Genetic Epidemiology, Psychiatric Genetics, Asthma Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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24762786
TITLE
Quality control and conduct of genome-wide association meta-analyses.
ABSTRACT
Rigorous organization and quality control (QC) are necessary to facilitate successful genome-wide association meta-analyses (GWAMAs) of statistics aggregated across multiple genome-wide association studies. This protocol provides guidelines for (i) organizational aspects of GWAMAs, and for (ii) QC at the study file level, the meta-level across studies and the meta-analysis output level. Real-world examples highlight issues experienced and solutions developed by the GIANT Consortium that has conducted meta-analyses including data from 125 studies comprising more than 330,000 individuals. We provide a general protocol for conducting GWAMAs and carrying out QC to minimize errors and to guarantee maximum use of the data. We also include details for the use of a powerful and flexible software package called EasyQC. Precise timings will be greatly influenced by consortium size. For consortia of comparable size to the GIANT Consortium, this protocol takes a minimum of about 10 months to complete.
DATE PUBLISHED
2014 May
HISTORY
PUBSTATUS PUBSTATUSDATE
aheadofprint 2014/04/24
entrez 2014/04/26 06:00
pubmed 2014/04/26 06:00
medline 2014/12/15 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Winkler TW Winkler Thomas W TW Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany.
Day FR Day Felix R FR Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
Croteau-Chonka DC Croteau-Chonka Damien C DC 1] Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA. [2] Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.
Wood AR Wood Andrew R AR Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK.
Locke AE Locke Adam E AE Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, USA.
Mägi R Mägi Reedik R Estonian Genome Center, University of Tartu, Tartu, Estonia.
Ferreira T Ferreira Teresa T Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Fall T Fall Tove T 1] Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. [2] Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.
Graff M Graff Mariaelisa M Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Justice AE Justice Anne E AE Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA.
Luan J Luan Jian'an J Medical Research Council (MRC) Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK.
Gustafsson S Gustafsson Stefan S Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
Randall JC Randall Joshua C JC Wellcome Trust Sanger Institute, Cambridge, UK.
Vedantam S Vedantam Sailaja S 1] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [2] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Workalemahu T Workalemahu Tsegaselassie T Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts, USA.
Kilpeläinen TO Kilpeläinen Tuomas O TO The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Scherag A Scherag André A 1] Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital of Essen, University of Duisburg-Essen, Essen, Germany. [2] Clinical Epidemiology, Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany.
Esko T Esko Tonu T 1] Estonian Genome Center, University of Tartu, Tartu, Estonia. [2] Divisions of Endocrinology and Genetics and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA. [4] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Kutalik Z Kutalik Zoltán Z 1] Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland. [2] Institute of Social and Preventive Medicine (IUMSP), Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. [3] Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Heid IM Heid Iris M IM 1] Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, Regensburg, Germany. [2].
