Journal
HUMAN HEREDITY
Volume 55, Issue 1, Pages 27-36Publisher
KARGER
DOI: 10.1159/000071807
Keywords
haplotypes; case-control studies; linkage disequilibrium; candidate gene analysis; htSNP
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Funding
- NATIONAL CANCER INSTITUTE [U01CA063464, R01CA063464] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM058897] Funding Source: NIH RePORTER
- NCI NIH HHS [CA63464] Funding Source: Medline
- NIGMS NIH HHS [GM58897] Funding Source: Medline
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We describe an approach for picking haplotype-tagging single nucleotide polymorphisms (htSNPs) that is presently being taken in two large nested case-control studies within a multiethnic cohort (MEC), which are engaged in a search for associations between risk of prostate and breast cancer and common genetic variations in candidate genes. Based on a preliminary sample of 70 control subjects chosen at random from each of the 5 ethnic groups in the MEC we estimate haplotype frequencies using a variant of the Excoffier-Slatkin E-M algorithm after genotyping a high density of SNPs selected every 3-5 kb in and surrounding a candidate gene. In order to evaluate the performance of a candidate set of htSNPS (which will be genotyped in the much larger case-control sample) we treat the haplotype frequencies estimate above as known, and carry out a formal calculation of the uncertainty of the number of copies of common haplotypes carried by an individual, summarizing this calculation as a coefficient of determination, R-h(2). A candidate date set of htSNPS of a given size is chosen so as to maximize the minimum value of R-h(2) over the common haploh types, h. Copyright (C) 2003 S. Karger AG, Basel.
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