Trait: liver disease

Experimental Factor Ontology (EFO) Information
Identifier EFO_0001421
Description A disease involving the liver.
Trait category
Digestive system disorder
Synonyms 40 synonyms
  • Disease of liver
  • Disease, Liver
  • Diseases, Liver
  • Disorder of liver
  • Dysfunction, Liver
  • Dysfunctions, Liver
  • Hepatopathy
  • LD - Liver disease
  • LIVER DIS
  • Liver Diseases
  • Liver Disorder
  • Liver Dysfunction
  • Liver Dysfunctions
  • Liver and Intrahepatic Bile Duct Disorder
  • Liver disorder NOS
  • Liver disorder NOS (disorder)
  • Liver disorder in pregnancy
  • Liver disorder in pregnancy (disorder)
  • Liver disorder in pregnancy - delivered (disorder)
  • Liver disorder in pregnancy NOS (disorder)
  • Liver disorder in pregnancy unspecified (disorder)
  • Liver disorder in pregnancy, unspecified as to episode of care
  • Liver disorder in pregnancy, with delivery
  • Unspecified disorder of liver
  • [X]Diseases of the liver
  • [X]Diseases of the liver (disorder)
  • disease of liver
  • disease of liver [Ambiguous]
  • disease of the liver (disorder)
  • disease or disorder of liver
  • disorder of liver
  • disorder of liver (disorder)
  • hepatic disease
  • hepatic disorder
  • liver and intrahepatic bile duct disorder
  • liver disease
  • liver disease or disorder
  • liver disorder
  • liver disorder antepartum
  • liver disorder in pregnancy - delivered
Mapped terms 18 mapped terms
  • DOID:409
  • ICD10:K75
  • ICD10:K76
  • ICD10CM:K70-K77
  • ICD9:573.8
  • ICD9:573.9
  • MEDGEN:893061
  • MESH:D008107
  • MONDO:0005154
  • MeSH:D008107
  • NCIT:C3196
  • NCIt:C3196
  • NCIt:C50634
  • SCTID:235856003
  • SNOMEDCT:15230009
  • SNOMEDCT:199117000
  • SNOMEDCT:235856003
  • UMLS:C4021780
Child trait(s) 3 child traits

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
Note: This table shows all PGS for "liver disease" and any child terms of this trait in the EFO hierarchy by default.
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
PGS000704
(HC171)
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Alcoholic cirrhosis alcoholic liver cirrhosis 183,271
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000704/ScoringFiles/PGS000704.txt.gz - Check Terms/Licenses
PGS000726
(PGS12_CIR)
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Cirrhosis cirrhosis of liver 12
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000726/ScoringFiles/PGS000726.txt.gz
PGS000776
(GRS9_Cirr)
 PGP000180 |
Innes H et al. Gastroenterology (2020)
 Cirrhosis cirrhosis of liver 9
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000776/ScoringFiles/PGS000776.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
PGS001293
(GBE_HC1123)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Other diseases of liver (time-to-event) liver disease 92
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001293/ScoringFiles/PGS001293.txt.gz
PGS001777
(3-SNP_cirr)
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Cirrhosis (alcohol related) alcoholic liver cirrhosis 3
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001777/ScoringFiles/PGS001777.txt.gz
PGS001860
(portability-PLR_571.5)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Other chronic nonalcoholic liver disease liver disease 497
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001860/ScoringFiles/PGS001860.txt.gz
PGS002071
(portability-ldpred2_571.5)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Other chronic nonalcoholic liver disease liver disease 352,506
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002071/ScoringFiles/PGS002071.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
PGS004621
(cirrhosis_pgs_eur)
 PGP000594 |
Ghouse J et al. Nat Genet (2024)
 Cirrhosis cirrhosis of liver 1,089,806
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004621/ScoringFiles/PGS004621.txt.gz
PGS004913
(PRSALC)
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Alcohol-associated liver cirrhosis alcoholic liver cirrhosis 20
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004913/ScoringFiles/PGS004913.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 —
PPM001596 PGS000704
(HC171)
 PSS000792|
European Ancestry|
87,413 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alcoholic cirrhosis — AUROC: 0.55471 — Age, sex, PCs(1-10) —
PPM001607 PGS000704
(HC171)
 PSS000793|