Loos RJ Loos Ruth J F RJ 1] The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [4].
Genetic Investigation of Anthropometric Traits (GIANT) Consortium
INVESTIGATORS
LASTNAME FORENAME INITIALS AFFILIATION
Abecasis Goncalo R GR
Absher Devin D
Alavere Helene H
Albrecht Eva E
Allen Hana Lango HL
Almgren Peter P
Amin Najaf N
Amouyel Philippe P
Anderson Denise D
Arnold Alice M AM
Arveiler Dominique D
Aspelund Thor T
Asselbergs Folkert W FW
Assimes Themistocles L TL
Atalay Mustafa M
Attwood Antony P AP
Atwood Larry D LD
Bakker Stephan J L SJ
Balkau Beverley B
Balmforth Anthony J AJ
Barlassina Cristina C
Barroso Inês I
Basart Hanneke H
Bauer Sabrina S
Beckmann Jacques S JS
Beilby John P JP
Bennett Amanda J AJ
Ben-Shlomo Yoav Y
Bergman Richard N RN
Bergmann Sven S
Berndt Sonja I SI
Biffar Reiner R
Di Blasio Anna Maria AM
Boehm Bernhard O BO
Boehnke Michael M
Boeing Heiner H
Boerwinkle Eric E
Bolton Jennifer L JL
Bonnefond Amélie A
Bonnycastle Lori L LL
Boomsma Dorret I DI
Borecki Ingrid B IB
Bornstein Stefan R SR
Bouatia-Naji Nabila N
Boucher Gabrielle G
Bragg-Gresham Jennifer L JL
Brambilla Paolo P
Bruinenberg Marcel M
Buchanan Thomas A TA
Buechler Christa C
Cadby Gemma G
Campbell Harry H
Caulfield Mark J MJ
Cavalcanti-Proença Christine C
Cesana Giancarlo G
Chanock Stephen J SJ
Chasman Daniel I DI
Chen Yii-Der Ida YD
Chines Peter S PS
Clegg Deborah J DJ
Coin Lachlan L
Collins Francis S FS
Connell John M JM
Cookson William W
Cooper Matthew N MN
Croteau-Chonka Damien C DC
Cupples L Adrienne LA
Cusi Daniele D
Day Felix R FR
Day Ian N M IN
Dedoussis George V GV
Dei Mariano M
Deloukas Panos P
Dermitzakis Emmanouil T ET
Dimas Antigone S AS
Dimitriou Maria M
Dixon Anna L AL
Dörr Marcus M
van Duijn Cornelia M CM
Ebrahim Shah S
Edkins Sarah S
Eiriksdottir Gudny G
Eisinger Kristina K
Eklund Niina N
Elliott Paul P
Erbel Raimund R
Erdmann Jeanette J
Erdos Michael R MR
Eriksson Johan G JG
Esko Tõnu T
Estrada Karol K
Evans David M DM
de Faire Ulf U
Fall Tove T
Farrall Martin M
Feitosa Mary F MF
Ferrario Marco M MM
Ferreira Teresa T
Ferrières Jean J
Fischer Krista K
Fisher Eva E
Fowkes Gerry G
Fox Caroline S CS
Franke Lude L
Franks Paul W PW
Fraser Ross M RM
Frau Francesca F
Frayling Timothy T
Freimer Nelson B NB
Froguel Philippe P
Fu Mao M
Gaget Stefan S
Ganna Andrea A
Gejman Pablo V PV
Gentilini Davide D
Geus Eco J C EJ
Gieger Christian C
Gigante Bruna B
Gjesing Anette P AP
Glazer Nicole L NL
Goddard Michael E ME
Goel Anuj A
Grallert Harald H
Gräßler Jürgen J
Grönberg Henrik H
Groop Leif C LC
Groves Christopher J CJ
Gudnason Vilmundur V
Guiducci Candace C
Gustafsson Stefan S
Gyllensten Ulf U
Hall Alistair S AS
Hall Per P
Hallmans Göran G
Hamsten Anders A
Hansen Torben T
Haritunians Talin T
Harris Tamara B TB
van der Harst Pim P
Hartikainen Anna-Liisa AL
Hassanali Neelam N
Hattersley Andrew T AT
Havulinna Aki S AS
Hayward Caroline C
Heard-Costa Nancy L NL
Heath Andrew C AC
Hebebrand Johannes J
Heid Iris M IM
den Heijer Martin M
Hengstenberg Christian C
Herzig Karl-Heinz KH
Hicks Andrew A AA
Hingorani Aroon A
Hinney Anke A
Hirschhorn Joel N JN
Hofman Albert A
Holmes Christopher C CC
Homuth Georg G
Hottenga Jouke-Jan JJ
Hovingh Kees G KG
Hu Frank B FB
Hu Yi-Juan YJ
Huffman Jennifer E JE
Hui Jennie J
Huikuri Heikki H
Humphries Steve E SE
Hung Joseph J
Hunt Sarah E SE
Hunter David D
Hveem Kristian K
Hyppönen Elina E
Igl Wilmar W
Illig Thomas T
Ingelsson Erik E
Iribarren Carlos C
Isomaa Bo B
Jackson Anne U AU
Jacobs Kevin B KB
James Alan L AL
Jansson John-Olov JO
Jarick Ivonne I
Jarvelin Marjo-Riitta MR
Jöckel Karl-Heinz KH
Johansson Åsa
Johnson Toby T
Jolley Jennifer J
Jørgensen Torben T
Jousilahti Pekka P
