Polygenic Score (PGS) ID: PGS000939

Predicted Trait
Reported Trait Hiatus hernia
Mapped Trait(s) Hiatus hernia (HP_0002036)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC310
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_HC310
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,553
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
—
[
  • 38,161 cases
  • , 231,543 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
PPM007522 PSS004427|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hiatus hernia — AUROC: 0.64044 [0.61719, 0.66369] R²: 0.04433
Incremental AUROC (full-covars): -0.00233
PGS R2 (no covariates): 0.00066
PGS AUROC (no covariates): 0.51517 [0.49142, 0.53893]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007523 PSS004428|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hiatus hernia — AUROC: 0.63197 [0.57447, 0.68948] R²: 0.03898
Incremental AUROC (full-covars): 0.00432
PGS R2 (no covariates): 0.00207
PGS AUROC (no covariates): 0.53874 [0.47063, 0.60684]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007524 PSS004429|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hiatus hernia — AUROC: 0.66967 [0.6596, 0.67973] R²: 0.07255
Incremental AUROC (full-covars): 0.00184
PGS R2 (no covariates): 0.00362
PGS AUROC (no covariates): 0.53601 [0.525, 0.54702]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007525 PSS004430|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hiatus hernia — AUROC: 0.66241 [0.64416, 0.68066] R²: 0.06499
Incremental AUROC (full-covars): 0.00273
PGS R2 (no covariates): 0.0024
PGS AUROC (no covariates): 0.53088 [0.51112, 0.55065]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007526 PSS004431|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hiatus hernia — AUROC: 0.64829 [0.6425, 0.65408] R²: 0.05826
Incremental AUROC (full-covars): 0.00672
PGS R2 (no covariates): 0.00515
PGS AUROC (no covariates): 0.54418 [0.53797, 0.55038]		 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
PSS004427 — —
[
  • 590 cases
  • , 5,907 controls
]
 — African unspecified — UKB —
PSS004428 — —
[
  • 82 cases
  • , 1,622 controls
]
 — East Asian — UKB —
PSS004429 — —
[
  • 3,001 cases
  • , 21,904 controls
]
 — European non-white British ancestry UKB —
PSS004430 — —
[
  • 920 cases
  • , 6,911 controls
]
 — South Asian — UKB —
PSS004431 — —
[
  • 9,526 cases
  • , 57,899 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)