European Ancestry|
135,300 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alcoholic cirrhosis HR: 1.18 [1.11, 1.27] C-index: 0.711 — Age as time scale, sex, batch, PCs(1-10) —
PPM001656 PGS000726
(PGS12_CIR)
 PSS000861|
European Ancestry|
30,469 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Cirrhosis OR: 1.32 — Odds Ratio (OR, top 20% vs. bottom 20%): 2.26 [1.87, 2.73] Age, sex, PCs (1-5) —
PPM001657 PGS000726
(PGS12_CIR)
 PSS000861|
European Ancestry|
30,469 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Biopsy-confirmed cirrhosis OR: 1.39 — Odds Ratio (OR, top 20% vs. bottom 20%): 2.21 [1.59, 3.08] Age, sex, PCs (1-5) —
PPM001658 PGS000726
(PGS12_CIR)
 PSS000861|
European Ancestry|
30,469 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Esophageal varices OR: 1.45 — Odds Ratio (OR, top 20% vs. bottom 20%): 3.1 [1.97, 4.9] Age, sex, PCs (1-5) —
PPM001659 PGS000726
(PGS12_CIR)
 PSS000861|
European Ancestry|
30,469 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Hepatocellular carcioma OR: 1.39 — Odds Ratio (OR, top 20% vs. bottom 20%): 2.51 [1.59, 3.97] Age, sex, PCs (1-5) —
PPM001660 PGS000726
(PGS12_CIR)
 PSS000861|
European Ancestry|
30,469 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Death from liver disease OR: 1.29 — Odds Ratio (OR, top 20% vs. bottom 20%): 2.03 [1.24, 3.32] Age, sex, PCs (1-5) —
PPM001661 PGS000726
(PGS12_CIR)
 PSS000866|
African Ancestry|
1,442 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Cirrhosis — — Odds Ratio (OR, 20-80% vs. bottom 20%): 3.63 [1.55, 8.5]
Odds Ratio (OR, top 20% risk vs. bottom 20%): 2.44 [0.92, 6.48]		 Age, sex, PCs (1-5) —
PPM001662 PGS000726
(PGS12_CIR)
 PSS000863|
Ancestry Not Reported|
13,826 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Cirrhosis — — Odds Ratio (OR, top 1% vs. bottom 20%): 3.16 [2.03, 4.9] Age, sex, PCs (1-5) —
PPM001663 PGS000726
(PGS12_CIR)
 PSS000862|
Ancestry Not Reported|
13,047 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Biopsy-confirmed cirrhosis — — Odds Ratio (OR, top 1% vs. bottom 20%): 6.12 [3.55, 10.58] Age, sex, PCs (1-5) —
PPM001664 PGS000726
(PGS12_CIR)
 PSS000864|
European Ancestry|
213 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Cirrhosis in individuals with hepatitis B — — Odds ratio (OR, top 20% vs. bottom 20%): 4.83 [1.12, 20.0] Age, sex, PCs (1-5) —
PPM001665 PGS000726
(PGS12_CIR)
 PSS000865|
European Ancestry|
661 individuals
 PGP000136 |
Emdin CA et al. Gastroenterology (2020)
 Reported Trait: Cirrhosis in individuals with hepatitis C — — Odds ratio (OR, top 20% vs. bottom 20%): 2.2 [1.2, 4.05] Age, sex, PCs (1-5) —
PPM002011 PGS000776
(GRS9_Cirr)
 PSS000996|
Ancestry Not Reported|
107,014 individuals
 PGP000180 |
Innes H et al. Gastroenterology (2020)
 Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) — C-index: 0.62 [0.59, 0.64] Hazard Ratio (HR, top 20% vs bottom 20%): 3.12 [2.37, 4.12] — —
PPM002012 PGS000776
(GRS9_Cirr)
 PSS000996|
Ancestry Not Reported|
107,014 individuals
 PGP000180 |
Innes H et al. Gastroenterology (2020)
 Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) — — Hazard Ratio (HR, top 20% vs bottom 20%): 3.16 [2.38, 4.21] Age, sex, BMI, diabetes, units of alcohol consumed per week —
PPM002013 PGS000776
(GRS9_Cirr)
 PSS000996|
Ancestry Not Reported|
107,014 individuals
 PGP000180 |
Innes H et al. Gastroenterology (2020)
 Reported Trait: Incident liver cirrhosis in individuals at-risk for nonalcoholic fatty liver disease (time to first hospitilisation) — C-index: 0.677 [0.653, 0.7] — Age, sex —
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
PPM008963 PGS001293
(GBE_HC1123)
 PSS004134|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.63246 [0.57311, 0.69181] R²: 0.03109
Incremental AUROC (full-covars): -0.0062
PGS R2 (no covariates): 0.0
PGS AUROC (no covariates): 0.50545 [0.44895, 0.56196]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008964 PGS001293
(GBE_HC1123)
 PSS004135|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.69904 [0.62545, 0.77263] PGS R2 (no covariates): 0.01113
Incremental AUROC (full-covars): 0.02137
R²: 0.05749
PGS AUROC (no covariates): 0.60324 [0.52305, 0.68342]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008965 PGS001293
(GBE_HC1123)
 PSS004136|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.63842 [0.61377, 0.66307] R²: 0.02524
Incremental AUROC (full-covars): 0.02435
