Polygenic Score (PGS) ID: PGS001777

Predicted Trait
Reported Trait Cirrhosis (alcohol related)
Mapped Trait(s) alcoholic liver cirrhosis (EFO_1000802)
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name 3-SNP_cirr
Development Method
Name Variants associated with alcohol related cirrhosis
Parameters NR
Variants
Original Genome Build NR
Number of Variants 3
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000258
Citation (link to publication) Whitfield JB et al. J Hepatol (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
48,682 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: GCST003153
Europe PMC: 26482880
 2,138 individuals European NR
Europe PMC: 29562163
 46,544 individuals,
42.0 % Male samples
 European MyCode

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
PPM009254 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) β: 0.897 (0.172) AUROC: 0.635 (0.025) Odds Ratio (OR, top 20% vs bottom 20%): 3.81 [2.05, 7.07] — —
PPM009255 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 0.8 (0.088) AUROC: 0.635 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 3.44 [2.48, 4.77] — —
PPM009256 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) — AUROC: 0.554 (0.036) Odds Ratio (OR, top 20% vs bottom 20%): 2.08 [1.11, 3.89] — —
PPM009247 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 1.092 (0.099) AUROC: 0.665 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 5.99 [4.18, 8.6] — —
PPM009248 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.669 (0.09) AUROC: 0.606 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 2.81 [2.03, 3.89] — —
PPM009249 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.729 (0.08) AUROC: 0.619 (0.014) Odds Ratio (OR, top 20% vs bottom 20%): 3.1 [2.32, 4.14] — —
PPM009250 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis β: 0.748 (0.073) AUROC: 0.636 (0.015) Odds Ratio (OR, top 20% vs bottom 20%): 3.37 [2.38, 4.78] BMI, coffee —
PPM009251 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 1.132 (0.116) AUROC: 0.671 (0.016) Odds Ratio (OR, top 20% vs bottom 20%): 6.18 [4.05, 9.41] — —
PPM009252 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (females) β: 0.974 (0.192) AUROC: 0.65 (0.027) Odds Ratio (OR, top 20% vs bottom 20%): 5.4 [2.67, 10.92] — —
PPM009253 PSS007668|
European Ancestry|
1,766 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis (males) β: 0.575 (0.107) AUROC: 0.592 (0.017) Odds Ratio (OR, top 20% vs bottom 20%): 2.47 [1.68, 3.62] — —
PPM009257 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in diabetics — — Odds Ratio (OR, high vs. low PRS): 5.32 [2.06, 13.7] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009258 PSS007667|
European Ancestry|
1,390 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in non-diabetics — — Odds Ratio (OR, high vs. low PRS): 4.77 [3.45, 6.58] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009259 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in diabetics — — Odds Ratio (OR, high vs. low PRS): 3.74 [2.16, 6.48] — PRS Thresholds: Low (<= 0), High( >0.70)
PPM009260 PSS007669|
European Ancestry|
6,898 individuals
 PGP000258 |
Whitfield JB et al. J Hepatol (2021)
 Reported Trait: Cirrhosis in non-diabetics — — Odds Ratio (OR, high vs. low PRS): 2.37 [1.86, 3.03] — PRS Thresholds: Low (<= 0), High( >0.70)

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
PSS007667 — —
[
  • 917 cases
  • , 473 controls
]
,
72.3 % Male samples
 — European — GenomALC —
PSS007668 — —
[
  • 1,162 cases
  • , 604 controls
]
,
62.06 % Male samples
 — European — GenomALC —
PSS007669 — —
[
  • 594 cases
  • , 6,304 controls
]
,
77.02 % Male samples
 — European — UKB —