Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.
paper
Cited
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- Authors
- Matsuzaki, Hajime; Loi, Halina; Dong, Shoulian; Tsai, Ya-Yu; Fang, Joy; Law, Jane; Di, Xiaojun; Liu, Wei-Min; Yang, Geoffrey; Liu, Guoying; Huang, Jing; Kennedy, Giulia C; Ryder, Thomas B; Marcus, Gregory A; Walsh, P Sean; Shriver, Mark D; Puck, Jennifer M; Jones, Keith W; Mei, Rui
- Year
- 2004
- Journal
- Genome research
- PMID
- 14993208
- DOI
- 10.1101/gr.2014904
- PMCID
- PMC353229
The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to 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, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome 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.
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| Title | Year | PMID |
|---|---|---|
| Description of the data from the Collaborative Study on the Genetics of Alcoholism (COGA) and single-nucleotide polymorphism genotyping for Genetic Analysis Workshop 14. | 2005 | 16451628 |
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