Polygenic Score (PGS) ID: PGS000866

Predicted Trait
Reported Trait Hepatic fat content
Mapped Trait(s) liver fat measurement (EFO_0010821)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name PRS-HFC_SOS
Development Method
Name Variants with validated effects on hepatic fat accumulation and/or nonalcoholic fatty liver disease severity and with experimental data supporting the casuality of the association
Parameters NR
Variants
Original Genome Build NR
Number of Variants 4
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000212
Citation (link to publication) Dongiovanni P et al. J Intern Med (2017)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 65.2%
African: 19.9%
East Asian: 7.6%
Hispanic or Latin American: 6.5%
Not Reported: 0.8%
17,458 individuals (100%)
Score Development/Training
European: 100%
631 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 18820647
 1,032 individuals African American or Afro-Caribbean DaHS
Europe PMC: 18820647
 696 individuals European DaHS
Europe PMC: 18820647
 383 individuals Hispanic or Latin American DaHS
GWAS Catalog: GCST001008
Europe PMC: 21423719
 7,176 individuals European AGES, AMISH, FHS, FamHS
GWAS Catalog: GCST010096
Europe PMC: 24531328
 2,448 individuals African American or Afro-Caribbean DaHS
GWAS Catalog: GCST010096
Europe PMC: 24531328
 1,365 individuals European DaHS
GWAS Catalog: GCST010096
Europe PMC: 24531328
 753 individuals Hispanic or Latin American DaHS
GWAS Catalog: GCST003153
Europe PMC: 26482880
 2,138 individuals European NR
GWAS Catalog: GCST001928
Europe PMC: 23535911
 1,326 individuals East Asian NR
GWAS Catalog: GCST010096
Europe PMC: 24531328
 141 individuals Not reported DaHS
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
— 631 individuals European LiverBC All individuals were identified as being morbidly obese, defined by the presence of a body mass index ≥ 40 kg m−2 or ≥35 kg m−2 in patients with metabolic comorbidities (type 2 diabetes, dyslipidemia or arterial hypertension). — — — —

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
PPM002410 PSS001090|
European Ancestry|
3,329 individuals
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Reported Trait: Alanine aminotransferase levels — — Association p-value (<): 1.00e-14 Age, sex, ethnicity, body mass index, statin use —

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
PSS001090 All individuals were identified as being severly obese. Homeostasis model assessment-insulin resistance index was calculated from fasting levels of glucose and insulin. Plasma levels of lipids and lipoproteins were measured by standard enzymatic assays. — 3,329 individuals,
30.0 % Male samples
 Mean = 48.0 years
Sd = 6.0 years		 European — SOS —