Parallel Genotyping of Over 10,000 SNPs Using a One-Primer Assay on a High-Density Oligonucleotide Array

  1. Hajime Matsuzaki1,
  2. Halina Loi1,
  3. Shoulian Dong1,
  4. Ya-Yu Tsai2,
  5. Joy Fang1,
  6. Jane Law1,
  7. Xiaojun Di1,
  8. Wei-Min Liu1,
  9. Geoffrey Yang1,
  10. Guoying Liu1,
  11. Jing Huang1,
  12. Giulia C. Kennedy1,
  13. Thomas B. Ryder1,
  14. Gregory A. Marcus1,
  15. P. Sean Walsh1,
  16. Mark D. Shriver3,
  17. Jennifer M. Puck4,
  18. Keith W. Jones1, and
  19. Rui Mei1,5
  1. 1 Affymetrix, Inc., Santa Clara, California 95051, USA
  2. 2 Center for Inherited Disease Research (CIDR), Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA
  3. 3 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
  4. 4 Genetics and Molecular Biology Branch, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

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.

Footnotes

  • [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: S.A. Tishkoff, J.S. Friedlaender, T.G. Schurr, and W.S. Watkins.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2014904.

  • 5 Corresponding author. E-MAIL rui_mei{at}affymetrix.com; FAX (408) 481-0422.

    • Accepted January 6, 2004.
    • Received October 6, 2003.
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