Identification of key contributors in complex population structures

PloS One
Markus NeuditschkoStefan Rieder

Abstract

Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures. Based on the Eigenvalue Decomposition (EVD) of a genomic relationship matrix we describe a novel approach to evaluate the genetic contribution of individuals to population structure. We combined the identification of key contributors with model-based clustering and population network visualization into an integrated three-step approach, which allows identification of high-resolution population structures and substructures around such key contributors. The approach was applied and validated in four disparate datasets including a simulated population (5,100 individuals and 10,000 SNPs), a highly structured experimental sheep population (1,421 individuals and 44,693 SNPs) and two large complex pedigree populations namely...Continue Reading

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Citations

Oct 27, 2017·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Apr 7, 2020·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey

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Methods Mentioned

BETA
PCA

Software Mentioned

istruct
ermline
paran
MultiColoredNodes
mpute
edig P ed
R
eagle
Principal Coordinate axes analysis PCoA
A dmixture

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