| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_0003095 |
| Description | Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly known as nonalcoholic fatty liver disease or NAFLD) is a type of liver disease that is not caused by alcohol. It typically does not cause symptoms in the early stages, but it can cause health problems due to fat accumulation, inflammation, and scarring in the liver. | Trait category |
Digestive system disorder
|
| Synonyms |
13 synonyms
|
| Mapped terms |
13 mapped terms
|
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
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 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000655/ScoringFiles/PGS000655.txt.gz |
| PGS000872 (PRS-5) |
PGP000215 | Bianco C et al. J Hepatol (2020) |
Non-alcoholic fatty liver disease | non-alcoholic fatty liver disease | 5 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000872/ScoringFiles/PGS000872.txt.gz | |
| PGS002282 (GRS68_NAFLD) |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Nonalcoholic fatty liver disease | non-alcoholic fatty liver disease | 68 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002282/ScoringFiles/PGS002282.txt.gz |
| PGS002283 (GRS15_NAFLD) |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Nonalcoholic fatty liver disease | non-alcoholic fatty liver disease | 15 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002283/ScoringFiles/PGS002283.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| 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 | — |
| PPM002418 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | PGS000872 (PRS-5) |
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 | — |
| PPM021276 | PGS000872 (PRS-5) |
PSS011674| European Ancestry| 5,209 individuals |
PGP000622 | Åberg F et al. Liver Int (2023) |Ext. |
Reported Trait: Liver-related hospitalization, hepatocellular cancer or liver-related death | HR: 5.05 [1.55, 16.5] | — | — | Enhanced liver fibrosis (ELF) test, chronic liver disease (CLivD) score | PGS did not increase predictive performance over ELF test + CLivD score |
| PPM012973 | PGS002282 (GRS68_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels | β: 0.13 (0.002) | — | — | — | — |
| PPM012975 | PGS002282 (GRS68_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x physical activity interaction | β: -0.28 (0.053) | — | — | — | — |
| PPM012976 | PGS002282 (GRS68_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x grip strength interaction | β: -0.0067 (0.002) | — | — | — | — |
| PPM012977 | PGS002282 (GRS68_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x BMI interaction | β: 0.037 (0.002) | — | — | — | — |
| PPM012981 | PGS002282 (GRS68_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: Nonalcoholic fatty liver disease in those with normal weight and high level of physical activity | — | — | Odds Ratio (OR, high vs. low GRS): 1.6 | Sex, age, socioeconomic status, assessment center, genotyping array, and the first 10 principal components | — |
| PPM012974 | PGS002283 (GRS15_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels | β: 0.094 (0.002) | — | — | — | — |
| PPM012978 | PGS002283 (GRS15_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x physical activity interaction | β: -0.3 (0.053) | — | — | — | — |
| PPM012979 | PGS002283 (GRS15_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x grip strength interaction | β: -0.011 (0.002) | — | — | — | — |
| PPM012980 | PGS002283 (GRS15_NAFLD) |
PSS009638| European Ancestry| 25,716 individuals |
PGP000312 | Schnurr TM et al. Hepatol Commun (2022) |
Reported Trait: ALT levels x BMI interaction | β: 0.039 (0.002) | — | — | — | — |
|
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 | — | [
|
— | European | — | eMERGE | — |
| 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). | — | [
|
— | European | — | UKB | — |
| PSS011674 | — | — | [
|
— | European (Finnish) |
— | Health2000 | — |
| PSS011182 | — | — | 381,825 individuals | — | European | — | UKB | — |
| PSS009638 | — | — | 25,716 individuals, 41.5 % Male samples |
Mean = 56.0 years Sd = 7.7 years |
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. | — | [ ,
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 | — | [ ,
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). | — | [ ,
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). | — | [
|
— | 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). | — | [
|
— | 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). | — | [
|
— | European | — | UKB | — |
| PSS000583 | Case inclusion ICD codes: ICD9=571.5, ICD9=571.8, ICD9=571.9, ICD10=K75.81, ICD10=K76.0, ICD10=K76.9 | — | [ ,
42.6 % Male samples |
— | European | — | eMERGE | — |