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.
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.]