Polygenic Score (PGS) ID: PGS002245

Predicted Trait
Reported Trait Liver fat (MRI-derived)
Mapped Trait(s) liver fat measurement (EFO_0010821)
Released in PGS Catalog: Jan. 24, 2022
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Score Details

Score Construction
PGS Name PGS8_LF
Development Method
Name GWAS lead variants
Parameters p<5*10^(-8)
Variants
Original Genome Build hg19
Number of Variants 8
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000273
Citation (link to publication) Haas ME et al. Cell Genom (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
32,974 individuals (100%)
PGS Evaluation
European: 100%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90029073
 32,974 individuals European UKB

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
PPM012775 PSS009552|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident non alcoholic fatty liver disease HR: 1.33 [1.27, 1.39] C-index: 0.598 [0.584, 0.612] — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012776 PSS009553|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident non alcoholic steatohepatitis HR: 1.67 [1.48, 1.87] C-index: 0.684 — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012777 PSS009554|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident cirrhosis HR: 1.41 [1.33, 1.5] C-index: 0.694 — age, age squared, sex, genotyping array, 10 principal components of ancestry —
PPM012778 PSS009551|
European Ancestry|
361,852 individuals
 PGP000273 |
Haas ME et al. Cell Genom (2021)
 Reported Trait: Incident hepatocellular carcinoma HR: 1.72 C-index: 0.77 — age, age squared, sex, genotyping array, 10 principal components of ancestry —

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
PSS009554 Hospitalization or death due to (ICD10; ICD9 codes): cirrhosis (K74.6; 5715), alcoholic cirrhosis or liver damage (K70.3; 5712, 5713), esophageal varices (I85.0,I85.9; 4560, 4561) or portal hypertension (K76.6; 5723) Median = 8.6 years
[
  • 977 cases
  • , 360,875 controls
]
 — European — UKB —
PSS009551 Hospitalization due to liver cell carcinoma (ICD10 C22.0) Median = 8.6 years
[
  • 171 cases
  • , 361,681 controls
]
 — European — UKB —
PSS009552 Hospitalization due to nonalcoholic fatty liver (ICD10 K76.0) Median = 8.6 years
[
  • 1,635 cases
  • , 360,217 controls
]
 — European — UKB —
PSS009553 Hospitalization due to other specified inflammatory liver diseases including nonalcoholic steatohepatitis (ICD10 K75.8) Median = 8.6 years
[
  • 208 cases
  • , 361,644 controls
]
 — European — UKB —