PGS Publication: PGP000119

Publication Information (EuropePMC)
Title GWAS and enrichment analyses of non-alcoholic fatty liver disease identify new trait-associated genes and pathways across eMERGE Network.
PubMed ID 31311600(Europe PMC)
doi 10.1186/s12916-019-1364-z
Publication Date July 17, 2019
Journal BMC Med
Author(s) Namjou B, Lingren T, Huang Y, Parameswaran S, Cobb BL, Stanaway IB, Connolly JJ, Mentch FD, Benoit B, Niu X, Wei WQ, Carroll RJ, Pacheco JA, Harley ITW, Divanovic S, Carrell DS, Larson EB, Carey DJ, Verma S, Ritchie MD, Gharavi AG, Murphy S, Williams MS, Crosslin DR, Jarvik GP, Kullo IJ, Hakonarson H, Li R, eMERGE Network, Xanthakos SA, Harley JB.
Released in PGS Catalog: Dec. 15, 2020

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000655
(NAFLD-10)
PGP000119 |
Namjou B et al. BMC Med (2019)
Non-alcoholic fatty liver disease non-alcoholic fatty liver disease 10
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000655/ScoringFiles/PGS000655.txt.gz
PGS000656
(NAS-11)
PGP000119 |
Namjou B et al. BMC Med (2019)
Non-alcoholic fatty liver disease activity score non-alcoholic fatty liver disease severity measurement 11
-
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000656/ScoringFiles/PGS000656.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM)
Evaluated Score PGS Sample Set ID
(PSS)
Performance Source Trait PGS Effect Sizes
(per SD change)
Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001342 PGS000656
(NAS-11)
PSS000584|
European Ancestry|
235 individuals
PGP000119 |
Namjou B et al. BMC Med (2019)
Reported Trait: Nonalcoholic fatty liver disease severity (NAFLD activity score above 5) AUROC: 0.76 sex, age, PCs (1-3), BMI, study site/medical centre
PPM001341 PGS000655
(NAFLD-10)
PSS000584|
European Ancestry|
235 individuals
PGP000119 |
Namjou B et al. BMC Med (2019)
Reported Trait: Nonalcoholic fatty liver disease severity (NAFLD activity score above 5) AUROC: 0.724 Odds Ratio (OR, highest vs. lowest quintile): 8.5 [3.45, 20.96] sex, age, PCs (1-3), BMI, study site/medical centre
PPM001340 PGS000655
(NAFLD-10)
PSS000583|
European Ancestry|
9,677 individuals
PGP000119 |
Namjou B et al. BMC Med (2019)
Reported Trait: Nonalcoholic fatty liver disease AUROC: 0.596 Odds Ratio (OR, highest vs. lowest quintile): 2.16 [1.81, 2.58] sex, age, PCs (1-3), BMI, study site/medical centre

Evaluated Samples

PGS Sample Set ID
(PSS)
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000584 Controls are cases with Nonalcoholic fatty liver disease activity score <5 and cases are those with a score >5. Case inclusion ICD codes: ICD9=571.5, ICD9=571.8, ICD9=571.9, ICD10=K75.81, ICD10=K76.0, ICD10=K76.9
[
  • 79 cases
  • , 156 controls
]
European eMERGE
PSS000583 Case inclusion ICD codes: ICD9=571.5, ICD9=571.8, ICD9=571.9, ICD10=K75.81, ICD10=K76.0, ICD10=K76.9
[
  • 1,106 cases
  • , 8,571 controls
]
,
42.6 % Male samples
European eMERGE