Polygenic Score (PGS) ID: PGS000704

Predicted Trait
Reported Trait Alcoholic cirrhosis
Mapped Trait(s) alcoholic liver cirrhosis (EFO_1000802)
Additional Trait Information Unadjusted weights
Released in PGS Catalog: Feb. 3, 2021
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Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name HC171
Development Method
Name snpnet (multi-PRS)
Parameters Weighted combination of multiple biomarker PRS. 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 183,271
Effect Weight Type weights.HC171
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
223,327 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

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
223,327 individuals European
(British)		 UKB — — — — Training

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
PPM001596 PSS000792|
European Ancestry|
87,413 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alcoholic cirrhosis — AUROC: 0.55471 — Age, sex, PCs(1-10) —
PPM001607 PSS000793|
European Ancestry|
135,300 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Alcoholic cirrhosis HR: 1.18 [1.11, 1.27] C-index: 0.711 — Age as time scale, sex, batch, PCs(1-10) —

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
PSS000792 — — 87,413 individuals — European — UKB —
PSS000793 ICD-10 K70 —
[
  • 845 cases
  • , 134,455 controls
]
 — European
(Finnish)		 — FinnGen —