SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

Lachance, Joseph; Tishkoff, Sarah A.

doi:10.1002/bies.201300014

i

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

Supporting Files

Jul 09 2013
By Lachance, Joseph ; Tishkoff, Sarah A.

File Language:

Details

Alternative Title:

Bioessays
Personal Author:

Lachance, Joseph ; Tishkoff, Sarah A.
Description:

Whole genome sequencing and SNP genotyping arrays can paint strikingly different pictures of demographic history and natural selection. This is because genotyping arrays contain biased sets of pre-ascertained SNPs. In this short review, we use comparisons between high-coverage whole genome sequences of African hunter-gatherers and data from genotyping arrays to highlight how SNP ascertainment bias distorts population genetic inferences. Sample sizes and the populations in which SNPs are discovered affect the characteristics of observed variants. We find that SNPs on genotyping arrays tend to be older and present in multiple populations. In addition, genotyping arrays cause allele frequency distributions to be shifted towards intermediate frequency alleles, and estimates of linkage disequilibrium are modified. Since population genetic analyses depend on allele frequencies, it is imperative that researchers are aware of the effects of SNP ascertainment bias. With this in mind, we describe multiple ways to correct for SNP ascertainment bias.
Subjects:

Africa African Hunter-gatherers Alleles Article Bias (Epidemiology) Biological Evolution Gene Frequency Genetics, Population Haplotypes Human Genetics Humans Linkage Disequilibrium Polymorphism, Single Nucleotide Population Genetics Selection, Genetic SNP Ascertainment Bias Whole Genome Sequencing
Source:

Bioessays. 35(9):780-786.
Pubmed ID:

23836388
Pubmed Central ID:

PMC3849385
Document Type:

Journal Article
Funding:

DP1 ES022577/ES/NIEHS NIH HHS/United States ; DP1 ES022577-04/DP/NCCDPHP CDC HHS/United States ; F32 HG006648/HG/NHGRI NIH HHS/United States ; F32HG006648-02/HG/NHGRI NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States
Volume:

35
Issue:

9
Collection(s):

CDC Public Access
Main Document Checksum:

urn:sha256:6e7ad20ef04ce0c9113b473cc00019017b194073fb4c71cfd06021aa54df66e4
Download URL:

https://stacks.cdc.gov/view/cdc/29791/cdc_29791_DS1.pdf
File Type:

[PDF - 446.60 KB ]

File Language:

ON THIS PAGE

Details Supporting Files

CDC STACKS serves as an archival repository of CDC-published products including scientific findings, journal articles, guidelines, recommendations, or other public health information authored or co-authored by CDC or funded partners.

As a repository, CDC STACKS retains documents in their original published format to ensure public access to scientific information.