Polygenic Score (PGS) ID: PGS000872

Predicted Trait
Reported Trait Non-alcoholic fatty liver disease
Mapped Trait(s) non-alcoholic fatty liver disease (EFO_0003095)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name PRS-5
Development Method
Name 4 variants from Dongiovanni et al (PGS000865)
Parameters Adjusted for the addition of rs72613567 (HSD17B13)
Variants
Original Genome Build NR
Number of Variants 5
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000215
Citation (link to publication) Bianco C et al. J Hepatol (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 90.5%
African: 5.4%
East Asian: 2.1%
Hispanic or Latin American: 1.8%
Not Reported: 0.2%
64,002 individuals (100%)
Score Development/Training
Multi-ancestry (including European): 51.9%
  • European
  • African
  • Hispanic or Latin American
Not Reported: 48.1%
5,268 individuals (100%)
PGS Evaluation
European: 87.5%
Not Reported: 12.5%
8 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
Europe PMC: 29562163
 46,544 individuals,
42.0 % Male samples
 European MyCode
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
Europe PMC: 29280273
 2,736 individuals European, African American or Afro-Caribbean, Hispanic or Latin American DaHS — — — — This dataset was used to obtain effect weights for 4 of the 5 SNPs within PRS-5
— 2,532 individuals Not reported NR — — — — This dataset was used to obtain the effect weight for rs72613567 (HSD17B13) within PRS-5

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
PPM002418 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Cirrhosis OR: 4.4 [3.5, 5.6] — — — —
PPM002420 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Cirrhosis OR: 4.5 [3.6, 5.7] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002432 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 9.4 [5.4, 16.2] — — Age, sex, body mass index, type 2 diabetes —
PPM002419 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 11.9 [6.6, 21.3] — — — —
PPM002421 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 11.7 [6.54, 21.0] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre —
PPM002422 PSS001096|
European Ancestry|
364,048 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 4.8 [2.6, 8.9] — — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre, diagnosis of cirrhosis —
PPM002428 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Fatty liver disease OR: 9.0 [6.0, 13.4] — — — —
PPM002429 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Severe fibrosis in individuals within stage F3-F4 of fatty liver disease OR: 12.6 [8.2, 19.3] — — — —
PPM002430 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 9.1 [5.2, 16.0] — — — —
PPM002431 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Fatty liver disease OR: 10.7 [6.6, 17.3] — — Age, sex, body mass index, type 2 diabetes —
PPM002433 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 3.3 [1.6, 6.9] — — Age, sex, body mass index, type 2 diabetes —
PPM002440 PSS001094|
European Ancestry|
2,564 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 2.9 [2.1, 3.8] AUROC: 0.65 — Age, sex, body mass index, type 2 diabetes Only 2,245 participants were available for this analysis.
PPM002443 PSS001097|
European Ancestry|
356,943 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 3.4 [2.5, 4.7] AUROC: 0.63 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002445 PSS001101|
European Ancestry|
355,450 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with no cirrhosis OR: 1.9 [1.1, 3.2] AUROC: 0.54 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002447 PSS001098|
European Ancestry|
85,890 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with a body mass index ≥30 OR: 5.5 [3.6, 8.5] AUROC: 0.69 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002449 PSS001103|
European Ancestry|
25,039 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma in individuals with type 2 diabetes OR: 4.6 [2.9, 7.3] AUROC: 0.71 — Age, sex, body mass index, type 2 diabetes, PCs(1-10), array batch, assessment centre PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM002451 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 8.61 [3.31, 22.37] AUROC: 0.65 — — —
PPM002453 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 6.36 [1.67, 24.31] — — Age, sex, body mass index, type 2 diabetes —
PPM002455 PSS001095|
Ancestry Not Reported|
429 individuals
 PGP000215 |
Bianco C et al. J Hepatol (2020)
 Reported Trait: Hepatocellular carcinoma OR: 2.4 [1.19, 4.83] — — — PRS-5 was treated as a binary variable with a cutoff of ≥0.495
PPM019102 PSS011182|
European Ancestry|
381,825 individuals
 PGP000505 |
Liu Z et al. Liver Int (2023)
|Ext.		 Reported Trait: Non-alcoholic fatty liver disease — — p-value (inferior to): 0.001 age, sex, ethnicity, Townsend deprivation index (quintiles), education level, household income, employment status, self-reported smoking status, self-reported frequency of alcohol intake, sedentary behaviour, body mass index, baseline diabetes, baseline hypertension, serum triglyceride level, C-reactive protein level, and eGFR —
PPM019103 PSS011182|
European Ancestry|
381,825 individuals
 PGP000505 |
Liu Z et al. Liver Int (2023)
|Ext.		 Reported Trait: Severe liver disease — — p-value (inferior to): 0.001 age, sex, ethnicity, Townsend deprivation index (quintiles), education level, household income, employment status, self-reported smoking status, self-reported frequency of alcohol intake, sedentary behaviour, body mass index, baseline diabetes, baseline hypertension, serum triglyceride level, C-reactive protein level, and eGFR —
PPM019104 PSS011182|
European Ancestry|
381,825 individuals
 PGP000505 |
Liu Z et al. Liver Int (2023)
|Ext.		 Reported Trait: Serum uric acid levels x PRS interaction for liver disease HR: 1.03 [1.01, 1.05] — — age, sex, ethnicity, Townsend deprivation index (quintiles), education level, household income, employment status, self-reported smoking status, self-reported frequency of alcohol intake, sedentary behaviour, body mass index, baseline diabetes, baseline hypertension, serum triglyceride level, C-reactive protein level, and eGFR —
PPM019105 PSS011182|
European Ancestry|
381,825 individuals
 PGP000505 |
Liu Z et al. Liver Int (2023)
|Ext.		 Reported Trait: Serum uric acid levels x PRS interaction for severe liver disease HR: 1.06 [1.03, 1.1] — — age, sex, ethnicity, Townsend deprivation index (quintiles), education level, household income, employment status, self-reported smoking status, self-reported frequency of alcohol intake, sedentary behaviour, body mass index, baseline diabetes, baseline hypertension, serum triglyceride level, C-reactive protein level, and eGFR —
PPM019101 PSS011182|
European Ancestry|
381,825 individuals
 PGP000505 |
Liu Z et al. Liver Int (2023)
|Ext.		 Reported Trait: Liver disease — — p-value (inferior to): 0.001 age, sex, ethnicity, Townsend deprivation index (quintiles), education level, household income, employment status, self-reported smoking status, self-reported frequency of alcohol intake, sedentary behaviour, body mass index, baseline diabetes, baseline hypertension, serum triglyceride level, C-reactive protein level, and eGFR —

