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Published online before print June 12, 2001, 10.1101/gr.GR-1578R
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Vol. 11, Issue 7, 1262-1268, July 2001

METHODS
High-Throughput Genotyping with Single Nucleotide Polymorphisms

Koustubh Ranade,1,10,11,12 Mau-Song Chang,2 Chih-Tai Ting,3 Dee Pei,4 Chin-Fu Hsiao,5 Michael Olivier,1 Robert Pesich,1 Joan Hebert,1 Yii-Der I. Chen,6 Victor J. Dzau,7 David Curb,8 Richard Olshen,9 Neil Risch,1 David R. Cox,1 and David Botstein1,11,13

1 Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA; 2 Department of Medicine, Veterans General Hospital, Taipei, Taiwan; 3 Department of Medicine, Veterans General Hospital, Taichung, Taiwan; 4 Department of Endocrinology and Metabolism, Tri-Service General Hospital, Taipei, Taiwan; 5 National Health Research Institute, Taipei, Taiwan; 6 Division of Endocrinology, Stanford University School of Medicine, Stanford, California 94305, USA; 7 Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; 8 Hawaii Center for Health Research, Honolulu, Hawaii 96813, USA; 9 Health Research and Policy, Stanford University School of Medicine, Stanford, California 94305, USA

To make large-scale association studies a reality, automated high-throughput methods for genotyping with single-nucleotide polymorphisms (SNPs) are needed. We describe PCR conditions that permit the use of the TaqMan or 5' nuclease allelic discrimination assay for typing large numbers of individuals with any SNP and computational methods that allow genotypes to be assigned automatically. To demonstrate the utility of these methods, we typed >1600 individuals for a G-to-T transversion that results in a glutamate-to-aspartate substitution at position 298 in the endothelial nitric oxide synthase gene, and a G/C polymorphism (newly identified in our laboratory) in intron 8 of the 11-beta hydroxylase gene. The genotyping method is accurate---we estimate an error rate of fewer than 1 in 2000 genotypes, rapid---with five 96-well PCR machines, one fluorescent reader, and no automated pipetting, over one thousand genotypes can be generated by one person in one day, and flexible---a new SNP can be tested for association in less than one week. Indeed, large-scale genotyping has been accomplished for 23 other SNPs in 13 different genes using this method. In addition, we identified three "pseudo-SNPs" (WIAF1161, WIAF2566, and WIAF335) that are probably a result of duplication.

10 Present address: Pharmaceutical Research Institute, Bristol-Myers Squibb, Applied Genomics, Princeton, NJ 08543-5400.

11 Corresponding authors.

12 E-MAIL koustubh.ranade{at}bms.com; FAX (609) 818-5839.

13 E-MAIL botstein{at}genome.stanford.edu; FAX (650) 723-7016.

11:1262-1268 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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