|Genome Mapping Section
DOE Human Genome Program Contractor-Grantee Workshop
74. Completing the Sequence-Ready Map of Chromosome 19
Laurie Gordon, Anca Georgescu, Mari
Christensen, Sha Hammond, Hummy Badri, Bernadette Lato, Matthew Groza,
Linda Ashworth, Mark Wagner, and Anne Olsen
Chromosome 19 is the most GC-rich chromosome, suggesting an especially high gene density. This prediction is supported by transcript mapping results (Deloukas et al., Science 282, 744-746, 1998), that indicate chromosome 19 has the highest number of gene-based STSs relative to size of all the chromosomes. Thus this chromosome should be an extremely rewarding sequencing target in terms of gene discovery and elucidation of gene structure and organization.
We are nearing completion of a sequence-ready map of chromosome 19. The current map consists of 72 BAC/cosmid contigs with an average size of 710 kb. The contigs have been ordered along the chromosome by high resolution FISH, so their location is well defined relative to the cytogenetic map. The ordered contigs span a total of 51 Mb, or 93% of the non-centromeric portion of the chromosome. The average size of remaining gaps is an estimated 80 kb. For gap closure, probes developed from the ends of contigs are hybridized to high-density BAC colony filters, and positive BACs are incorporated into the existing map by analysis of restriction digests.
All contigs have been restriction mapped with EcoRI, resulting in a high-resolution restriction map of almost an entire chromosome. The distribution of EcoRI sites varies along the chromosome, with relatively larger fragments more common in light band regions. Several EcoRI polymorphisms between clones from different sources have been detected in the process of assembling restriction maps. The average depth of coverage of restriction mapped contigs is 8.5-fold. The high depth of coverage and mix of cosmid and BAC clones generally enables selection of an optimum set of spanning clones with minimum overlap for sequencing. About 30 Mb of chromosome 19 have been sequenced or are currently in the sequencing queue. The average size of contigs being sequenced is 830 kb. An average overlap between sequence tiling path clones of 10% is estimated from the map. All sequence tiling path clones are digested with three additional restriction enzymes to provide data for confirmation of final sequence assembly. Updated chromosome 19 data, including all restriction maps, are available on the LLNL Genome Center web site at http://bbrp.llnl.gov/bbrp/genome/html/chrom_map.html.
Work performed under the auspices of the US DOE by Lawrence Livermore National Laboratory under contract W-7405-ENG-48.
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