PGS R2 (no covariates): 0.01187
PGS AUROC (no covariates): 0.59189 [0.56464, 0.61913]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008966 PGS001293
(GBE_HC1123)
 PSS004137|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.60451 [0.56674, 0.64227] R²: 0.01731
Incremental AUROC (full-covars): 0.00746
PGS R2 (no covariates): 0.00179
PGS AUROC (no covariates): 0.53523 [0.49417, 0.57629]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008967 PGS001293
(GBE_HC1123)
 PSS004138|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other diseases of liver — AUROC: 0.58372 [0.56726, 0.60017] R²: 0.00961
Incremental AUROC (full-covars): 0.01977
PGS R2 (no covariates): 0.00443
PGS AUROC (no covariates): 0.5536 [0.53634, 0.57086]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009254 PGS001777
(3-SNP_cirr)
 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) β: 0.897 (0.172) AUROC: 0.635 (0.025) Odds Ratio (OR, top 20% vs bottom 20%): 3.81 [2.05, 7.07] — —
PPM009255 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 0.8 (0.088) AUROC: 0.635 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 3.44 [2.48, 4.77] — —
PPM009256 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) — AUROC: 0.554 (0.036) Odds Ratio (OR, top 20% vs bottom 20%): 2.08 [1.11, 3.89] — —
PPM009247 PGS001777
(3-SNP_cirr)
 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 1.092 (0.099) AUROC: 0.665 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 5.99 [4.18, 8.6] — —
PPM009248 PGS001777
(3-SNP_cirr)
 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.669 (0.09) AUROC: 0.606 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 2.81 [2.03, 3.89] — —
PPM009249 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.729 (0.08) AUROC: 0.619 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 3.1 [2.32, 4.14] — —
PPM009250 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.748 (0.073) AUROC: 0.636 (0.015) Odds Ratio (OR, top 20% vs bottom 20%): 3.37 [2.38, 4.78] BMI, coffee —
PPM009251 PGS001777
(3-SNP_cirr)
 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 1.132 (0.116) AUROC: 0.671 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 6.18 [4.05, 9.41] — —
PPM009252 PGS001777
(3-SNP_cirr)
 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) β: 0.974 (0.192) AUROC: 0.65 (0.027) Odds Ratio (OR, top 20% vs bottom 20%): 5.4 [2.67, 10.92] — —
PPM009253 PGS001777
(3-SNP_cirr)
 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 0.575 (0.107) AUROC: 0.592 (0.017) Odds Ratio (OR, top 20% vs bottom 20%): 2.47 [1.68, 3.62] — —
PPM009257 PGS001777
(3-SNP_cirr)
 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in diabetics — — Odds Ratio (OR, high vs. low PRS): 5.32 [2.06, 13.7] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009258 PGS001777
(3-SNP_cirr)
 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in non-diabetics — — Odds Ratio (OR, high vs. low PRS): 4.77 [3.45, 6.58] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009259 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in diabetics — — Odds Ratio (OR, high vs. low PRS): 3.74 [2.16, 6.48] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009260 PGS001777
(3-SNP_cirr)
 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in non-diabetics — — Odds Ratio (OR, high vs. low PRS): 2.37 [1.86, 3.03] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009769 PGS001860
(portability-PLR_571.5)
 PSS009335|
European Ancestry|
19,586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0413 [0.0273, 0.0553] sex, age, birth date, deprivation index, 16 PCs —
PPM009770 PGS001860
(portability-PLR_571.5)
 PSS009109|
European Ancestry|
4,060 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.034 [0.0032, 0.0648] sex, age, birth date, deprivation index, 16 PCs —
PPM009771 PGS001860
(portability-PLR_571.5)
 PSS008663|
European Ancestry|
6,543 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0281 [0.0038, 0.0523] sex, age, birth date, deprivation index, 16 PCs —
PPM009772 PGS001860
(portability-PLR_571.5)
 PSS008437|
Greater Middle Eastern Ancestry|
1,185 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0168 [-0.0407, 0.0741] sex, age, birth date, deprivation index, 16 PCs —
PPM009773 PGS001860
(portability-PLR_571.5)
 PSS008217|
South Asian Ancestry|
6,209 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0246 sex, age, birth date, deprivation index, 16 PCs —
