A SNP resource for human chromosome 22: Extracting dense clusters of SNPs from the genomic sequence

The recent publication of the complete sequence of human chromosome 22 prov ides a platform from which to investigate genomic sequence variation. We re port the identification and characterization of 12,267 potential variants ( SNPs and other small insertions/deletions) of human chromosome 22, discover ed in the overlaps of 460 clones used for the chromosome sequencing. We fou nd, on average, I potential variant every 1.07 kb and approximately 18% of the potential variants involve insertions/deletions. The SNPs have been pos itioned both relative to each other, and to genes, predicted genes, repeat sequences, other genetic markers, and the 2730 SNPs previously identified o n the chromosome. A subset of the SNPs were verified experimentally using e ither PCR-RFLP or genomic Invader assays. These experiments confirmed 92% o f 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.].