Methods

Genotyping African haplotypes in ATM using a co-spotted single-base extension assay†

  1. Maneesh Jain‡,
  2. Yvonne R. Thorstenson*,
  3. David M. Faulkner,
  4. Nader Pourmand,
  5. Ted Jones,
  6. Melinda Au§,
  7. Peter J. Oefner,
  8. Kevin P. White,
  9. Ronald W. Davis

Article first published online: 31 JUL 2003

DOI: 10.1002/humu.10250

Issue

Human Mutation

Human Mutation

Volume 22, Issue 3, pages 214–221, September 2003

Additional Information

How to Cite

Jain, M., Thorstenson, Y. R., Faulkner, D. M., Pourmand, N., Jones, T., Au, M., Oefner, P. J., White, K. P. and Davis, R. W. (2003), Genotyping African haplotypes in ATM using a co-spotted single-base extension assay. Hum. Mutat., 22: 214–221. doi: 10.1002/humu.10250

Author Information

  1. Stanford Genome Technology Center, Palo Alto, California

  1. ‡

    Par Allele Genomics, Inc., 384 Oyster Pt. Blvd. 8, South San Francisco, CA 94080

  2. §

    Exelixis, Inc., P.O. Box 511, South San Francisco, CA 94083

  3. Genetics Department, NSB 386, Yale University, New Haven, CT 06520

*Stanford Genome Technology Center, 855 California Ave., Palo Alto, CA 94304

  1. †

    Communicated by Ann-Christine Syvanen

Publication History

  1. Issue published online: 31 JUL 2003
  2. Article first published online: 31 JUL 2003
  3. Manuscript Accepted: 24 APR 2003
  4. Manuscript Received: 11 DEC 2002

Funded by

  • NIH. Grant Number: HG00205

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Keywords:

  • SNP;
  • genotyping;
  • arrayed SBE;
  • ATM;
  • haplotype;
  • single-base extension

Abstract

Human genetic analysis, including population genetic studies, increasingly calls for cost-effective, high-throughput methods for the rapid screening of single nucleotide polymorphisms (SNPs) across many individuals. The modified single-base extension assay described here (arrayed SBE) is a highly accurate and robust method for SNP genotyping that can deliver genotypes at 3.5 cents each, following PCR. Specifically, amino-modified probe/target pairs were prehybridized, then co-spotted in a microarray format prior to enzymatic addition of allele-specific nucleotides. Probe/target identity was determined solely by its physical location on the array rather than by hybridization to a complementary target, resulting in a call rate of 99–100%. These innovations result in an inexpensive, accurate assay with exceptional signal-to-noise ratios, depending on the glass surface employed. Comparison of glass slides from three different manufacturers indicated that aldehyde-based Zyomyx slides provided superior performance for this assay. Arrayed SBE was applied to study the geographic distribution of three African-specific haplotypes in the human ATM gene. Four selectively neutral markers, which define the haplotypes H5, H6, and H7, were screened in a total of 415 individuals. Region-specific haplotype frequencies were consistent with patterns of human migration across and outside of Africa, suggesting a possible haplotype origin in East Africa. Arrayed SBE was a robust tool for this analysis that could be applied to any situation requiring the genotyping of a few SNPs in many individuals. Hum Mutat 22:214–221, 2003. © 2003 Wiley-Liss, Inc.

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