Trait: cirrhosis of liver

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 21 synonyms
  • CL - Cirrhosis of liver
  • Cirrhoses, Hepatic
  • Cirrhoses, Liver
  • Cirrhosis of liver (disorder)
  • Cirrhosis of liver NOS
  • Cirrhosis of liver NOS (disorder)
  • Cirrhosis of liver without mention of alcohol
  • Cirrhosis of liver, NOS
  • Cirrhosis, Hepatic
  • Cirrhosis, Liver
  • Fibroses, Liver
  • Fibrosis, Liver
  • Hepatic Cirrhoses
  • Hepatic cirrhosis
  • Hepatic cirrhosis, NOS
  • Liver Cirrhoses
  • Liver Fibroses
  • Liver Fibrosis
  • cirrhosis
  • cirrhosis of liver
  • liver cirrhosis
Mapped terms 14 mapped terms
  • DOID:5082
  • ICD10:K74
  • ICD10:K74.60
  • ICD9:571.5
  • MESH:D008103
  • MONDO:0005155
  • MeSH:D008103
  • MedDRA:10009213
  • NCIT:C2951
  • NCIt:C2951
  • OMIM:215600
  • SCTID:19943007
  • SNOMEDCT:19943007
  • UMLS:C0023890
Child trait(s) alcoholic liver cirrhosis

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 "cirrhosis of liver" 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 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 - 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
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

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
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
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]
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]
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)

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
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.
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
PSS000792 87,413 individuals European UKB
PSS000793 ICD-10 K70
[
  • 845 cases
  • , 134,455 controls
]
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).
[
  • 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
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