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| PMID |
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| TITLE |
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| Model-based assessment of replicability for genome-wide association meta-analysis. |
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| ABSTRACT |
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| Genome-wide association meta-analysis (GWAMA) is an effective approach to enlarge sample sizes and empower the discovery of novel associations between genotype and phenotype. Independent replication has been used as a gold-standard for validating genetic associations. However, as current GWAMA often seeks to aggregate all available datasets, it becomes impossible to find a large enough independent dataset to replicate new discoveries. Here we introduce a method, MAMBA (Meta-Analysis Model-based Assessment of replicability), for assessing the "posterior-probability-of-replicability" for identified associations by leveraging the strength and consistency of association signals between contributing studies. We demonstrate using simulations that MAMBA is more powerful and robust than existing methods, and produces more accurate genetic effects estimates. We apply MAMBA to a large-scale meta-analysis of addiction phenotypes with 1.2 million individuals. In addition to accurately identifying replicable common variant associations, MAMBA also pinpoints novel replicable rare variant associations from imputation-based GWAMA and hence greatly expands the set of analyzable variants. |
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| DATE PUBLISHED |
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| HISTORY |
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| PUBSTATUS |
PUBSTATUSDATE |
| received |
2019/12/17 |
| accepted |
2021/01/07 |
| entrez |
2021/03/31 06:11 |
| pubmed |
2021/04/01 06:00 |
| medline |
2021/04/20 06:00 |
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| AUTHORS |
|
| NAME |
COLLECTIVENAME |
LASTNAME |
FORENAME |
INITIALS |
AFFILIATION |
AFFILIATIONINFO |
| McGuire D |
|
McGuire |
Daniel |
D |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Jiang Y |
|
Jiang |
Yu |
Y |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Liu M |
|
Liu |
Mengzhen |
M |
|
Department of Psychology, University of Minnesota, Minneapolis, MN, USA. |
| Weissenkampen JD |
|
Weissenkampen |
J Dylan |
JD |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Eckert S |
|
Eckert |
Scott |
S |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Yang L |
|
Yang |
Lina |
L |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Chen F |
|
Chen |
Fang |
F |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
|
GWAS and Sequencing Consortium of Alcohol and Nicotine Use (GSCAN) |
|
|
|
|
|
| Berg A |
|
Berg |
Arthur |
A |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. |
| Vrieze S |
|
Vrieze |
Scott |
S |
|
Department of Psychology, University of Minnesota, Minneapolis, MN, USA. |
| Jiang B |
|
Jiang |
Bibo |
B |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. bjiang@phs.psu.edu. |
| Li Q |
|
Li |
Qunhua |
Q |
|
Department of Statistics, Penn State University, University Park, PA, USA. qunhua.li@psu.edu. |
| Liu DJ |
|
Liu |
Dajiang J |
DJ |
|
Department of Public Health Sciences, Penn State College of Medicine, Hershey, PA, USA. dajiang.liu@psu.edu. |
|
| INVESTIGATORS |
|
| LASTNAME |
FORENAME |
INITIALS |
AFFILIATION |
| Liu |
Mengzhen |
M |
|
| Jiang |
Yu |
Y |
|
| Wedow |
Robbee |
R |
|
| Li |
Yue |
Y |
|
| Brazel |
David M |
DM |
|
| Chen |
Fang |
F |
|
| Datta |
Gargi |
G |
|
| Davila-Velderrain |
Jose |
J |
|
| McGuire |
Daniel |
D |
|
| Tian |
Chao |
C |
|
| Zhan |
Xiaowei |
X |
|
| Choquet |
H Éléne |
HÉ |
|
| Docherty |
Anna R |
AR |
|
| Faul |
Jessica D |
JD |
|
| Foerster |
Johanna R |
JR |
|
| Fritsche |
Lars G |
LG |
|
| Gabrielsen |
Maiken Elvestad |
ME |
|
| Gordon |
Scott D |
SD |
|
| Haessler |
Jeffrey |
J |
|
| Hottenga |
Jouke-Jan |
JJ |
|
| Huang |
Hongyan |
H |
|
| Jang |
Seon-Kyeong |
SK |
|
| Jansen |
Philip R |
PR |
|
| Ling |
Yueh |
Y |
|
| Ma Gi |
Reedik |
R |
|
| Matoba |
Nana |
N |
|
| McMahon |
George |
G |
|
| Mulas |
Antonella |
A |
|
| Orru |
Valeria |
V |
|
| Palviainen |
Teemu |
T |
|
| Pandit |
Anita |
A |
|
| Reginsson |
Gunnar W |
GW |
|
| Skogholt |
Anne Heidi |
