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Review
. 2004 Mar;1(3):218-24.
doi: 10.1186/1479-7364-1-3-218.

Population genetic analysis of ascertained SNP data

Rasmus Nielsen  1
Affiliations
Review

Population genetic analysis of ascertained SNP data

Rasmus Nielsen. Hum Genomics. 2004 Mar.

Abstract

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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Figures

Figure 1
Figure 1
The expected frequency of mutant alleles (unfolded frequency spectrum) of allele frequency X in the standard neutral model assuming a sample of size n = 20 chromosomes and an ascertainment sample size of d = 2 (black), d = 5 (dark grey), d = 10 (light grey) and d = 20 (white; no ascertainment bias). In (a) it is assumed that the ascertainment sample is a subset of the typed sample and in (b) it is assumed that it is not.
Figure 2
Figure 2
The expected folded frequency spectrum in the standard neutral model assuming a sample of size n = 20 chromosomes and an ascertainment sample size of d = 2 (black), d = 5 (dark grey), d = 10 (light grey) and d = 20 (white; no ascertainment bias). In (a) it is assumed that the ascertainment sample is a subset of the typed sample and in (b) it is assumed that it is not.
Figure 3
Figure 3
The expected frequency of mutant alleles (unfolded frequency spectrum) of allele frequency X in a neutral model of two populations exchanging M = 1 migrants per generation, assuming: (a) a sample of size n = 20 chromosomes and no ascertainment bias; (b) an ascertainment sample of two chromosomes from each population; and (c) an ascertainment sample of four chromosomes from Population 1.
Figure 4
Figure 4
The observed frequency (grey) of a mutant allele in a sample of 1,000 SNPs simulated under the standard neutral model with the ascertainment scheme of Equation 2 and assuming n = 20 and d = 4: The black bars show the corresponding expected frequencies assuming no ascertainment bias and the white bars show the estimated frequencies using the correction given in Equation 4.
See this image and copyright information in PMC

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