PGS Publication: PGP000258

Publication Information (EuropePMC)
Title A genetic risk score and diabetes predict development of alcohol-related cirrhosis in drinkers.
PubMed ID 34656649(Europe PMC)
doi 10.1016/j.jhep.2021.10.005
Publication Date Oct. 13, 2021
Journal J Hepatol
Author(s) Whitfield JB, Schwantes-An TH, Darlay R, Aithal GP, Atkinson SR, Bataller R, Botwin G, Chalasani NP, Cordell HJ, Daly AK, Day CP, Eyer F, Foroud T, Gleeson D, Goldman D, Haber PS, Jacquet JM, Liang T, Liangpunsakul S, Masson S, Mathurin P, Moirand R, McQuillin A, Moreno C, Morgan MY, Mueller S, Müllhaupt B, Nagy LE, Nahon P, Nalpas B, Naveau S, Perney P, Pirmohamed M, Seitz HK, Soyka M, Stickel F, Thompson A, Thursz MR, Trépo E, Morgan TR, Seth D, GenomALC Consortium.
Released in PGS Catalog: Nov. 25, 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:
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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

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution Scoring File (FTP Link)
PGS001777
(3-SNP_cirr)
PGP000258 |
Whitfield JB et al. J Hepatol (2021)
Cirrhosis (alcohol related) alcoholic liver cirrhosis 3
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001777/ScoringFiles/PGS001777.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
PPM009258 PGS001777
(3-SNP_cirr)
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)
PPM009247 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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]
PPM009254 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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]
PPM009257 PGS001777
(3-SNP_cirr)
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)
PPM009259 PGS001777
(3-SNP_cirr)
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 PGS001777
(3-SNP_cirr)
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