Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions

PloS One
Jun Zhang


Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA) has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs) without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the simila...Continue Reading


Sep 1, 1978·Science·P MenozziLuigi Luca Cavalli-Sforza
Dec 5, 1998·American Journal of Human Genetics·Esteban ParraMark D Shriver
Mar 11, 2000·American Journal of Human Genetics·Mary Sara McPeek, L Sun
Jan 17, 2002·Genetic Epidemiology·L SunMary Sara McPeek
Feb 15, 2002·American Journal of Human Genetics·Heather E Collins-SchrammMichael F Seldin
Sep 6, 2002·Genetic Epidemiology·Xiaofeng ZhuRichard S Cooper
Feb 5, 2003·Human Heredity·Lei SunMary Sara McPeek
Jan 1, 1964·Cold Spring Harbor Symposia on Quantitative Biology·Luigi Luca Cavalli-SforzaA W EDWARDS
Nov 25, 2003·American Journal of Human Genetics·Noah A RosenbergJonathan K Pritchard
Apr 22, 2004·European Journal of Human Genetics : EJHG·Dina L NewmanCarole Ober
Feb 16, 2005·Genetic Epidemiology·Hua TangNeil J Risch
Mar 10, 2006·Clinical Biomechanics·Allan T WrigleyJoan M Stevenson
Apr 17, 2007·American Journal of Human Genetics·Marc BauchetMark D Shriver
Sep 26, 2007·PLoS Genetics·Peristera PaschouPetros Drineas
Jan 23, 2008·PLoS Genetics·Alkes L PriceJoel N Hirschhorn
Sep 2, 2008·Nature·John NovembreCarlos Bustamante
Sep 12, 2008·Molecular Ecology Notes·Daniel FalushJonathan K Pritchard
Mar 25, 2009·Genome Research·Joseph K PickrellJonathan K Pritchard
May 16, 2009·American Journal of Human Genetics·Shameek BiswasJoshua M Akey
May 21, 2009·Genetic Epidemiology·Ann B LeeKathryn Roeder
Jun 9, 2009·PLoS Genetics·Graham CoopJonathan K Pritchard
Dec 4, 2009·PloS One·Jun ZhangMary Sara McPeek
Dec 1, 2008·Journal of the American Statistical Association·Carlos M CarvalhoMike West


Jan 25, 2012·PloS One·Hoicheong SiuMomiao Xiong
Feb 9, 2017·Nature Communications·Eunjung HanCatherine A Ball
Feb 28, 2020·Forensic Science International. Genetics·Peter PfaffelhuberFranz Baumdicker

Methods Mentioned


Related Concepts

In Silico
Genetics, Population
Variation (Genetics)
Single Nucleotide Polymorphism
Principal Component Analysis
Genome-Wide Association Study
Biological Markers
Forensic Medicine

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