DOE Human Genome Program Contractor-Grantee Workshop VIII
February 27-March 2, 2000  Santa Fe, NM

47. Human Chromosome 16 Mapping Update

Cliff S. Han, Robert D. Sutherland, Phillip B. Jewett, Mary L. Campbell, Linda J. Meincke, Judy G. Tesmer, Mark O. Mundt, Larry L. Deaven, and Norman A. Doggett

Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545

chan@telomere.lanl.gov

We have used sequence-based markers from an integrated YAC STS-content/somatic cell hybrid breakpoint physical map and radiation hybrid maps of human chromosome 16 to construct a new sequence-ready BAC map of this chromosome. The integrated physical map was previously generated in our laboratory and contains 1150 STSs, providing a marker on average every 78 Kb on the euchromatic arms of chromosome 16. The other two maps utilized for this effort were the radiation hybrid maps of chromosome 16 from Whitehead Institute and Stanford University. To create large sequenceable targets of this chromosome we used a systematic approach to screen high density BAC filters with probes generated from overlapping oligonucleotides (overgos). We first identified all available sequences in the three maps. These include sequences from genes, ESTs, STSs, and cosmid end sequences. We then used BLAST to identify 36 bp unique fragments of DNA for overgo probes. A total of 906 overgos were selected from the long arm of chromosome 16. After a total of 212 hybridizations we have constructed an initial probe-content BAC map of chromosome 16q consisting of 828 overgo markers and 3363 BACs providing greater than 85% coverage of the long arm of this chromosome. Gaps in the map are being closed with the following methods: 1) PCR screening the RPCI-11 library with the BAC end sequence-derived STSs. 2) BAC end sequence database searches with draft sequences of BAC clones near the gaps. 3) Screening the RPCI-11 library with overgos generated from the BAC end sequences near the gaps. To date, 400 PCR screening and 5 pooled overgo hybridization have been completed for the gap closing effort, extending the coverage of the BAC map to over 90%.

Supported by the US DOE, OBER under contract W-7405-ENG-36.