JCVI: A SNP Resource for Human chromosome 22: Extracting Dense Clusters of SNPs from the Genomic Sequence
 
 
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Citation

Dawson, E., Chen, Y., Hunt, S., Smink, L. J., Hunt, A., Rice, K., Livingston, S., Bumpstead, S., Bruskiewich, R., Sham, P., Ganske, R., Adams, M., Kawasaki, K., Shimizu, N., Minoshima, S., Roe, B., Bentley, D., Dunham, I.

A SNP Resource for Human chromosome 22: Extracting Dense Clusters of SNPs from the Genomic Sequence

Genome Res. 2001 Jan 01; 11(1): 170-8.

PubMed Citation

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 www.sanger.ac.uk and in dbSNP.]