Trait: non-alcoholic fatty liver disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003095
Description A term referring to fatty replacement of the hepatic parenchyma which is not related to alcohol use. [NCIT: C84444]
Trait category
Digestive system disorder
Synonyms 6 synonyms
  • NAFLD
  • NAFLD - Nonalcoholic Fatty Liver Disease
  • Nonalcoholic Fatty Liver Disease
  • fatty liver disease, nonalcoholic
  • non-alcoholic fatty liver
  • non-alcoholic fatty liver disease
Mapped terms 13 mapped terms
  • DOID:0080208
  • EFO:1001248
  • ICD9:571.8
  • MESH:D065626
  • MONDO:0013209
  • MeSH:D065626
  • MedDRA:10029530
  • NCIT:C84444
  • NCIt:C84444
  • OMIM:613282
  • OMIM:613387
  • Orphanet:33271
  • SCTID:197315008

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution 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

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)
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
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
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)
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)

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
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
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.
[
  • 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
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