Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations

Donna M. Toleno; Peter L. Morrell; Michael T. Clegg

doi:10.1093/bioinformatics/btm260

Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations

Donna M. Toleno, Peter L. Morrell, Michael T. Clegg

Agronomy and Plant Genetics

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Abstract

Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time. Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

Original language	English (US)
Pages (from-to)	1807-1814
Number of pages	8
Journal	Bioinformatics
Volume	23
Issue number	14
DOIs	https://doi.org/10.1093/bioinformatics/btm260
State	Published - Jul 15 2007

Bibliographical note

Funding Information:
The authors thank M. Brandt, C. Torres, L. DeRose, S. MacDonald and two anonymous reviewers for helpful comments on previous versions of the manuscript. This work was supported by National Science Foundation grant DEB-0129247.

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title = "Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations",

abstract = "Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time. Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.",

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AU - Morrell, Peter L.

AU - Clegg, Michael T.

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Y1 - 2007/7/15

N2 - Motivation: Errors in nucleotide sequence and SNP genotyping data are problematic when inferring haplotypes. Previously published methods for error detection in haplotype data make use of pedigree information; however, for many samples, individuals are not related by pedigree. This article describes a method for detecting errors in haplotypes by considering the recombinational history implied by the patterns of variation, three SNPs at a time. Results: Coalescent simulations provide evidence that the method is robust to high levels of recombination as well as homologous gene conversion, indicating that patterns produced by both proximate and distant SNPs may be useful for detecting unlikely three-site haplotypes.

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Error detection in SNP data by considering the likelihood of recombinational history implied by three-site combinations

Abstract

Bibliographical note

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