Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0001422 |
Description | A disorder characterized by replacement of the liver parenchyma with fibrous tissue and regenerative nodules. It is usually caused by alcoholism, hepatitis B, and hepatitis C. Complications include the development of ascites, esophageal varices, bleeding, and hepatic encephalopathy. [NCIT: P378] | Trait categories |
Cancer
Digestive system disorder
|
Synonyms |
22 synonyms
|
Mapped terms |
16 mapped terms
|
Child trait(s) | alcoholic liver cirrhosis |
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) |
---|---|---|---|---|---|---|
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 |
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 | |
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 |
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 |
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 |
---|---|---|---|---|---|---|---|---|---|
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 | — |
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) |
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 | — |
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 |
---|---|---|---|---|---|---|---|---|
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 | [ ,
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. |
PSS011418 | ICD10: K70.2, K70.3, K70.4, K74.0, K74.1, K74.2, K74.6, K76.6, or I85 | — | [
|
— | European | — | 7 cohorts
|
— |
PSS007667 | — | — | [ ,
72.3 % Male samples |
— | European | — | GenomALC | — |
PSS007668 | — | — | [ ,
62.06 % Male samples |
— | European | — | GenomALC | — |
PSS007669 | — | — | [ ,
77.02 % Male samples |
— | European | — | UKB | — |
PSS000792 | — | — | 87,413 individuals | — | European | — | UKB | — |
PSS000793 | ICD-10 K70 | — | [
|
— | European (Finnish) |
— | FinnGen | — |
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). | — | [
|
— | 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). | — | [
|
— | 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). | — | [
|
— | NR | — | PHB | — |
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). | — | [
|
— | 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). | — | [
|
— | 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). | — | [
|
— | African unspecified | — | PHB | — |
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 | — | [
|
— | European | — | UKB | — |
PSS011709 | — | — | [
|
— | European | — | IB-liver | — |
PSS011710 | — | — | [
|
— | European | — | IB-liver | — |