Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium
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Correcting for ascertainment biases when analyzing SNP data : applications to the estimation of linkage disequilibrium. / Nielsen, Rasmus; Signorovitch, James.
I: Theoretical Population Biology, Bind 63, Nr. 3, 2003, s. 245-255.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - Correcting for ascertainment biases when analyzing SNP data
T2 - applications to the estimation of linkage disequilibrium
AU - Nielsen, Rasmus
AU - Signorovitch, James
PY - 2003
Y1 - 2003
N2 - As large-scale sequencing efforts turn from single genome sequencing to polymorphism discovery, single nucleotide polymorphisms (SNPs) are becoming an increasingly important class of population genetic data. But because of the ascertainment biases introduced by many methods of SNP discovery, most SNP data cannot be analyzed using classical population genetic methods. Statistical methods must instead be developed that can explicitly take into account each method of SNP discovery. Here we review some of the current methods for analyzing SNPs and derive sampling distributions for single SNPs and pairs of SNPs for some common SNP discovery schemes. We also show that the ascertainment scheme has a large effect on the estimation of linkage disequilibrium and recombination, and describe some methods of correcting for ascertainment biases when estimating recombination rates from SNP data.
AB - As large-scale sequencing efforts turn from single genome sequencing to polymorphism discovery, single nucleotide polymorphisms (SNPs) are becoming an increasingly important class of population genetic data. But because of the ascertainment biases introduced by many methods of SNP discovery, most SNP data cannot be analyzed using classical population genetic methods. Statistical methods must instead be developed that can explicitly take into account each method of SNP discovery. Here we review some of the current methods for analyzing SNPs and derive sampling distributions for single SNPs and pairs of SNPs for some common SNP discovery schemes. We also show that the ascertainment scheme has a large effect on the estimation of linkage disequilibrium and recombination, and describe some methods of correcting for ascertainment biases when estimating recombination rates from SNP data.
U2 - 10.1016/S0040-5809(03)00005-4
DO - 10.1016/S0040-5809(03)00005-4
M3 - Journal article
C2 - 12689795
AN - SCOPUS:0042991419
VL - 63
SP - 245
EP - 255
JO - Theoretical Population Biology
JF - Theoretical Population Biology
SN - 0040-5809
IS - 3
ER -
ID: 222644701