Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data

Genetics
Rasmus NielsenAndrew G Clark

Abstract

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.

References

Jul 14, 2001·Science·J C StephensG F Vovis
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Dec 6, 2002·Genome Research·Joshua M AkeyMark D Shriver
Jan 10, 2003·Nucleic Acids Research·Gudmundur A Thorisson, Lincoln D Stein
Mar 1, 2003·Nature Genetics·L Luca Cavalli-Sforza, Marcus W Feldman
Apr 12, 2003·Theoretical Population Biology·Rasmus Nielsen, James Signorovitch
Jul 5, 2003·American Journal of Human Genetics·Tara C MatiseArthur L Holden

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Citations

Feb 3, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Karl J SchmidThomas Altmann
Feb 17, 2010·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·M MoraguesJoanne R Russell
Sep 27, 2008·Journal of Molecular Evolution·John J WelchDavid Waxman
Jul 25, 2008·Genetica·Patrícia H Brito, Scott V Edwards
Mar 18, 2005·Nature·Rasmus Nielsen
Oct 19, 2007·Nature Reviews. Genetics·Rasmus NielsenAndrew G Clark
Oct 19, 2013·Nature Reviews. Genetics·Outi SavolainenJuha Merilä
Jan 5, 2006·European Journal of Human Genetics : EJHG·Albert Tenesa, Malcolm G Dunlop
Nov 5, 2008·Proceedings of the National Academy of Sciences of the United States of America·William M MuirHans H Cheng
Jul 9, 2008·Animal Biotechnology·Kent M Reed
Mar 5, 2005·Bioinformatics·Per UnnebergFredrik Sterky
Dec 20, 2008·Molecular Biology and Evolution·Alan M Moses, Richard Durbin
Feb 27, 2010·Molecular Biology and Evolution·Andrew D Kern, David Haussler
Jun 19, 2010·Molecular Biology and Evolution·Anders AlbrechtsenRasmus Nielsen
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
May 28, 2013·Molecular Biology and Evolution·Mark LipsonBonnie Berger
Mar 13, 2009·Genome Research·Rasmus NielsenAndrew G Clark
Jan 21, 2010·Genome Research·Hua ChenDavid Reich
Oct 28, 2005·Genome Research·Andrew G ClarkRasmus Nielsen
Oct 28, 2005·Genome Research·Rasmus NielsenCarlos Bustamante
Oct 28, 2005·Genome Research·Christopher S CarlsonDeborah A Nickerson
Jul 11, 2006·Genome Research·Joanna L KelleyJoshua M Akey
Mar 14, 2007·Genome Research·Albert TenesaPeter M Visscher
Nov 28, 2013·Annual Review of Genetics·Joseph J VittiPardis C Sabeti
Jun 9, 2006·Annual Review of Genomics and Human Genetics·David Serre, Thomas J Hudson
Jul 3, 2008·Annual Review of Genomics and Human Genetics·Michael C Campbell, Sarah A Tishkoff
Jun 5, 2007·PLoS Genetics·Scott H WilliamsonRasmus Nielsen
Jun 3, 2008·PLoS Genetics·Adam R BoykoCarlos D Bustamante
Nov 10, 2013·PLoS Genetics·Laurent ExcoffierMatthieu Foll
Sep 6, 2008·PloS One·Francesca LucaAndrea Novelletto
May 17, 2006·Genetics·Yeon-Kyeong YooJung-Joo Hwang
Nov 18, 2006·Genetics·Kevin R Thornton, Jeffrey D Jensen
Feb 5, 2009·Genetics·Melissa M GrayRobert K Wayne

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