| Predicted Trait | |
| Reported Trait | Alcoholic cirrhosis |
| Mapped Trait(s) | alcoholic liver cirrhosis (EFO_1000802) |
| Additional Trait Information | Unadjusted weights |
| 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 | |
| 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 |
|---|---|---|---|---|---|---|---|---|
Europe PMC: 10.1038/s41588-020-00757-z |
223,327 individuals | European (British) |
UKB | — | — | — | — | Training |
|
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) | — |
| PPM022382 | PSS011933| Multi-ancestry (including European)| 312,599 individuals |
PGP000708 | Ding C et al. Nat Commun (2023) |Ext. |
Reported Trait: Alcohol-related cirrhosis | HR: 1.67 [1.55, 1.8] | — | — | sex, age, ethnicity, Townsend deprivation index at recruitment, physical activity, smoking, total weekly alcohol intake, beverage type, drinking with/without meal, daily alcohol consumption group, diabetes, BMI, first 10 principal genetic components, and genotyping array | — |
| PPM022383 | PSS011933| Multi-ancestry (including European)| 312,599 individuals |
PGP000708 | Ding C et al. Nat Commun (2023) |Ext. |
Reported Trait: Alcoholic hepatitis | HR: 1.32 [1.12, 1.57] | — | — | sex, age, ethnicity, Townsend deprivation index at recruitment, physical activity, smoking, total weekly alcohol intake, beverage type, drinking with/without meal, daily alcohol consumption group, diabetes, BMI, first 10 principal genetic components, and genotyping array | — |
| PPM022384 | PSS011933| Multi-ancestry (including European)| 312,599 individuals |
PGP000708 | Ding C et al. Nat Commun (2023) |Ext. |
Reported Trait: Alcohol-related cirrhosis x alcohol consumption interaction | — | — | Hazard ratio (HR, heavy binge drinking and high PRS vs. below daily limit drinking and low PRS): 12.41 [4.96, 31.05] | total weekly alcohol intake, diabetes, BMI, sex, age, ethnicity, Townsend deprivation index, physical activity, smoke, alcohol type, drinking with/without meals, genotyping array, and first 10 ancestry principal components | — |
|
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 | — | [
|
— | European (Finnish) |
— | FinnGen | — |
| PSS011933 | — | — | 294,816 individuals | — | European | — | UKB | — |
| PSS011933 | — | — | 17,783 individuals | — | Not reported | — | UKB | — |