Polygenic Score (PGS) ID: PGS000949

Predicted Trait
Reported Trait Inguinal hernia (time-to-event)
Mapped Trait(s) Inguinal hernia (HP_0000023)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1094
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_HC1094
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,085
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
—
[
  • 15,095 cases
  • , 254,609 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
PPM007569 PSS004104|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE inguinal hernia — AUROC: 0.77669 [0.74183, 0.81155] R²: 0.12906
Incremental AUROC (full-covars): 0.0025
PGS R2 (no covariates): 0.00602
PGS AUROC (no covariates): 0.56793 [0.52138, 0.61447]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007570 PSS004105|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE inguinal hernia — AUROC: 0.91597 [0.86802, 0.96391] R²: 0.32274
Incremental AUROC (full-covars): 0.00132
PGS R2 (no covariates): 0.01604
PGS AUROC (no covariates): 0.6059 [0.48166, 0.73015]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007571 PSS004106|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE inguinal hernia — AUROC: 0.81509 [0.80403, 0.82615] R²: 0.19099
Incremental AUROC (full-covars): 0.00779
PGS R2 (no covariates): 0.01076
PGS AUROC (no covariates): 0.5791 [0.56214, 0.59607]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007572 PSS004107|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE inguinal hernia — AUROC: 0.80083 [0.78118, 0.82049] R²: 0.17463
Incremental AUROC (full-covars): 0.00263
PGS R2 (no covariates): 0.00658
PGS AUROC (no covariates): 0.56567 [0.53271, 0.59863]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007573 PSS004108|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE inguinal hernia — AUROC: 0.80466 [0.79851, 0.8108] R²: 0.19027
Incremental AUROC (full-covars): 0.01341
PGS R2 (no covariates): 0.01302
PGS AUROC (no covariates): 0.58201 [0.5728, 0.59123]		 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
PSS004104 — —
[
  • 170 cases
  • , 6,327 controls
]
 — African unspecified — UKB —
PSS004105 — —
[
  • 23 cases
  • , 1,681 controls
]
 — East Asian — UKB —
PSS004106 — —
[
  • 1,142 cases
  • , 23,763 controls
]
 — European non-white British ancestry UKB —
PSS004107 — —
[
  • 327 cases
  • , 7,504 controls
]
 — South Asian — UKB —
PSS004108 — —
[
  • 3,805 cases
  • , 63,620 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)