Nucleic Acids Research, 2002, Vol. 30, No. 12 e53
© 2002 Oxford University Press
High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology
Stanford Human Genome Center, Stanford University School of Medicine, 975 California Avenue, Palo Alto, CA 94305, USA, 1Department of Internal Medicine, National Taiwan University, Taipei, Taiwan, 2Division of Cardiology, Department of Internal Medicine, Taipei Veterans General Hospital, Taipei, Taiwan, 3Department of Medicine, Taichung Veterans General Hospital, Taichung, Taiwan, 4Department of Medicine, TriService General Hospital, Taipei, Taiwan, 5Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94304, USA, 6Hawaii Center for Health Research, Honolulu, HI 96813, USA, 7Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA, 8Compaq Computer Corporation, 181 Lytton Avenue, Palo Alto, CA 94301, USA and 9Third Wave Technologies Inc., 502 South Rosa Road, Madison, WI 53719, USA
The feasibility of large-scale genome-wide association studies of complex human disorders depends on the availability of accurate and efficient genotyping methods for single nucleotide polymorphisms (SNPs). We describe a new platform of the invader assay, a biplex assay, where both alleles are interrogated in a single reaction tube. The assay was evaluated on over 50 different SNPs, with over 20 SNPs genotyped in study cohorts of over 1500 individuals. We assessed the usefulness of the new platform in high-throughput genotyping and compared its accuracy to genotyping results obtained by the traditional monoplex invader assay, TaqMan genotyping and sequencing data. We present representative data for two SNPs in different genes (CD36 and protein tyrosine phosphatase 1ß) from a study cohort comprising over 1500 individuals with high or low-normal blood pressure. In this high-throughput application, the biplex invader assay is very accurate, with an error rate of <0.3% and a failure rate of 1.64%. The set-up of the assay is highly automated, facilitating the processing of large numbers of samples simultaneously. We present new analysis tools for the assignment of genotypes that further improve genotyping success. The biplex invader assay with its automated set-up and analysis offers a new efficient high-throughput genotyping platform that is suitable for association studies in large study cohorts.
* To whom correspondence should be addressed at present address: Human and Molecular Genetics Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA. Tel: +1 414 456 4968; Fax: +1 414 456 6516; Email: molivier{at}mcw.edu Present address: Koustubh Ranade, Pharmaceutical Research Institute, Bristol-Myers Squibb, Princeton, NJ 08543-5839, USA
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