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Vol. 11, Issue 1, 170-178, January 2001

RESOURCES
A SNP Resource for Human Chromosome 22: Extracting Dense Clusters of SNPs From the Genomic Sequence

Elisabeth Dawson,1,7 Yuan Chen,1,7 Sarah Hunt,1,7 Luc J. Smink,1 Adrienne Hunt,1 Kate Rice,1 Simon Livingston,1 Suzannah Bumpstead,1 Richard Bruskiewich,1 Pak Sham,2 Rocky Ganske,3 Mark Adams,4 Kazuhiko Kawasaki,5 Nobuyoshi Shimizu,5 Shinsei Minoshima,5 Bruce Roe,6 David Bentley,1 and Ian Dunham1,8

1 The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; 2 Section of Genetic Epidemiology and Biostatistics, Department of Psychiatry, Institute of Psychiatry, London SE5 8AF, UK; 3 Third Wave Technologies, Inc., Madison, Wisconsin 53719-1256, USA; 4 The Institute for Genomic Research, Rockville, Maryland 20850, USA; 5 Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan; 6 Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, USA

The recent publication of the complete sequence of human chromosome 22 provides a platform from which to investigate genomic sequence variation. We report the identification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22, discovered in the overlaps of 460 clones used for the chromosome sequencing. We found, on average, 1 potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been positioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified on the chromosome. A subset of the SNPs were verified experimentally using either PCR-RFLP or genomic Invader assays. These experiments confirmed 92% of the potential variants in a panel of 92 individuals. [Details of the SNPs and RFLP assays can be found at http://www.sanger.ac.uk and in dbSNP.]

7 These authors contributed equally to this work.

8 Corresponding author.

11:170-178 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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