Document Detail


Correcting coalescent analyses for panel-based SNP ascertainment.
MedLine Citation:
PMID:  23335334     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Single-nucleotide polymorphism (SNP) data are routinely obtained by sequencing a region of interest in a small panel, constructing a chip with probes specific to sites found to vary in the panel, and using the chip to assay subsequent samples. The size of the chip is often reduced by removing low-frequency alleles from the set of SNPs. Using coalescent estimation of the scaled population size parameter, Θ, as a test case, we demonstrate the loss of information inherent in this procedure and develop corrections for coalescent analysis of SNPs obtained via a panel. We show that more accurate Θ-estimates can be recovered if the panel size is known, but at considerable computational cost as the panel individuals must be explicitly modeled in the analysis. We extend this technique to apply to the case where rare alleles have been omitted from the SNP panel. We find that when appropriate corrections for panel ascertainment and rare-allele omission are used, the biases introduced by ascertainment are largely correctable, but recovered estimates are less accurate than would be obtained with fully sequenced data. This method is then applied to recombinant multiple population data to investigate the effects of recombination and migration on the estimate of Θ.
Authors:
James R McGill; Elizabeth A Walkup; Mary K Kuhner
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2013-01-18
Journal Detail:
Title:  Genetics     Volume:  193     ISSN:  1943-2631     ISO Abbreviation:  Genetics     Publication Date:  2013 Apr 
Date Detail:
Created Date:  2013-04-02     Completed Date:  2013-11-27     Revised Date:  2014-04-01    
Medline Journal Info:
Nlm Unique ID:  0374636     Medline TA:  Genetics     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1185-96     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Animals
Data Interpretation, Statistical
Gene Frequency
Humans
Models, Genetic
Oligonucleotide Array Sequence Analysis / methods*
Polymorphism, Single Nucleotide*
Population / genetics
Sample Size
Grant Support
ID/Acronym/Agency:
R01 HG004839/HG/NHGRI NIH HHS
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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