In:
Genome Research, Cold Spring Harbor Laboratory, Vol. 14, No. 3 ( 2004-03), p. 414-425
Abstract:
The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilizedto investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, andwas further driven by strict empirical measurements of accuracy, reproducibility, andaverage call rate, which we estimate to be 〉 9.5%, 〉 99.9%, and 〉 95%, respectively. With average heterozygosity of 0.38 andgenome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.
Type of Medium:
Online Resource
ISSN:
1088-9051
Language:
English
Publisher:
Cold Spring Harbor Laboratory
Publication Date:
2004
detail.hit.zdb_id:
1483456-X
SSG:
12
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