AH |
|
| Smith |
Jennifer A |
JA |
|
| Taylor |
Amy E |
AE |
|
| Turman |
Constance |
C |
|
| Willemsen |
Gonneke |
G |
|
| Young |
Hannah |
H |
|
| Young |
Kendra A |
KA |
|
| Zajac |
Gregory J M |
GJM |
|
| Zhao |
Wei |
W |
|
| Zhou |
Wei |
W |
|
| Bjornsdottir |
Gyda |
G |
|
| Boardman |
Jason D |
JD |
|
| Boehnke |
Michael |
M |
|
| Boomsma |
Dorret I |
DI |
|
| Chen |
Chu |
C |
|
| Cucca |
Francesco |
F |
|
| Davies |
Gareth E |
GE |
|
| Eaton |
Charles B |
CB |
|
| Ehringer |
Marissa A |
MA |
|
| Esko |
To Nu |
TN |
|
| Fiorillo |
Edoardo |
E |
|
| Gillespie |
Nathan A |
NA |
|
| Gudbjartsson |
Daniel F |
DF |
|
| Haller |
Toomas |
T |
|
| Harris |
Kathleen Mullan |
KM |
|
| Heath |
Andrew C |
AC |
|
| Hewitt |
John K |
JK |
|
| Hickie |
Ian B |
IB |
|
| Hokanson |
John E |
JE |
|
| Hopfer |
Christian J |
CJ |
|
| Hunter |
David J |
DJ |
|
| Iacono |
William G |
WG |
|
| Johnson |
Eric O |
EO |
|
| Kamatani |
Yoichiro |
Y |
|
| Kardia |
Sharon L R |
SLR |
|
| Keller |
Matthew C |
MC |
|
| Kellis |
Manolis |
M |
|
| Kooperberg |
Charles |
C |
|
| Kraft |
Peter |
P |
|
| Krauter |
Kenneth S |
KS |
|
| Laakso |
Markku |
M |
|
| Lind |
Penelope A |
PA |
|
| Loukola |
Anu |
A |
|
| Lutz |
Sharon M |
SM |
|
| Madden |
Pamela A F |
PAF |
|
| Martin |
Nicholas G |
NG |
|
| McGue |
Matt |
M |
|
| McQueen |
Matthew B |
MB |
|
| Medland |
Sarah E |
SE |
|
| Metspalu |
Andres |
A |
|
| Mohlke |
Karen L |
KL |
|
| Nielsen |
Jonas B |
JB |
|
| Okada |
Yukinori |
Y |
|
| Peters |
Ulrike |
U |
|
| Polderman |
Tinca J C |
TJC |
|
| Posthuma |
Danielle |
D |
|
| Reiner |
Alexander P |
AP |
|
| Rice |
John P |
JP |
|
| Rimm |
Eric |
E |
|
| Rose |
Richard J |
RJ |
|
| Runarsdottir |
Valgerdur |
V |
|
| Stallings |
Michael C |
MC |
|
| Stanˇca Kova |
Alena |
A |
|
| Stefansson |
Hreinn |
H |
|
| Thai |
Khanh K |
KK |
|
| Tindle |
Hilary A |
HA |
|
| Tyrfingsson |
Thorarinn |
T |
|
| Wall |
Tamara L |
TL |
|
| Weir |
David R |
DR |
|
| Weisner |
Constance |
C |
|
| Whitfield |
John B |
JB |
|
| Winsvold |
Bendik Slagsvold |
BS |
|
| Yin |
Jie |
J |
|
| Zuccolo |
Luisa |
L |
|
| Bierut |
Laura J |
LJ |
|
| Hveem |
Kristian |
K |
|
| Lee |
James J |
JJ |
|
| Munafo |
Marcus R |
MR |
|
| Saccone |
Nancy L |
NL |
|
| Willer |
Cristen J |
CJ |
|
| Cornelis |
Marilyn C |
MC |
|
| David |
Sean P |
SP |
|
| Hinds |
David |
D |
|
| Jorgenson |
Eric |
E |
|
| Kaprio |
Jaakko |
J |
|
| Stitzel |
Jerry A |
JA |
|
| Stefansson |
Kari |
K |
|
| Thorgeirsson |
Thorgeir E |
TE |
|
| Abecasis |
Goncalo |
G |
|
| Liu |
Dajiang J |
DJ |
|
| Vrieze |
Scott |
S |
|
|
| JOURNAL |
|
| VOLUME: 12 |
| ISSUE: 1 |
| TITLE: Nature communications |
| ISOABBREVIATION: Nat Commun |
| YEAR: 2021 |
| MONTH: 03 |
| DAY: 30 |
| MEDLINEDATE: |
| SEASON: |
| CITEDMEDIUM: Internet |
| ISSN: 2041-1723 |
| ISSNTYPE: Electronic |
|
| MEDLINE JOURNAL |
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| MEDLINETA: Nat Commun |
| COUNTRY: England |
| ISSNLINKING: 2041-1723 |
| NLMUNIQUEID: 101528555 |
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| PUBLICATION TYPE |
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| PUBLICATIONTYPE TEXT |
| Journal Article |
| Research Support, N.I.H., Extramural |
|
| COMMENTS AND CORRECTIONS |
|
|
| GRANTS |
|
| GRANTID |
AGENCY |
COUNTRY |
| R21 DA040177 |
NIDA NIH HHS |
United States |
| R01 DA037904 |
NIDA NIH HHS |
United States |
| R01 GM126479 |
NIGMS NIH HHS |
United States |
| R56 HG011035 |
NHGRI NIH HHS |
United States |
| R01 HG008983 |
NHGRI NIH HHS |
United States |
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| GENERAL NOTE |
|
|
| KEYWORDS |
|
|
| MESH HEADINGS |
|
| DESCRIPTORNAME |
QUALIFIERNAME |
| Algorithms |
|
| Computational Biology |
methods |
| Genetic Association Studies |
methods |
| Genome-Wide Association Study |
methods |
| Genotype |
methods |
| Meta-Analysis as Topic |
methods |
| Models, Genetic |
methods |
| Phenotype |
methods |
| Polymorphism, Single Nucleotide |
methods |
| Reproducibility of Results |
methods |
| Sample Size |
methods |
| Software |
methods |
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| SUPPLEMENTARY MESH |
|
|
| GENE SYMBOLS |
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| CHEMICALS |
|
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| OTHER ID's |
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