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
PSS001103 All individuals had type 2 diabetes (T2D). Diabetes was defined as individuals having either of following criteria: 1) self-reported type 2 or unspecified diabetes (codes 1220 and 1223 in data-field 20002); 2) ICD10 diagnoses codes E11 and E14 (data-field 41270); 3) insulin treatment or use of oral glucose lowering drugs (data-fields 6153, 6177 and 20003); 4) serum glucose level ≥11.1 mmol/L (200mg/dL); 5) HbA1c ≥ 48 mmol/mol (6.5%). Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 80 cases
  • , 24,959 controls
]
 — European — UKB —
PSS011182 — — 381,825 individuals — European — UKB —
PSS001094 Cases were individuals with liver disease. Of the 1,699 cases, 1,473 had fatty liver disease (FLD) whilst 226 had hepatocellular carcinoma (HCC). Of the 1,473 individuals with FLD, 297 had severe fibrosis and were therefore classified as being within stage 3-4 of FLD. Severe fibrosis was defined in the presence of histological fibrosis F3-F4 (when liver biopsy was available) or in presence of clinical, endoscopic or radiological signs of portal hypertension or cirrhosis, or liver stiffness ≥8.4 kPa evaluated by Fibroscan. Diagnosis of HCC was based on EASL-EORTC Clinical Practice Guidelines. —
[
  • 1,699 cases
  • , 865 controls
]
,
57.76 % Male samples
 — European — NR Cases were obtained from the Nonalcoholic Fatty Liver Disease (NAFLD) Case-Control Cross-Sectional Cohort.
PSS001095 All individuals had liver disease. Of the 158 cases, 72 had cirrhosis whilst 84 had hepatocellular cancer. Diagnosis of HCC was based on EASL-EORTC Clinical Practice Guidelines —
[
  • 158 cases
  • , 271 controls
]
,
43.59 % Male samples
 — Not reported — NR —
PSS001096 Cases were individuals with liver disease. Of the 1,628 cases, 1,426 individuals had cirrhosis whilst 202 had hepatocellular cancer (HCC). Cirrhosis was defined as ICD-10 codes I85.0, I85.9, K70.3, K70.4, K72.1, K74.1, K74.2, K74.6, K76.6, K76.7 using hospitalization records (data-field 41270). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 1,628 cases
  • , 362,420 controls
]
,
46.22 % Male samples
 — European — UKB —
PSS001097 Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 197 cases
  • , 356,746 controls
]
 — European — UKB —
PSS001098 All individuals had a body mass index ≥30. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 87 cases
  • , 85,803 controls
]
 — European — UKB —
PSS001101 All individuals had no diagnosis of cirrhosis. Cases were individuals with hepatocellular cancer (HCC). HCC was defined by combining International Classification of Diseases, Tenth Revision (ICD-10) code C22.0 from both UK cancer registry (data-field 40006), and hospitalization records (data-field 41270). —
[
  • 95 cases
  • , 355,355 controls
]
 — European — UKB —