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Human Genome News Archive Edition

Human Genome News, July-Aug. 1995; 7(2):5

Chromosome 9 Workshop Produces New Maps

This article was excerpted from the electronic meeting report.

The Fourth International Workshop on Chromosome 9, held April 23-25 in Williamsburg, Virginia, was organized by Margaret Pericak-Vance (Duke University) and attended by 33 people from 7 countries. Sponsors included the U.K. Medical Research Council, DOE, NIH National Center for Human Genome Research, and the Human Genome Organisation (via a grant from the European Community).

Speaking of the meeting's success, A. Jamie Cuticchia [formerly Genome Data Base (GDB), now at Mitre Corporation] said, "The chromosome 9 workshop is noteworthy because for the first time on record every participant submitted data to GDB before the meeting. Recognizing that searchable data is critical in creating integrated maps, the chromosome 9 community required that ALL data be submitted in advance."

Continuing a previously effective format, individual participants made brief presentations of their interests and research highlights since the last meeting, and leaders of small working groups provided information on the latest findings. Chromosomal subgroups worked independently and then jointly to produce consensus physical and genetic maps. A new subsection on morbid anatomy was added to handle emerging correlations of mapped disorders with localized potential candidate genes. Selected meeting highlights follow.

Mapping

Global Map. The composite genetic linkage map was modified and updated during the meeting using a set of defined linkage data and SIGMA, a software program developed by Michael Cinkosky (formerly Los Alamos National laboratory, now at University of Utah Medical Center). Lack of telomeric markers continues to be a problem, but recent efforts have clarified the order of and distance between markers near each telomere; genetic distance in these regions has been reduced significantly as well. The map is most remarkable for uneven marker distribution, with several clusters of anonymous markers. This suggests that certain genomic regions have enhanced clonability properties, unusually high polymorphism rates among markers, low genetic-recombination rates, or a combination of these factors.

Morbid Anatomy. Six new Mendelian disease loci were identified by genetic linkage or physical mapping to chromosome 9. These are hyperglycinemia, isolated, nonketotic type 1 (GLDC); venous malformations (VMCM); familial melanoma (CDKN2); arthrogryposis (AMCD1); male pseudohermaphroditism (HSD17B3); and Osler-Rendu-Weber disease, type 1 (ENG).

Comparative Mapping. Publication of the results of 50 cross-hybridizations between products of human chromosome 9 and the mouse genome has provided a detailed comparative map. The chromosome now has known syntenies with eight segments derived from four mouse chromosomes. The information is sufficient for polarity determination in these homologous segments; none is astride the human centromere.

Resources

Hybrids. Allen Bale (Yale University) reported the submission of four hybrids containing defined 9q deletions to Coriell. Other hybrids, available from David Callen (Adelaide Children's Hospital), contain possibly useful breakpoints on chromosome 9 involving balanced translocations with chromosome 16.

Clones. The chromosome 9 cosmid library from Lawrence Livermore National Laboratory continues to be a valuable tool. A new section of the chromosome 9 home page will include a list and free text information about cosmids in this library identified by the 300-microtitre plate notation. new data or comments about the section should be sent to john attwood(john@mrc-hbgu.ucl.ac.uk). A second chromosome 9 cosmid library has been constructed in the vector supercos [Murrell et al., Genomics 25, 59-65 (1995)]. Some YACs from the chromosome 9 specific library constructed by MaryKay McCormick (Massachusetts General Hospital) are freely available, and others are distributed on a collaborative basis. In addition to the 160 or so cloned genes known on chromosome 9 and listed in GDB, 215 ESTs were added in the past year. The total of 330 ESTs presently identified includes 108 from Charles Auffray (Genethon). ESTs become increasingly valuable resources as the rate of EST mapping increases in genomic radiation hybrids.

Polymorphic Markers. GDB lists 341 polymorphic loci on chromosome 9. Of these, 286 are short tandem repeats (159 dinucleotides, 22 trinucleotides, and 105 tetranucleotides). Several new polymorphic markers were contributed at the meeting, including approximate map positions for 43 new tetranucleotide repeats from the Utah Marker Development Group (UMDG).

Meiotic Breakpoints. Two groups reported algorithms concerned with defining meiotic breakpoints in the CEPH families. Steve Gerken (UMDG) aims to construct maps, and Attwood plans to produce a panel of well-supported breakpoints that can be used for rapid placement of new polymorphic markers. All breakpoints generated by Attwood are available via the Chromosome 9 Home Page (see sidebar for address), which contains an interactive form for requesting breakpoint details for any specified chromosomal region.

Community Goals

Specific community goals set at the workshop include (1) extending information on the ease of using genetic markers and (2) coordinating across numerous groups the refining of meiotic breakpoint mapping of many microsatellite markers.

Chromosome 9 Workshop Information Available

Workshop reports, abstracts, maps, and figures are available by anonymous ftp (ftp no longer available) in the subdirectory /pub/c9workshop/1995 or via the Chromosome 9 Home Page (http://www.gene.ucl.ac.uk/chr9home.html). An integrated chromosome 9 map can be found in the location database LDB (accessible via the chromosome 9 Home Page and http://cedar.genetics.soton.ac.uk/public_html. The map can also be obtained by anonymous ftp as the file /pub/chrom9/map from ftp://cedar.genetics.soton.ac.uk. SIGMA is available via anonymous ftp (ftp.ncgr.org).

1996 Chromosome 9 Workshop Planned

A fifth workshop is tentatively planned for fall 1996 to bring various mapping issues to closure. Brandon Wainwright (Center for Molecular Biology and Biotechnology) will host the meeting in Brisbane, Australia, because of the number and diversity of chromosome 9 research groups there.


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