Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array

Hajime Matsuzaki, Halina Loi, Shoulian Dong, Ya Yu Tsai, Joy Fang, Jane Law, Xiaojun Di, Wei Min Liu, Geoffrey Yang, Guoying Liu, Jing Huang, Giulia C. Kennedy, Thomas B. Ryder, Gregory A. Marcus, P. Sean Walsh, Mark D. Shriver, Jennifer M. Puck, Keith W. Jones, Rui Mei

Research output: Contribution to journalArticlepeer-review

257 Scopus citations


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 >9.5%, >99.9%, and >95%, respectively. 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.

Original languageEnglish (US)
Pages (from-to)414-425
Number of pages12
JournalGenome research
Issue number3
StatePublished - Mar 2004

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)


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