entire functional 12 First South-North Human Genome Conference (euchromatic) portion of the human Y or Resources "male" chromosome, which at 60 Mb is one 6 E-Mail Searcher Verifies Protein Sequence Homology of the smallest. The new map, consisting of 8 GnomeView; Newsgronp, p.13; NCBI Repository, p_ 13 196 overlapping YAC clones, is expected to facilitate positional cloning of genes for a For Your Information given phenotype, speed gene identification, 14 Calendar of Genome Events; Training Calendar and provide material for large-scale sequenc­ 15 Funding Announcements, Guidelines for U.s. Genome Funding ing. The work was supported by the NIH 16 SubscriptionIDocument Request, Calendar Acronyms 2 Human Genome News, November 1992 Genome News Y chromosome and appears relatively con­ Use of a total human YAC library elimi­ stant in size. By contrast, the heterochro­ nated the labor-intensive step of construct­ matic region has no known function; ing chromosome-specific YAC libraries. consists of short, repetitive sequences; The YAC library, containing 10,368 clones and varies tremendously among males with an average insert size of 650 kb, was STS-Content (undetectable in some and twice the size then analyzed by "STS-content mapping" Mapping of the euchromatic region in others). and screened for landmarks using 160 Strategy Used deletion-mapped STSs. YAC clones were Because most of the Y chromosome does ordered by determining overlap (common For Y and 21 not undergo meiotic recombination, a STSs). Based on their presence or Physical Maps: genetic linkage map is precluded, and absence in the YACs, 207 Y-DNA probes Y-linked gene identification has been • STS probe sets were assigned to 127 ordered intervals assembled and based on physical mapping of naturally with an average spacing of about 220 kb. occurring deletions. Deletion mapping, in ordered. The authors estimate that the physical which DNA loci are ordered along the map spans at least 28 Mb; previous esti­ • Total human chromosome, is a practical approach YAC library mates based on cytological observations because Y chromosome deletions occur were in the 30- to 40-Mb range. screened for fairly frequently in the population. STS landmarks. This mapping strategy enabled investiga­ STS-8ased Deletion Map • YACclones 1 tors to isolate specific YACs from a com­ ordered by In the first of two Science articles, Page plex library, order and arrange them in determining and colleagues described deletion map­ larger units to form "contigs," and place STS overlaps. ping based on sequence tagged site the STSs along the chromosome. These (STS) detection; an STS is a short DNA ordered points on the physical map will sequence that can be detected by the provide landmarks for all future investiga­ polymerase chain reaction (PCR)-a fast, tions of the Y chromosome, the authors sensitive assay. An STS can be mapped stated. They also noted that this method to a specific point that becomes a chromo­ can be applied to other human chromo­ somal landmark easily disseminated somes if large numbers of STSs can be through publication in journals and com­ generated for them. puter databases. The researchers assembled a set of STS • CHROMOSOME 21 MAP probes to screen DNA from 96 patients In the October 1 issue of Nature,3 French who had either visible Y chromosome researcher Daniel Cohen of Genethon and abnormalities or sex chromosome consti­ 35 others from 12 institutions [including tutions (XX males and XV females) that American researchers Stylianos Antonara­ did not correlate with their outward sexual kis (Johns Hopkins School of Medicine); appearance. To establish the relative STS David Cox (University of California, San order, investigators compared sets of posi­ Francisco); Harold Riethman (Wistar Insti­ tive pOints (indicating the presence of an tute); and Katheleen Gardiner and David STS) and negative points for each patient. Patterson (Eleanor Roosevelt Institute)] report a complete physical map of the long The deletion map is expected to be useful arm of human chromosome 21. The small­ in identifying Y chromosomal genes, est and one of the best studied of the studying the origin of chromosomal disor­ human chromosomes, chromosome 21 ders, and tracing the evolution of the has been associated with several genetic Y chromosome. This newsletter Is prepared diseases, including Down's syndrome, at the request of the DOE Physical (Ordered Clone) Map some forms of Alzheimer's disease, amyo­ Office of HeaRh and Environ· trophic lateral sclerosis (Lou Gehrig's mental Research and the In their second Science article,2 the researchers describe how ordered STS disease), and progressive myoclonus epi­ NIH National Center for lepsy. The new physical clone map will Human Genome Research probes, generated during deletion map­ by the Biomedical and Envl· ping, provided the framework for rapid speed identification of the chromosomal ronmentallnfonnation Anal· construction of the chromosomal physical regions involved in these and other dis­ ysis Section of the Heai1h map. Investigators began by preparing a eases aiter the regions are further localized and Safety Research DiVi· by genetic linkage or cytogenetic analysis. sion at Oak Ridge National library of YAC clones from the genomic Laboratory. which isman· DNA of a human XYYYY male to obtain The map, containing 191 STSs spaced at aged by Martin Martetta a Y chromosome representation fourfold about 220 was constructed from human Energy Systems. Inc .• for kb, the U.S. Department of greater than could have been achieved YAC libraries having insert sizes of 400 kb Energy. Uilder Contract with a comparably sized library for an to 2 Mb. The new map contains an average DE·AC05·840R21400.0 XYmale. of five clones in each interval between two Human Genome News, November 1992 3 Genome News STSs, an indication of the "robustness" of in a common format. Collated by Washing­ the contig. ton University (SI. Louis) geneticist Helen Donis-Keller and her staff, the linkage The work was conducted at laboratories in map contains restriction fragment length France, the United States, Spain, and Japan. polymorphism (RFLP) and microsatellite It was supported by the French Ministry of DNA markers. Research and Technology and the Associa­ tion Francaise Contre les Myopathies Markers Used for Genetic Mapping through the Genethon program and by According to the Science article, the major grants from NCHGR and other NIH institutes. difference between a previously published genome map and the new one lies in the • CHILDHOOD LEUKEMIA GENE number and type of markers used. This Researchers constructing a human chromo­ map incorporates over 4 times more some 11 physical map consisting of ordered markers, some 300 of which are variable DNA clones have determined the base-pair repeats of short (2 to 4 bp) DNA units sequence of fragments spanning the chro­ called microsatellites. mosomal region 11 q23. The area is fre­ quently broken in patients with some forms The first human genetic linkage maps were of childhood leukemia; this breakage may based on protein polymorph isms
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