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

被引:58
作者
Dawson, E
Chen, Y
Hunt, S
Smink, LJ
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
机构
[1] Sanger Ctr, Cambridge CB10 1SA, England
[2] Inst Psychiat, Dept Psychiat, Sect Genet Epidemiol & Biostat, London SE5 8AF, England
[3] Third Wave Technol Inc, Madison, WI 53719 USA
[4] Inst Genome Res, Rockville, MD 20850 USA
[5] Keio Univ, Sch Med, Dept Mol Biol, Shinjuku Ku, Tokyo 1608582, Japan
[6] Univ Oklahoma, Dept Chem & Biochem, Norman, OK 73019 USA
基金
英国惠康基金;
关键词
D O I
10.1101/gr.156901
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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, I 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.].
引用
收藏
页码:170 / 178
页数:9
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