Polygenic Score (PGS) ID: PGS000655

Predicted Trait
Reported Trait Non-alcoholic fatty liver disease
Mapped Trait(s) non-alcoholic fatty liver disease (EFO_0003095)
Released in PGS Catalog: Dec. 15, 2020
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Score Details

Score Construction
PGS Name NAFLD-10
Development Method
Name Genome-wide significant variants
Parameters SNPs with p<0.05 in this paper's cohort
Variants
Original Genome Build GRCh37
Number of Variants 10
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000119
Citation (link to publication) Namjou B et al. BMC Med (2019)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
9,677 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST008468
Europe PMC: 31311600
 9,677 individuals European eMERGE

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) 		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
PPM001341 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 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 —