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Originally published as Genetics Published Articles Ahead of Print on September 15, 2004.
Genetics, Vol. 168, 2373-2382, December 2004, Copyright © 2004
doi:10.1534/genetics.104.031039
Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data
Rasmus Nielsen*,
,1,
Melissa J. Hubisz* and
Andrew G. Clark
* Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14853
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York
Center for Bioinformatics, University of Copenhagen, 2100 Copenhagen, Denmark
1 Corresponding author: Center for Bioinformatics, Universitetsparken 15, 2100 Kbh Ø, Denmark.
E-mail: rasmus{at}binf.ku.dk
Most of the available SNP data have eluded valid population genetic analysis because most population genetical methods do not correctly accommodate the special discovery process used to identify SNPs. Most of the available SNP data have allele frequency distributions that are biased by the ascertainment protocol. We here show how this problem can be corrected by obtaining maximum-likelihood estimates of the true allele frequency distribution. In simple cases, the ML estimate of the true allele frequency distribution can be obtained analytically, but in other cases computational methods based on numerical optimization or the EM algorithm must be used. We illustrate the new correction method by analyzing some previously published SNP data from the SNP Consortium. Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project.
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