Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array |
| |
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 |
| |
Institution: | Affymetrix, Inc., Santa Clara, California 95051, USA. |
| |
Abstract: | 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. |
| |
Keywords: | |
本文献已被 PubMed 等数据库收录! |
|