Challenges in conducting genome-wide association studies in highly admixed multi-ethnic populations: the Generation R Study

European Journal of Epidemiology
Carolina Medina-GomezFernando Rivadeneira

Abstract

Genome-wide association studies (GWAS) have been successful in identifying loci associated with a wide range of complex human traits and diseases. Up to now, the majority of GWAS have focused on European populations. However, the inclusion of other ethnic groups as well as admixed populations in GWAS studies is rapidly rising following the pressing need to extrapolate findings to non-European populations and to increase statistical power. In this paper, we describe the methodological steps surrounding genetic data generation, quality control, study design and analytical procedures needed to run GWAS in the multiethnic and highly admixed Generation R Study, a large prospective birth cohort in Rotterdam, the Netherlands. Furthermore, we highlight a number of practical considerations and alternatives pertinent to the quality control and analysis of admixed GWAS data.

References

Oct 19, 2001·Molecular Biology and Evolution·A D Overall, R A Nichols
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Feb 12, 2004·European Journal of Human Genetics : EJHG·Louise HoskingChun-Fang Xu
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Oct 24, 2007·Nature Genetics·Patrick SulemKari Stefansson
Dec 21, 2007·European Journal of Epidemiology·Vincent W V JaddoeAlbert Hofman
Oct 15, 2008·Human Molecular Genetics·Paul I W de BakkerBenjamin F Voight
Feb 14, 2009·American Journal of Human Genetics·Lucy HuangPaul Scheet
Sep 15, 2010·PloS One·Sara L PulitPaul I W de Bakker
Nov 9, 2010·Genetic Epidemiology·Yun LiGonçalo R Abecasis
Nov 19, 2010·Nature Protocols·Carl A AndersonKrina T Zondervan
Jun 29, 2011·Nature Reviews. Genetics·Michael F SeldinAlkes L Price
Sep 6, 2011·Human Molecular Genetics·Jingyuan FuCisca Wijmenga
Nov 30, 2011·Genetic Epidemiology·Andrew P Morris
Mar 3, 2012·G3 : Genes - Genomes - Genetics·Bryan HowieMatthew Stephens
Apr 10, 2012·Nature Genetics·Jonathan P BradfieldUNKNOWN Early Growth Genetics Consortium
Jul 4, 2012·American Journal of Human Genetics·Timothy ThorntonNeil Risch
Oct 18, 2012·Genetic Epidemiology·Eric Yi LiuYun Li
Mar 2, 2013·Human Molecular Genetics·Diana L CousminerUNKNOWN Early Growth Genetics (EGG) Consortium
May 15, 2013·Nature Genetics·Ikuyo KouShiro Ikegawa
May 30, 2013·European Journal of Human Genetics : EJHG·Dorret I BoomsmaCornelia M van Duijn
Dec 10, 2013·The Journal of Allergy and Clinical Immunology·Ralf Jp van der ValkUNKNOWN EArly Genetics & Lifecourse Epidemiology (EAGLE) Consortium
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Apr 26, 2014·Nature Protocols·Thomas W WinklerUNKNOWN Genetic Investigation of Anthropometric Traits (GIANT) Consortium

❮ Previous
Next ❯

Citations

Dec 23, 2015·Journal of Child Psychology and Psychiatry, and Allied Disciplines·Eszter SzekelyPhilip Shaw
Aug 25, 2015·Journal of the American Academy of Child and Adolescent Psychiatry·Sabine E MousDanielle Posthuma
May 5, 2016·European Journal of Human Genetics : EJHG·Matthew Traylor, Cathryn M Lewis
Jun 25, 2016·International Journal of Obesity : Journal of the International Association for the Study of Obesity·G NoppeE F C van Rossum
Oct 22, 2016·Biological Psychiatry·Evangelos VassosGerome Breen
Aug 28, 2016·European Journal of Epidemiology·Abbas Dehghan
Nov 30, 2016·Molecular Psychiatry·A A E VinkhuyzenJ J McGrath
Oct 26, 2016·Journal of Lipid Research·Ardashel LatsuzbaiaJanine F Felix
Jun 20, 2017·Journal of Child Psychology and Psychiatry, and Allied Disciplines·Philip R JansenHenning Tiemeier
Oct 25, 2017·European Journal of Epidemiology·M Arfan IkramAlbert Hofman
Jun 9, 2018·Pediatric Allergy and Immunology : Official Publication of the European Society of Pediatric Allergy and Immunology·Sara S ShagiwalLiesbeth Duijts
Jun 23, 2018·Human Molecular Genetics·Simon HaworthNicholas J Timpson
Oct 25, 2017·European Journal of Epidemiology·Tonya WhiteHenning Tiemeier
Apr 12, 2018·Annual Review of Genomics and Human Genetics·Daniel M Jordan, Ron Do
May 10, 2019·Nature Reviews. Genetics·Vivian TamDavid Meyre
Nov 16, 2017·American Journal of Physical Anthropology·Brunilda DhamoEdwin M Ongkosuwito
Oct 28, 2019·Genetic Epidemiology·Emileigh L WillemsStephanie A Santorico
Mar 13, 2020·Annals of Neurology·C Louk de MolRinze F Neuteboom
May 10, 2020·Genes, Brain, and Behavior·María Fernanda Vinueza-VelozChris I De Zeeuw
Jan 11, 2017·European Journal of Epidemiology·Marjolein N KooijmanVincent W V Jaddoe
Sep 28, 2018·BMC Cancer·Anne-Lotte L F van der KooiUNKNOWN PanCareLIFE Consortium
Apr 5, 2019·European Journal of Epidemiology·Clair A EnthovenCaroline C W Klaver
Aug 19, 2017·Scientific Reports·Alexander NeumannHenning Tiemeier
Jan 29, 2019·Environmental Health Perspectives·Todd A JuskoMatthew P Longnecker
Mar 20, 2019·JMIR Research Protocols·Eva ClemensMarry M van den Heuvel-Eibrink
Feb 23, 2020·Human Genetics·Madina SeidualyJong Bhak
Apr 28, 2017·BJPsych Open·Anna A E VinkhuyzenJohn J McGrath
May 11, 2020·Journal of Neural Transmission·Yoshiro MorimotoHiroki Ozawa
Apr 24, 2018·Genetic Epidemiology·Eszter SzekelyPhilip Shaw
Oct 18, 2020·Nutrients·Veronica A MullinsFloyd H Chilton
Apr 27, 2017·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Brandon MapesM Eileen Dolan
Dec 21, 2019·International Journal of Psychophysiology : Official Journal of the International Organization of Psychophysiology·Keanan J JoynerChristopher J Patrick
Feb 15, 2021·Human Reproduction·Anne-Lotte L F van der KooiEline van Dulmen-den Broeder
Mar 10, 2021·International Journal of Psychophysiology : Official Journal of the International Organization of Psychophysiology·Keanan J JoynerChristopher J Patrick

❮ Previous
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Methods Mentioned

BETA
chip
genotyping
MDS

Software Mentioned

Genome Studio
Hapmap
Admix
Efficient Mixed - Model Association eXpedited ( EMMAX )
REAP
MACH
Genome
minimac
Illumina Genome Studio
R

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