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An analysis of strategies for discovery of single‐nucleotide polymorphisms
Author(s) -
Eberle Michael A.,
Kruglyak Leonid
Publication year - 2000
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/1098-2272(2000)19:1+<::aid-gepi5>3.0.co;2-p
Subject(s) - single nucleotide polymorphism , minor allele frequency , snp , genetics , biology , allele , allele frequency , tag snp , population , computational biology , genotype , gene , medicine , environmental health
Strategies for the discovery of single‐nucleotide polymorphisms (SNPs) can be characterized by the number of individuals in the discovery sample, and by the minimal required number of observations of each allele. We examined the effect of different strategies on two key properties of the resulting SNP collection: (1) the probability that a SNP with a given population allele frequency is detected; and (2) the allele‐frequency distribution of the discovered SNPs. We show that strategies that accept all polymorphic sites lead to collections with a high fraction of SNPs with rare minor alleles, particularly in expanded populations. Such SNPs have a low probability of replication in a second sample. We discuss how to tailor a discovery strategy to the desired properties of a SNP collection. Genet. Epidemiol. 19(Suppl 1):S29–S35, 2000. © 2000 Wiley‐Liss, Inc.