Evaluation of a cosmid contig physical map of human chromosome 16

Raymond L. Stallings, Norman A. Doggett, David Callen, Sinoula Apostolou, L. Zhong Chen, Julie K. Nancarrow, Scott A. Whitmore, Peter Harris, Hannah Michison, Martijn Breuning, Jasper J. Saris, James Fickett, Michael Cinkosky, David C. Torney, Carl E. Hildebrand, Robert K. Moyzis

Research output: Contribution to journalArticle

43 Scopus citations

Abstract

A cosmid contig physical map of human chromosome 16 has been developed by repetitive sequence finger-printing of ∼4000 cosmid clones obtained from a chromosome 16-specific cosmid library. The arrangement of clones in contigs is determined by (1) estimating cosmid length and determining the likelihoods for all possible pairwise clone overlaps, using the fingerprint data, and (2) using an optimization technique to fit contig maps to these estimates. Two important questions concerning this contig map are how much of chromosome 16 is covered and how accurate are the assembled contigs. Both questions can be addressed by hybridization of single-copy sequence probes to gridded arrays of the cosmids. All of the fingerprinted clones have been arrayedon nylon membranes so that any region of interest can be identified by hybridization. The hybridization experiments indicate that ∼84% of the euchromatic arms of chromosome 16 are covered by contigs and singleton cosmids. Both grid hybridization (26 contigs) and pulsed-field gel electrophoresis experiments (11 configs) confirmed the assembled contigs, indicating that false positive overlaps occur infrequently in the present map. Furthermore, regional localization of 93 contigs and singleton cosmids to a somatic cell hybrid mapping panel indicates that there is no bias in the coverage of the euchromatic arms.

Original languageEnglish (US)
Pages (from-to)1031-1039
Number of pages9
JournalGenomics
Volume13
Issue number4
DOIs
StatePublished - Aug 1992

ASJC Scopus subject areas

  • Genetics

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    Stallings, R. L., Doggett, N. A., Callen, D., Apostolou, S., Chen, L. Z., Nancarrow, J. K., Whitmore, S. A., Harris, P., Michison, H., Breuning, M., Saris, J. J., Fickett, J., Cinkosky, M., Torney, D. C., Hildebrand, C. E., & Moyzis, R. K. (1992). Evaluation of a cosmid contig physical map of human chromosome 16. Genomics, 13(4), 1031-1039. https://doi.org/10.1016/0888-7543(92)90016-L