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| PMID |
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| TITLE |
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| Quality control and conduct of genome-wide association meta-analyses. |
|
| ABSTRACT |
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| 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. |
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| DATE PUBLISHED |
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| HISTORY |
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| PUBSTATUS |
PUBSTATUSDATE |
| entrez |
2014/04/26 06:00 |
| pubmed |
2014/04/26 06:00 |
| medline |
2014/12/15 06:00 |
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| 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 |
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| 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 |
Å |
|
| 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 |
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|
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|
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|
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|
|
| 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 |
| DK078150 |
NIDDK NIH HHS |
United States |
| CZB/4/672 |
Chief Scientist Office |
United Kingdom |
| R01DK075787 |
NIDDK NIH HHS |
United States |
| U106179472 |
Medical Research Council |
United Kingdom |
| G1000143 |
Medical Research Council |
United Kingdom |
| MR/J012165/1 |
Medical Research Council |
United Kingdom |
| R01 DK075787 |
NIDDK NIH HHS |
United States |
| MC_UU_12015/1 |
Medical Research Council |
United Kingdom |
| R37 HL066289 |
NHLBI NIH HHS |
United States |
| MC_U106179471 |
Medical Research Council |
United Kingdom |
| 097117 |
Wellcome Trust |
United Kingdom |
| MC_UU_12015/2 |
Medical Research Council |
United Kingdom |
| 14136 |
Cancer Research UK |
United Kingdom |
| U106179471 |
Medical Research Council |
United Kingdom |
| MC_U106179472 |
Medical Research Council |
United Kingdom |
| G0401527 |
Medical Research Council |
United Kingdom |
| MR/K013351/1 |
Medical Research Council |
United Kingdom |
| T32 HL007055 |
NHLBI NIH HHS |
United States |
| R01 DK078150 |
NIDDK NIH HHS |
United States |
| T32 HL007427 |
NHLBI NIH HHS |
United States |
|
| 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 |
|
|
