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Understanding the accuracy of statistical haplotype inference with sequence data of known phase
Authors
Barrett
Carlson
+42 more
Chung
Clark
Clark
Clark
Clayton
Douglas
Excoffier
Excoffier
Gabriel
Halperin
Hawley
Hill
Hudson
Johnson
Kidd
Kimmel
Kukita
Lin
Long
Marchini
Marth
Martinez-Arias
Mateu
Morris
Myers
Niu
Niu
Patil
Raymond
Reich
Sabeti
Salem
Schaid
Scheet
Schouten
Stephens
Stephens
Stephens
Stephens
Tishkoff
Weir
Yan
Publication date
1 January 2007
Publisher
'Wiley'
Doi
Cite
View
on
PubMed
Abstract
Statistical methods for haplotype inference from multi-site genotypes of unrelated individuals have important application in association studies and population genetics. Understanding the factors that affect the accuracy of this inference is important, but their assessment has been restricted by the limited availability of biological data with known phase. We created hybrid cell lines monosomic for human chromosome 19 and produced single-chromosome complete sequences of a 48 kb genomic region in 39 individuals of African American (AA) and European American (EA) origin. We employ these phase-known genotypes and coalescent simulations to assess the accuracy of statistical haplotype reconstruction by several algorithms. Accuracy of phase inference was considerably low in our biological data even for regions as short as 25–50 kb, suggesting that caution is needed when analyzing reconstructed haplotypes. Moreover, the reliability of estimated confidence in phase inference is not high enough to allow for a reliable incorporation of site-specific uncertainty information in subsequent analyses. We show that, in samples of certain mixed ancestry (AA and EA populations), the most accurate haplotypes are probably obtained when increasing sample size by considering the largest, pooled sample, despite the hypothetical problems associated with pooling across those heterogeneous samples. Strategies to improve confidence in reconstructed haplotypes, and realistic alternatives to the analysis of inferred haplotypes, are discussed. Genet. Epidemiol . © 2007 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/57366/1/20185_ftp.pd
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