| 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. |
| Polygenic Score ID & Name | PGS Publication ID (PGP) | Reported Trait | Mapped Trait(s) (Ontology) | Number of Variants |
Ancestry distribution GWAS Dev Eval |
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 |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| 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] | — | — |
| 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] | — | — |
| 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) |
| 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) |
| 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) |
|
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 | — | — | [ ,
72.3 % Male samples |
— | European | — | GenomALC | — |
| PSS007668 | — | — | [ ,
62.06 % Male samples |
— | European | — | GenomALC | — |
| PSS007669 | — | — | [ ,
77.02 % Male samples |
— | European | — | UKB | — |