Polygenic Score (PGS) ID: PGS000948

Predicted Trait
Reported Trait Inguinal hernia
Mapped Trait(s) Inguinal hernia (HP_0000023)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC243
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_HC243
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,899
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
269,704 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 12,808 cases
  • , 256,896 controls
]
 European UKB — — — white British ancestry —

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
PPM007564 PSS004374|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inguinal hernia — AUROC: 0.78348 [0.74679, 0.82018] R²: 0.13075
Incremental AUROC (full-covars): 0.00435
PGS R2 (no covariates): 0.00705
PGS AUROC (no covariates): 0.56723 [0.51532, 0.61915]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007565 PSS004375|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inguinal hernia — AUROC: 0.9389 [0.90999, 0.9678] R²: 0.36887
Incremental AUROC (full-covars): -0.00042
PGS R2 (no covariates): 0.0169
PGS AUROC (no covariates): 0.60459 [0.46834, 0.74083]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007566 PSS004376|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inguinal hernia — AUROC: 0.82392 [0.8123, 0.83554] R²: 0.19164
Incremental AUROC (full-covars): 0.00848
PGS R2 (no covariates): 0.01125
PGS AUROC (no covariates): 0.58382 [0.56527, 0.60237]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007567 PSS004377|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inguinal hernia — AUROC: 0.79999 [0.77842, 0.82155] R²: 0.16477
Incremental AUROC (full-covars): 0.00323
PGS R2 (no covariates): 0.00427
PGS AUROC (no covariates): 0.55482 [0.52022, 0.58942]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007568 PSS004378|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Inguinal hernia — AUROC: 0.80639 [0.79996, 0.81282] R²: 0.1844
Incremental AUROC (full-covars): 0.01302
PGS R2 (no covariates): 0.01276
PGS AUROC (no covariates): 0.58203 [0.57214, 0.59192]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS004374 — —
[
  • 151 cases
  • , 6,346 controls
]
 — African unspecified — UKB —
PSS004375 — —
[
  • 20 cases
  • , 1,684 controls
]
 — East Asian — UKB —
PSS004376 — —
[
  • 947 cases
  • , 23,958 controls
]
 — European non-white British ancestry UKB —
PSS004377 — —
[
  • 284 cases
  • , 7,547 controls
]
 — South Asian — UKB —
PSS004378 — —
[
  • 3,287 cases
  • , 64,138 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)