Polygenic Score (PGS) ID: PGS004913

Predicted Trait
Reported Trait Alcohol-associated liver cirrhosis
Mapped Trait(s) alcoholic liver cirrhosis (EFO_1000802)
Released in PGS Catalog: June 12, 2024
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Score Details

Score Construction
PGS Name PRSALC
Development Method
Name PRSice-2
Parameters p <1.205E-05, r2 = 0.2
Variants
Original Genome Build NR
Number of Variants 20
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000645
Citation (link to publication) Schwantes-An TH et al. Hepatol Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
4,305 individuals (100%)
Score Development/Training
European: 100%
3,037 individuals (100%)
PGS Evaluation
European: 100%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90428821
[
  • 1,840 cases
  • , 2,465 controls
]
 European GenomALC, NIAAA
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
—
[
  • 2,432 cases
  • , 605 controls
]
,
67.3 % Male samples
 European GenomALC — Mean = 51.9 years
Sd = 10.7 years		 — — —

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
PPM021374 PSS011711|
European Ancestry|
9,448 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.02
Odds ratio (OR, top vs bottom PRS deciles): 2.75 [1.79, 4.21]		 Age, sex, 10 PCs —
PPM021375 PSS011709|
European Ancestry|
3,360 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Alcohol-associated liver cirrhosis — — R²: 0.029
Odds ratio (OR, top vs bottom PRS deciles): 4.4 [1.56, 12.44]		 Age, sex, 10 PCs —
PPM021376 PSS011710|
European Ancestry|
3,709 individuals
 PGP000645 |
Schwantes-An TH et al. Hepatol Commun (2024)
 Reported Trait: Metabolic dysfunction-associated steatotic liver disease cirrhosis — — Odds ratio (OR, top vs bottom PRS deciles): 3.94 [2.23, 6.95] Age, sex, BMI, 10 PCs —

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
PSS011709 — —
[
  • 121 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011710 — —
[
  • 470 cases
  • , 3,239 controls
]
 — European — IB-liver —
PSS011711 Cirrhosis cases were defined as having ICD10 code K70.3; “alcohol-associated cirrhosis of liver', or ICD-9 code 571.2, “Cirrhosis, liver, alcohol-associated or ICD10 code K70.1; “alcoholic hepatitis without ascites” or ICD-9 code 571.1, “acute alcoholic hepatitis.” Controls were defined as having (1) reported alcohol intake of ≥80 g/d (males) and ≥50 g/d (females) and/or (2) ICD10 diagnosis of F10.2 (mental and behavioral disorders due to alcohol) but with no recorded diagnosis of any liver disease as defined previously —
[
  • 467 cases
  • , 8,981 controls
]
 — European — UKB —