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Hum Genomics. 2004 Mar;1(3):218-24.

Population genetic analysis of ascertained SNP data.

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Department of Biological Statistics and Computational Biology, Cornell University, 439 Warren Hall, Ithaca, NY 14853-7801, USA.


The large single nucleotide polymorphism (SNP) typing projects have provided an invaluable data resource for human population geneticists. Almost all of the available SNP loci, however, have been identified through a SNP discovery protocol that will influence the allelic distributions in the sampled loci. Standard methods for population genetic analysis based on the available SNP data will, therefore, be biased. This paper discusses the effect of this ascertainment bias on allelic distributions and on methods for quantifying linkage disequilibrium and estimating demographic parameters. Several recently developed methods for correcting for the ascertainment bias will also be discussed.

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