Introduction to the Workshop
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The electronic form of this document may be cited in the following style:
Human Genome Program, U.S. Department of Energy, DOE Human Genome Program Contractor-Grantee Workshop IV, 1994.
Abstracts scanned from text submitted for November 1994 DOE Human Genome Program Contractor-Grantee Workshop. Inaccuracies have not been corrected.
Construction of an STS-Content YAC Map of Human Chromosome 16
N.A. Doggett, L.A. Duesing, J.G.Tesmer, L.J. Meincke, M.R. Altherr, A.A. Ford, D.C. Bruce, D.C. Torney, E.H. Knill, W.J. Bruno, R.D. Sutherland, M.G. Lowenstein, M.O. Mundt, D.F. Callen, G.R. Sutherland, L.L. Deaven, and R.K. Moyzis
Life Sciences Division and Center for Human Genome Studies, Los Alamos National Laboratory, Los Alamos, NM, Cytogenetics and Molecular Genetics, Woman's & Children's Hospital, Adelaide, SA, Australia
An STS-content YAC map has been constructed for human chromosome 16. The map consists of 515 CEPH MegaYACs, 220 flow sorted 16-specific YACs and 320 STSs, and provides nearly complete coverage of the euchromatic arms of this chromosome. STSs, which were derived largely from the end clones of cosmid contigs were first localized to a high resolution cytogenetic breakpoint map derived from 78 mouse/human somatic cell hybrids and 4 fragile sites which divide chromosome 16 into 90 intervals of average size 1 Mb. In the later stages of mapping STSs were derived from the ends of YAC clones which bordered gaps or from genes and markers that were known to lie near gap regions. The CEPH MegaYAC library was pooled into 95 top level pools based on a plate shuffling pooling scheme, and 672 secondary pools based on a plate shuffling and row column pooling scheme. An individual positive YAC is identified after screening the primary pool and a minimum of 14 secondary pools. For the flow-sorted 16 specific YAC library, a four-sets packing design was implemented which involved screening 47 pools in a single level to identify positive clones. The STS content map has been assembled in a spreadsheet program with YACs and STS oriented along the x and y axis respectively. In this manner STSs (rows) and YACs (columns) could easily be moved as newer data permitted refined ordering. This hand construction proved superior than automated methods such as segmap because available algorithms did not easily support the known ordering of STSs which had been localized to the breakpoint map. In the current map there is evidence for deletions occurring in 108 MegaYACs or ~21% of the MegaYACs. Due to the redundancy of coverage in the YAC map however, coverage exists for nearly all of these deleted regions in at least one YAC.
Supported by the US DOE (W-7405-ENG-36).