Relationship estimation from whole-genome sequence data

PLoS Genetics
Hong LiChad D Huff

Abstract

The determination of the relationship between a pair of individuals is a fundamental application of genetics. Previously, we and others have demonstrated that identity-by-descent (IBD) information generated from high-density single-nucleotide polymorphism (SNP) data can greatly improve the power and accuracy of genetic relationship detection. Whole-genome sequencing (WGS) marks the final step in increasing genetic marker density by assaying all single-nucleotide variants (SNVs), and thus has the potential to further improve relationship detection by enabling more accurate detection of IBD segments and more precise resolution of IBD segment boundaries. However, WGS introduces new complexities that must be addressed in order to achieve these improvements in relationship detection. To evaluate these complexities, we estimated genetic relationships from WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as controls. We identified several genomic regions with excess pairwise IBD in both the pedigree and control datasets using three established IBD methods: GERMLINE, fastIBD, and ISCA. These spurious IBD segments produced a 10-fold increase in the rate of detected fals...Continue Reading

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Citations

Oct 18, 2015·Theoretical Population Biology·M SunN A Sheehan
Feb 26, 2016·Genome Biology and Evolution·Larisa FedorovaAlexei Fedorov
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Jun 26, 2018·American Journal of Human Genetics·Monica D RamstetterAmy L Williams

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Methods Mentioned

BETA
PCA

Software Mentioned

Estimation of Recent Shared Ancestry ( ERSA )
ISCA
RELPAIR
BEAGLE
Beagle fastIBD
UCSC Genome Browser
ERSA2
GERMLINE
indep
fastIBD

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