PGS Publication: PGP000217

Publication Information (EuropePMC)
Title A Polygenic Risk Score to Refine Risk Stratification and Prediction for Severe Liver Disease by Clinical Fibrosis Scores.
PubMed ID 34091049(Europe PMC)
doi 10.1016/j.cgh.2021.05.056
Publication Date June 4, 2021
Journal Clin Gastroenterol Hepatol
Author(s) De Vincentis A, Tavaglione F, Jamialahmadi O, Picardi A, Antonelli Incalzi R, Valenti L, Romeo S, Vespasiani-Gentilucci U.
Released in PGS Catalog: Aug. 26, 2021

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

External PGS Evaluated 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)
PGS000865
(PRS-HFC)
 PGP000212 |
Dongiovanni P et al. J Intern Med (2017)
 Hepatic fat content liver fat measurement 4
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000865/ScoringFiles/PGS000865.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
PPM002473 PGS000865
(PRS-HFC)
 PSS001114|
European Ancestry|
266,687 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease HR: 1.25 [1.16, 1.35] — Hazard Ratio (HR, top 25% vs bottom 25%): 1.63 [1.28, 2.08] Age, sex —
PPM002474 PGS000865
(PRS-HFC)
 PSS001115|
European Ancestry|
13,268 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in individuals with diabetes HR: 1.55 [1.33, 1.8] — Hazard Ratio (HR, top 25% vs bottom 25%): 3.24 [1.93, 5.43] Age, sex —
PPM002475 PGS000865
(PRS-HFC)
 PSS001116|
European Ancestry|
64,655 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in obese individuals HR: 1.4 [1.25, 1.57] — Hazard Ratio (HR, top 25% vs bottom 25%): 2.29 [1.6, 3.29] Age, sex —
PPM002476 PGS000865
(PRS-HFC)
 PSS001114|
European Ancestry|
266,687 individuals
 PGP000217 |
De Vincentis A et al. Clin Gastroenterol Hepatol (2021)
|Ext.		 Reported Trait: Incident severe liver disease in individuals with a fatty liver index ≥ 60 HR: 1.34 [1.23, 1.47] — Hazard Ratio (HR, top 25% vs bottom 25%): 2.13 [1.57, 2.89] Age, sex —

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
PSS001114 Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. Median = 9.0 years
IQR = [8.3, 9.7] years
[
  • 543 cases
  • , 266,144 controls
]
,
45.0 % Male samples
 Mean = 56.5 years
Sd = 8.1 years		 European — UKB —
PSS001115 All individuals had diabetes. Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. —
[
  • 125 cases
  • , 13,143 controls
]
 — European — UKB —
PSS001116 All individuals were classified as obese. Cases were individuals with severe liver disease (SLD). SLD was defined as a composite diagnosis of cirrhosis, decompensated liver disease (i.e., esophageal varices with or without bleeding, portal hypertension, hepatorenal syndrome, liver failure), hepatocellular carcinoma and/or liver transplantation (ICD-10 C22.0, I85.0, I85.9, K70.3, K70.4, K72.1, K72.9, K74.1, K74.2, K74.6, K76.6, K76.7, Z94.4) in any of the aforementioned records. —
[
  • 238 cases
  • , 64,417 controls
]
 — European — UKB —