Jula Antti A
Justice Anne E AE
Kaakinen Marika M
Kähönen Mika M
Kajantie Eero E
Kanoni Stavroula S
Kao W H Linda WH
Kaplan Lee M LM
Kaplan Robert C RC
Kaprio Jaakko J
Kapur Karen K
Karpe Fredrik F
Kathiresan Sekar S
Kee Frank F
Keinanen-Kiukaanniemi Sirkka M SM
Ketkar Shamika S
Kettunen Johannes J
Khaw Kay-Tee KT
Kiemeney Lambertus A LA
Kilpeläinen Tuomas O TO
Kinnunen Leena L
Kivimaki Mika M
Kivmaki Mika M
Van der Klauw Melanie M MM
Kleber Marcus E ME
Knowles Joshua W JW
Koenig Wolfgang W
Kolcic Ivana I
Kolovou Genovefa G
König Inke R IR
Koskinen Seppo S
Kovacs Peter P
Kraft Peter P
Kraja Aldi T AT
Kristiansson Kati K
KrjutÅjkov Kaarel K
Kroemer Heyo K HK
Krohn Jon P JP
Krzelj Vjekoslav V
Kuh Diana D
Kulzer Jennifer R JR
Kumari Meena M
Kutalik Zoltán Z
Kuulasmaa Kari K
Kuusisto Johanna J
Kvaloy Kirsti K
Laakso Markku M
Laitinen Jaana H JH
Lakka Timo A TA
Lamina Claudia C
Langenberg Claudia C
Lantieri Olivier O
Lathrop G Mark GM
Launer Lenore J LJ
Lawlor Debbie A DA
Lawrence Robert W RW
Leach Irene M IM
Lecoeur Cecile C
Lee Sang Hong SH
Lehtimäki Terho T
Leitzmann Michael F MF
Lettre Guillaume G
Levinson Douglas F DF
Li Guo G
Li Shengxu S
Liang Liming L
Lin Dan-Yu DY
Lind Lars L
Lindgren Cecilia M CM
Lindström Jaana J
Liu Jianjun J
Liuzzi Antonio A
Locke Adam E AE
Lokki Marja-Liisa ML
Loley Christina C
Loos Ruth J F RJ
Lorentzon Mattias M
Luan Jian'an J
Luben Robert N RN
Ludwig Barbara B
Madden Pamela A PA
Mägi Reedik R
Magnusson Patrik K E PK
Mangino Massimo M
Manunta Paolo P
Marek Diana D
Marre Michel M
Martin Nicholas G NG
März Winfried W
Maschio Andrea A
Mathieson Iain I
McArdle Wendy L WL
McCaroll Steven A SA
McCarthy Anne A
McCarthy Mark I MI
McKnight Barbara B
Medina-Gomez Carolina C
Medland Sarah E SE
Meitinger Thomas T
Metspalu Andres A
van Meurs Joyce B J JB
Meyre David D
Midthjell Kristian K
Mihailov Evelin E
Milani Lili L
Min Josine L JL
Moebus Susanne S
Moffatt Miriam F MF
Mohlke Karen L KL
Molony Cliona C
Monda Keri L KL
Montgomery Grant W GW
Mooser Vincent V
Morken Mario A MA
Morris Andrew D AD
Morris Andrew P AP
Mühleisen Thomas W TW
Müller-Nurasyid Martina M
Munroe Patricia B PB
Musk Arthur W AW
Narisu Narisu N
Navis Gerjan G
Neale Benjamin M BM
Nelis Mari M
Nemesh James J
Neville Matt J MJ
Ngwa Julius S JS
Nicholson George G
Nieminen Markku S MS
Njølstad Inger I
Nohr Ellen A EA
Nolte Ilja M IM
North Kari E KE
Nöthen Markus M MM
Nyholt Dale R DR
O'Connell Jeffrey R JR
Ohlsson Claes C
Oldehinkel Albertine J AJ
van Ommen Gert-Jan GJ
Ong Ken K KK
Oostra Ben A BA
Ouwehand Willem H WH
Palmer Colin N A CN
Palmer Lyle J LJ
Palotie Aarno A
Paré Guillaume G
Parker Alex N AN
Paternoster Lavinia L
Pawitan Yudi Y
Pechlivanis Sonali S
Peden John F JF
Pedersen Nancy L NL
Pedersen Oluf O
Pellikka Niina N
Peltonen Leena L
Penninx Brenda B
Perola Markus M
Perry John R B JR
Person Thomas T
Peters Annette A
Peters Marjolein J MJ
Pichler Irene I
Pietiläinen Kirsi H KH
Platou Carl G P CG
Polasek Ozren O
Pouta Anneli A
Power Chris C
Pramstaller Peter P PP
Preuss Michael M
Price Jackie F JF
Prokopenko Inga I
Province Michael A MA
Psaty Bruce M BM
Purcell Shaun S
Pütter Carolin C
Qi Lu L
Quertermous Thomas T
Radhakrishnan Aparna A
Raitakari Olli O
Randall Joshua C JC
Rauramaa Rainer R
Rayner Nigel W NW
Rehnberg Emil E
Rendon Augusto A
Ridderstråle Martin M
Ridker Paul M PM
Ripatti Samuli S
Rissanen Aila A
Rivadeneira Fernando F
Rivolta Carlo C
Robertson Neil R NR
Rose Lynda M LM
Rudan Igor I
Saaristo Timo E TE
Sager Hendrik H
Salomaa Veikko V
Samani Nilesh J NJ
Sambrook Jennifer G JG
Sanders Alan R AR
Sandholt Camilla C
Sanna Serena S
Saramies Jouko J
Schadt Eric E EE
Scherag Andre A
Schipf Sabine S
Schlessinger David D
Schreiber Stefan S
Schunkert Heribert H
Schwarz Peter E H PE
