Polygenic Score (PGS) ID: PGS000726

Predicted Trait
Reported Trait Cirrhosis
Mapped Trait(s) cirrhosis of liver (EFO_0001422)
Released in PGS Catalog: Feb. 3, 2021
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Score Details

Score Construction
PGS Name PGS12_CIR
Development Method
Name Genome-wide significant variants
Parameters P < 5e-8, replication p < 0.05
Variants
Original Genome Build GRCh37
Number of Variants 12
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000136
Citation (link to publication) Emdin CA et al. Gastroenterology (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • African
  • Additional Asian Ancestries
  • Not Reported
440,073 individuals (100%)
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • Not Reported
346,840 individuals (100%)
PGS Evaluation
European: 50%
Not Reported: 33.3%
African: 16.7%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
Europe PMC: 33310085
 440,073 individuals European, African unspecified, Asian unspecified, NR ACG, ARIC, BioVU, UKB
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
—
[
  • 3,554 cases
  • , 343,286 controls
]
 European, NR BBJ, FinnGen, PHB Partners Healthcare Biobank definition of cirrhosis: 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). FinnGen definition of cirrhosis: Cirrhosis ascertained through ICD-10 code K74, ICD-9 code 571 (hepatic fibrosis and cirrhosis). Biobank Japan definition of cirrhosis: Cirrhosis ascertained through self-reported survey and review of medical records. — — — Replication Cohort

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) 		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
PPM001656 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 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 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 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 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 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 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 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 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 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) —

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
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 —