Skip to main content

High-throughput genotyping with single nucleotide polymorphisms.

Publication ,  Journal Article
Ranade, K; Chang, MS; Ting, CT; Pei, D; Hsiao, CF; Olivier, M; Pesich, R; Hebert, J; Chen, YD; Dzau, VJ; Curb, D; Olshen, R; Risch, N ...
Published in: Genome Res
July 2001

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.

Duke Scholars

Altmetric Attention Stats
Dimensions Citation Stats

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

July 2001

Volume

11

Issue

7

Start / End Page

1262 / 1268

Location

United States

Related Subject Headings

  • Taq Polymerase
  • Radiation Hybrid Mapping
  • Polymorphism, Single Nucleotide
  • Polymerase Chain Reaction
  • Humans
  • Genotype
  • Bioinformatics
  • Base Pair Mismatch
  • Alleles
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Ranade, K., Chang, M. S., Ting, C. T., Pei, D., Hsiao, C. F., Olivier, M., … Botstein, D. (2001). High-throughput genotyping with single nucleotide polymorphisms. Genome Res, 11(7), 1262–1268. https://doi.org/10.1101/gr.157801
Ranade, K., M. S. Chang, C. T. Ting, D. Pei, C. F. Hsiao, M. Olivier, R. Pesich, et al. “High-throughput genotyping with single nucleotide polymorphisms.Genome Res 11, no. 7 (July 2001): 1262–68. https://doi.org/10.1101/gr.157801.
Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, Olivier M, et al. High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 2001 Jul;11(7):1262–8.
Ranade, K., et al. “High-throughput genotyping with single nucleotide polymorphisms.Genome Res, vol. 11, no. 7, July 2001, pp. 1262–68. Pubmed, doi:10.1101/gr.157801.
Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, Olivier M, Pesich R, Hebert J, Chen YD, Dzau VJ, Curb D, Olshen R, Risch N, Cox DR, Botstein D. High-throughput genotyping with single nucleotide polymorphisms. Genome Res. 2001 Jul;11(7):1262–1268.

Published In

Genome Res

DOI

ISSN

1088-9051

Publication Date

July 2001

Volume

11

Issue

7

Start / End Page

1262 / 1268

Location

United States

Related Subject Headings

  • Taq Polymerase
  • Radiation Hybrid Mapping
  • Polymorphism, Single Nucleotide
  • Polymerase Chain Reaction
  • Humans
  • Genotype
  • Bioinformatics
  • Base Pair Mismatch
  • Alleles
  • 3105 Genetics