PGS Publication: PGP000136

Publication Information (EuropePMC)
Title Association of genetic variation with cirrhosis: a multi-trait genome-wide association and gene-environment interaction study.
PubMed ID 33310085(Europe PMC)
doi 10.1053/j.gastro.2020.12.011
Publication Date Dec. 10, 2020
Journal Gastroenterology
Author(s) Emdin CA, Haas M, Ajmera V, Simon TG, Homburger J, Neben C, Jiang L, Wei WQ, Feng Q, Zhou A, Denny J, Corey K, Loomba R, Kathiresan S, Khera AV.
Released in PGS Catalog: Feb. 3, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
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Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

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)
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

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
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) —

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 —