Scott Laura J LJ
Shi Jianxin J
Shin So-Youn SY
Shuldiner Alan R AR
Shungin Dmitry D
Signorini Stefano S
Silander Kaisa K
Sinisalo Juha J
Skrobek Boris B
Smit Jan H JH
Smith Albert Vernon AV
Smith George Davey GD
Snieder Harold H
Soranzo Nicole N
Sørensen Thorkild I A TI
Sovio Ulla U
Spector Timothy D TD
Speliotes Elizabeth K EK
Stančáková Alena A
Stark Klaus K
Stefansson Kari K
Steinthorsdottir Valgerdur V
Stephens Jonathan C JC
Stirrups Kathleen K
Stolk Ronald P RP
Strachan David P DP
Strawbridge Rona J RJ
Stringham Heather M HM
Stumvoll Michael M
Surakka Ida I
Swift Amy J AJ
Syvanen Ann-Christine AC
Tammesoo Mari-Liis ML
Teder-Laving Maris M
Teslovich Tanya M TM
Teumer Alexander A
Theodoraki Eirini V EV
Thomson Brian B
Thorand Barbara B
Thorleifsson Gudmar G
Thorsteinsdottir Unnur U
Timpson Nicholas John NJ
Tönjes Anke A
Tregouet David-Alexandre DA
Tremoli Elena E
Trip Mieke D MD
Tuomi Tiinamaija T
Tuomilehto Jaakko J
Tyrer Jonathan J
Uda Manuela M
Uitterlinden André G AG
Usala Gianluca G
Uusitupa Matti M
Valle Timo T TT
Vandenput Liesbeth L
Vatin Vincent V
Vedantam Sailaja S
de Vegt Femmie F
Vermeulen Sita H SH
Viikari Jorma J
Virtamo Jarmo J
Visscher Peter M PM
Vitart Veronique V
Van Vliet-Ostaptchouk Jana V JV
Voight Benjamin F BF
Vollenweider Peter P
Volpato Claudia B CB
Völzke Henry H
Waeber Gérard G
Waite Lindsay L LL
Wallaschofski Henri H
Walters G Bragi GB
Wang Zhaoming Z
Wareham Nicholas J NJ
Watanabe Richard M RM
Watkins Hugh H
Weedon Michael N MN
Welch Ryan R
Weyant Robert J RJ
Wheeler Eleanor E
White Charles C CC
Wichmann H-Erich HE
Widen Elisabeth E
Wild Sarah H SH
Willemsen Gonneke G
Willer Cristen J CJ
Wilsgaard Tom T
Wilson James F JF
van Wingerden Sophie S
Winkelmann Bernhard R BR
Winkler Thomas W TW
Witte Daniel R DR
Witteman Jacqueline C M JC
Wolffenbuttel Bruce H R BH
Wong Andrew A
Wood Andrew R AR
Workalemahu Tsegaselassie T
Wright Alan F AF
Yang Jian J
Yarnell John W G JW
Zgaga Lina L
Zhao Jing Hua JH
Zillikens M Carola MC
Zitting Paavo P
Zondervan Krina T KT
JOURNAL
VOLUME: 9
ISSUE: 5
TITLE: Nature protocols
ISOABBREVIATION: Nat Protoc
YEAR: 2014
MONTH: May
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1750-2799
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: Nat Protoc
COUNTRY: England
ISSNLINKING: 1750-2799
NLMUNIQUEID: 101284307
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
COMMENTS AND CORRECTIONS
REFTYPE REFSOURCE REFPMID NOTE
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GRANTS
GRANTID AGENCY COUNTRY
097117 Wellcome Trust United Kingdom
14136 Cancer Research UK United Kingdom
CZB/4/672 Chief Scientist Office United Kingdom
DK078150 NIDDK NIH HHS United States
G1000143 Medical Research Council United Kingdom
G1000758 Medical Research Council United Kingdom
MC_U106179471 Medical Research Council United Kingdom
MC_U106179472 Medical Research Council United Kingdom
MC_UU_12015/1 Medical Research Council United Kingdom
MC_UU_12015/2 Medical Research Council United Kingdom
MR/J012165/1 Medical Research Council United Kingdom
MR/K013351/1 Medical Research Council United Kingdom
R01 DK075787 NIDDK NIH HHS United States
R01 DK078150 NIDDK NIH HHS United States
R01DK075787 NIDDK NIH HHS United States
R37 HL066289 NHLBI NIH HHS United States
T32 HL007055 NHLBI NIH HHS United States
T32 HL007427 NHLBI NIH HHS United States
T32 HL007427 NHLBI NIH HHS United States
U106179471 Medical Research Council United Kingdom
U106179472 Medical Research Council United Kingdom
GENERAL NOTE
KEYWORDS
MESH HEADINGS
DESCRIPTORNAME QUALIFIERNAME
Genome-Wide Association Study methods
Meta-Analysis as Topic methods
Quality Control methods
Software methods
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's
OTHERID SOURCE
EMS59293 NLM
PMC4083217 NLM