Detect and adjust for population stratification in population-based association study using genomic control markers: an application of Affymetrix Genechip Human Mapping 10K array

European Journal of Human Genetics : EJHG
Ke HaoWing H Wong

Abstract

Population-based association design is often compromised by false or nonreplicable findings, partially due to population stratification. Genomic control (GC) approaches were proposed to detect and adjust for this confounder. To date, the performance of this strategy has not been extensively evaluated on real data. More than 10 000 single-nucleotide polymorphisms (SNPs) were genotyped on subjects from four populations (including an Asian, an African-American and two Caucasian populations) using GeneChip Mapping 10 K array. On these data, we tested the performance of two GC approaches in different scenarios including various numbers of GC markers and different degrees of population stratification. In the scenario of substantial population stratification, both GC approaches are sensitive using only 20-50 random SNPs, and the mixed subjects can be separated into homogeneous subgroups. In the scenario of moderate stratification, both GC approaches have poor sensitivities. However, the bias in association test can still be corrected even when no statistical significant population stratification is detected. We conducted extensive benchmark analyses on GC approaches using SNPs over the whole human genome. We found GC method can cluste...Continue Reading

References

Jul 3, 1995·American Journal of Medical Genetics·Y YuvalM Pras
Sep 30, 1994·Science·E S Lander, N J Schork
Sep 13, 1996·Science·N Risch, K Merikangas
Sep 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·N E Morton, A Collins
May 10, 2000·American Journal of Human Genetics·S A BacanuK Roeder
Jun 3, 2000·Genetics·J K PritchardP Donnelly
Apr 21, 2001·Biometrics·B Devlin, K Roeder
Mar 23, 2002·The Pharmacogenomics Journal·S T WeissL J Palmer
Dec 21, 2002·Science·Noah A RosenbergMarcus W Feldman
Sep 10, 2003·Nature Biotechnology·Giulia C KennedyKeith W Jones
Mar 31, 2004·Nature Genetics·Matthew L FreedmanDavid Altshuler
Mar 31, 2004·Nature Genetics·Jonathan MarchiniPeter Donnelly

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Citations

Mar 17, 2011·European Journal of Human Genetics : EJHG·Jian YangUNKNOWN GIANT Consortium
Jan 6, 2006·Genes and Immunity·Y StienstraG van der Steege
Oct 19, 2007·Critical Care Medicine·Jesús VillarRobert M Kacmarek
Aug 27, 2009·Critical Care Medicine·Carlos FloresUNKNOWN GRECIA and Gen-SEP groups
Dec 16, 2005·Genome Research·Efrosini SetakisDavid J Balding
Feb 8, 2007·Genes, Brain, and Behavior·X ChenM F Miles
Mar 10, 2007·Human Heredity·Ke Hao, Simon Cawley
Apr 26, 2012·International Journal of Biological Sciences·Weizhen LuoLongchao Zhang
Jun 30, 2012·International Journal of Biological Sciences·Weizhen LuoLongchao Zhang
Oct 29, 2010·International Journal of Hypertension·Claire E HastieAnna F Dominiczak
Sep 22, 2005·American Journal of Human Genetics·Dov ShiffmanJohn P Kane
Jul 28, 2007·Arteriosclerosis, Thrombosis, and Vascular Biology·Joshua W KnowlesJohn P Cooke
Sep 28, 2006·Human Heredity·Michael SteffensMax P Baur
Apr 19, 2005·Expert Review of Molecular Diagnostics·David W Craig, Dietrich A Stephan
Dec 4, 2008·Genetic Epidemiology·Tony DaddCathryn M Lewis
Apr 6, 2006·Electrophoresis·Juan J SanchezNiels Morling
Jan 23, 2008·Applied Microbiology and Biotechnology·Hyeung-Jin JangWilliam E Bentley
Apr 24, 2009·Biological Trace Element Research·Wayne Chris HawkesKevin Dawson
Sep 17, 2009·Applied Microbiology and Biotechnology·Hyeung-Jin JangWilliam E Bentley
Aug 21, 2013·Biological Trace Element Research·Wayne Chris HawkesZeynep Alkan
Dec 7, 2007·PLoS Computational Biology·Xiaohong LiBrian J Reid
Nov 20, 2019·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·María Gabriela Pizarro InostrozaJuan Vicente Delgado Bermejo

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