PPM009774 PGS001860
(portability-PLR_571.5)
 PSS007998|
East Asian Ancestry|
1,783 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0455 [-0.0012, 0.092] sex, age, birth date, deprivation index, 16 PCs —
PPM009775 PGS001860
(portability-PLR_571.5)
 PSS007782|
African Ancestry|
2,429 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.013 [-0.0529, 0.0269] sex, age, birth date, deprivation index, 16 PCs —
PPM009776 PGS001860
(portability-PLR_571.5)
 PSS008886|
African Ancestry|
3,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.0259 [-0.0576, 0.0058] sex, age, birth date, deprivation index, 16 PCs —
PPM011429 PGS002071
(portability-ldpred2_571.5)
 PSS009335|
European Ancestry|
19,586 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0415 [0.0275, 0.0555] sex, age, birth date, deprivation index, 16 PCs —
PPM011430 PGS002071
(portability-ldpred2_571.5)
 PSS009109|
European Ancestry|
4,060 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.029 [-0.0018, 0.0598] sex, age, birth date, deprivation index, 16 PCs —
PPM011431 PGS002071
(portability-ldpred2_571.5)
 PSS008663|
European Ancestry|
6,543 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0289 [0.0047, 0.0532] sex, age, birth date, deprivation index, 16 PCs —
PPM011432 PGS002071
(portability-ldpred2_571.5)
 PSS008437|
Greater Middle Eastern Ancestry|
1,185 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0227 [-0.0348, 0.08] sex, age, birth date, deprivation index, 16 PCs —
PPM011433 PGS002071
(portability-ldpred2_571.5)
 PSS008217|
South Asian Ancestry|
6,209 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.0224 [-0.0025, 0.0473] sex, age, birth date, deprivation index, 16 PCs —
PPM011434 PGS002071
(portability-ldpred2_571.5)
 PSS007998|
East Asian Ancestry|
1,783 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): 0.043 [-0.0037, 0.0895] sex, age, birth date, deprivation index, 16 PCs —
PPM011435 PGS002071
(portability-ldpred2_571.5)
 PSS007782|
African Ancestry|
2,429 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.0077 [-0.0476, 0.0323] sex, age, birth date, deprivation index, 16 PCs —
PPM011436 PGS002071
(portability-ldpred2_571.5)
 PSS008886|
African Ancestry|
3,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Other chronic nonalcoholic liver disease — — Partial Correlation (partial-r): -0.0167 [-0.0484, 0.015] sex, age, birth date, deprivation index, 16 PCs —
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) — — — —
PPM020806 PGS004621
(cirrhosis_pgs_eur)
 PSS011418|
European Ancestry|
1,153,995 individuals
 PGP000594 |
Ghouse J et al. Nat Genet (2024)
 Reported Trait: Cirrhosis OR: 1.42 AUROC: 0.68 — age,sex,10 PCs —
PPM021374 PGS004913
(PRSALC)
 PSS011711|
European Ancestry|
9,448 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.02
Odds ratio (OR, top vs bottom PRS deciles): 2.75 [1.79, 4.21]		 Age, sex, 10 PCs —
PPM021375 PGS004913
(PRSALC)
 PSS011709|
European Ancestry|
3,360 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.029
Odds ratio (OR, top vs bottom PRS deciles): 4.4 [1.56, 12.44]		 Age, sex, 10 PCs —
PPM021376 PGS004913
(PRSALC)
 PSS011710|
European Ancestry|
3,709 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Metabolic dysfunction-associated steatotic liver disease cirrhosis — — Odds ratio (OR, top vs bottom PRS deciles): 3.94 [2.23, 6.95] Age, sex, BMI, 10 PCs —

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
PSS008663 — — 6,543 individuals — European Italy (South Europe) 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 —
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 —
PSS007782 — — 2,429 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008437 — — 1,185 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009335 — — 19,586 individuals — European UK (+ Ireland) UKB —
PSS009638 — — 25,716 individuals,
41.5 % Male samples
 Mean = 56.0 years
Sd = 7.7 years		 European — UKB —
PSS011709 — —
[
  • 121 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011711 Cirrhosis cases were defined as having ICD10 code K70.3; “alcohol-associated cirrhosis of liver', or ICD-9 code 571.2, “Cirrhosis, liver, alcohol-associated or ICD10 code K70.1; “alcoholic hepatitis without ascites” or ICD-9 code 571.1, “acute alcoholic hepatitis.” Controls were defined as having (1) reported alcohol intake of ≥80 g/d (males) and ≥50 g/d (females) and/or (2) ICD10 diagnosis of F10.2 (mental and behavioral disorders due to alcohol) but with no recorded diagnosis of any liver disease as defined previously —
