The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

John S.K. Kauwe, Sarah Bertelsen, Laura Jean Bierut, Gerald Dunn, Anthony L. Hinrichs, Carol H. Jin, Brian K. Suarez

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Accurately resolving population structure in a sample is important for both linkage and association studies. In this study we investigated the power of single-nucleotide polymorphisms (SNPs) in detecting population structure in a sample of 286 unrelated individuals. We varied the number of SNPs to determine how many are required to approach the degree of resolution obtained with the Collaborative Study on the Genetics of Alcoholism (COGA) short tandem repeat polymorphisms (STRPs). In addition, we selected SNPs with varying minor allele frequencies (MAFs) to determine whether low or high frequency SNPs are more efficient in resolving population structure. We conclude that a set of at least 100 evenly spaced SNPs with MAFs of 40-50% is required to resolve population structure in this dataset. If SNPs with lower MAFs are used, then more than 250 SNPs may be required to obtain reliable results.

Original languageEnglish
Article numberS84
JournalBMC genetics
Volume6
Issue numberSUPPL.1
DOIs
StatePublished - Dec 30 2005

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