PGS Publication: PGP000180

Publication Information (EuropePMC)
Title Genome-Wide Association Study for Alcohol-Related Cirrhosis Identifies Risk Loci in MARC1 and HNRNPUL1.
PubMed ID 32561361(Europe PMC)
doi 10.1053/j.gastro.2020.06.014
Publication Date June 16, 2020
Journal Gastroenterology
Author(s) Innes H, Buch S, Hutchinson S, Guha IN, Morling JR, Barnes E, Irving W, Forrest E, Pedergnana V, Goldberg D, Aspinall E, Barclay S, Hayes PC, Dillon J, Nischalke HD, Lutz P, Spengler U, Fischer J, Berg T, Brosch M, Eyer F, Datz C, Mueller S, Peccerella T, Deltenre P, Marot A, Soyka M, McQuillin A, Morgan MY, Hampe J, Stickel F.
Released in PGS Catalog: May 28, 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
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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 PGS Scoring File (FTP Link)
PGS000776
(GRS9_Cirr)
PGP000180 |
Innes H et al. Gastroenterology (2020)
Cirrhosis cirrhosis of liver 9
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000776/ScoringFiles/PGS000776.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
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

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.