[
  • 467 cases
  • , 8,981 controls
]
 — European — UKB —
PSS011710 — —
[
  • 470 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011182 — — 381,825 individuals — European — UKB —
PSS007667 — —
[
  • 917 cases
  • , 473 controls
]
,
72.3 % Male samples
 — European — GenomALC —
PSS007668 — —
[
  • 1,162 cases
  • , 604 controls
]
,
62.06 % Male samples
 — European — GenomALC —
PSS007669 — —
[
  • 594 cases
  • , 6,304 controls
]
,
77.02 % Male samples
 — European — UKB —
PSS008217 — — 6,209 individuals — South Asian India (South Asia) UKB —
PSS009109 — — 4,060 individuals — European Poland (NE Europe) UKB —
PSS000861 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 1,137 cases
  • , 29,332 controls
]
 — European — PHB —
PSS000862 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 339 cases
  • , 12,708 controls
]
 — NR — PHB —
PSS000863 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 1,137 cases
  • , 12,689 controls
]
 — NR — PHB —
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 —
PSS000864 All individuals had hepatitis B. Cases included individuals cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 60 cases
  • , 153 controls
]
 — European — PHB —
PSS000865 All individuals had hepatitis B. Cases included individuals cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 233 cases
  • , 428 controls
]
 — European — PHB —
PSS000866 Cases included individuals with cirrhosis, biopsy confirmed cirrhosis and/or cirrhosis ascertained through ICD codes:Hospitalization or death due to physician diagnosed cirrhosis: K70.2 (alcoholic fibrosis and sclerosis of the liver), K70.3 (alcoholic cirrhosis), K70.4 (alcoholic hepatic failure), K74.0 (hepatic fibrosis), K74.1 (hepatic sclerosis), K74.2 (hepatic fibrosis with hepatic sclerosis), K74.6 (other and unspecific cirrhosis of liver), K76.6 (portal hypertension), or I85 (esophageal varices). —
[
  • 67 cases
  • , 1,375 controls
]
 — African unspecified — PHB —
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 —
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 —
PSS000996 All individuals (cases and controls) met the at-risk criteria for nonalcoholic fatty liver disease (NAFLD) defined as a BMI ≥30 kg/m2 or diagnosis of type 2 diabetes, or both, without evidence of any other cause of liver disease including excess alcohol . Cases were individuals who had been hospitalised with cirrhosis for the first time. A hospital admission for cirrhosis was defined according to the Ratib et al (PMID: 24419483) validated algorithm incorporating appropriate ICD discharge codes and OPCS Classification of Interventions and Procedures version 4 codes. Mean = 7.9 years
[
  • 562 cases
  • , 106,452 controls
]
,
43.0 % Male samples
 Median = 59.0 years
Range = [52.0, 64.0] years		 Not reported — UKB GRS dataset used to test/ evaluate performance of GRS. The GRS dataset is independent of the discovery analysis datasets containing UKB participants. Possible sample overlap between the GRS dataset and the phase 1 replication/validation analysis and phase 2 replication analysis datasets containing UKB participants.
PSS011674 — —
[
  • 56 cases
  • , 5,153 controls
]
 — European
(Finnish)		 — Health2000 —
PSS011418 ICD10: K70.2, K70.3, K70.4, K74.0, K74.1, K74.2, K74.6, K76.6, or I85 —
[
  • 12,910 cases
  • , 1,141,085 controls
]
 — European — 7 cohorts
  • AllofUs
  • ,CHB
  • ,EB
  • ,FinnGen
  • ,IHCS
  • ,MyCode
  • ,deCODE
 —
PSS004134 — —
[
  • 93 cases
  • , 6,404 controls
]
 — African unspecified — UKB —
PSS004135 — —
[
  • 37 cases
  • , 1,667 controls
]
 — East Asian — UKB —
PSS004136 — —
[
  • 460 cases
  • , 24,445 controls
]
 — European non-white British ancestry UKB —
PSS004137 — —
[
  • 193 cases
  • , 7,638 controls
]
 — South Asian — UKB —
PSS004138 — —
[
  • 1,158 cases
  • , 66,267 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS000792 — — 87,413 individuals — European — UKB —
PSS000793 ICD-10 K70 —
[
  • 845 cases
  • , 134,455 controls
]
 — European
(Finnish)		 — FinnGen —
PSS008886 — — 3,837 individuals — African unspecified Nigeria (West Africa) UKB —
PSS007998 — — 1,783 individuals — East Asian China (East Asia) UKB —