A SNP Resource for Human Chromosome 22: Extracting Dense Clusters of SNPs From the Genomic Sequence
- Elisabeth Dawson1,7,
- Yuan Chen1,7,
- Sarah Hunt1,7,
- Luc J. Smink1,
- Adrienne Hunt1,
- Kate Rice1,
- Simon Livingston1,
- Suzannah Bumpstead1,
- Richard Bruskiewich1,
- Pak Sham2,
- Rocky Ganske3,
- Mark Adams4,
- Kazuhiko Kawasaki5,
- Nobuyoshi Shimizu5,
- Shinsei Minoshima5,
- Bruce Roe6,
- David Bentley1, and
- Ian Dunham1,8
- 1The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK; 2Section of Genetic Epidemiology and Biostatistics, Department of Psychiatry, Institute of Psychiatry, London SE5 8AF, UK; 3Third Wave Technologies, Inc., Madison, Wisconsin 53719-1256, USA; 4The Institute for Genomic Research, Rockville, Maryland 20850, USA; 5Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160–8582, Japan; 6Department of Chemistry and Biochemistry, The University of Oklahoma, Norman, Oklahoma 73019, USA
Abstract
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.]
Footnotes
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↵7 These authors contributed equally to this work.
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↵8 Corresponding author.
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E-MAIL id1{at}sanger.ac.uk; FAX 01223-494919.
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Article and publication are at www.genome.org/cgi/doi/10.1101/gr.156901.
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- Received July 24, 2000.
- Accepted September 22, 2000.
- Cold Spring Harbor Laboratory Press
