Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools (original) (raw)

Abstract.

Detecting alleles that confer small increments in susceptibility to disease will require large-scale allelic association studies of single-nucleotide polymorphisms (SNPs) in candidate, or positional candidate, genes. However, current genotyping technologies are one to two orders of magnitude too expensive to permit the analysis of thousands of SNPs in large samples. We have developed and thoroughly validated a highly accurate protocol for SNP allele frequency estimation in DNA pools based upon the SNaPshot (Applied Biosystems) chemistry adaptation of primer extension. Using this assay, we were able to estimate the difference in allele frequencies between pooled cases and controls (Δ) with a mean error of 0.01. Moreover, when we genotyped seven different SNPs in a single multiplex reaction, the results were similar, with a mean error for Δ of 0.008. The assay performed well for alleles of low frequency alleles (_f_~0.05) and was accurate even with relatively poor quality DNA template extracted from mouthwashes. Our assay conditions are generalisable, universal, robust and, therefore, for the first time, permit high-throughput association analysis at a realistic cost.

Access this article

Log in via an institution

Subscribe and save

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

Author information

Authors and Affiliations

  1. Department of Psychological Medicine, University of Wales College of Medicine, Heath Park, Cardiff, CF14 4XN, UK, UK
    Nadine Norton, Nigel M. Williams, Hywel J. Williams, Gillian Spurlock, George Kirov, Derek W. Morris, Bastiaan Hoogendoorn, Michael J. Owen & Michael C. O'Donovan

Authors

  1. Nadine Norton
    You can also search for this author inPubMed Google Scholar
  2. Nigel M. Williams
    You can also search for this author inPubMed Google Scholar
  3. Hywel J. Williams
    You can also search for this author inPubMed Google Scholar
  4. Gillian Spurlock
    You can also search for this author inPubMed Google Scholar
  5. George Kirov
    You can also search for this author inPubMed Google Scholar
  6. Derek W. Morris
    You can also search for this author inPubMed Google Scholar
  7. Bastiaan Hoogendoorn
    You can also search for this author inPubMed Google Scholar
  8. Michael J. Owen
    You can also search for this author inPubMed Google Scholar
  9. Michael C. O'Donovan
    You can also search for this author inPubMed Google Scholar

Additional information

Electronic Publication

Rights and permissions

About this article

Cite this article

Norton, N., Williams, N.M., Williams, H.J. et al. Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools.Hum Genet 110, 471–478 (2002). https://doi.org/10.1007/s00439-002-0706-6

Download citation

Keywords