Polygenic Score (PGS) ID: PGS001253

Predicted Trait
Reported Trait Hearing difficulty
Mapped Trait(s) hearing loss (EFO_0004238)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC1002247
Released in PGS Catalog: Oct. 21, 2021
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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_BIN_FC1002247
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,098
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%
260,301 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
—
[
  • 72,820 cases
  • , 187,481 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
PPM008774 PSS003755|
African Ancestry|
6,121 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.58714 [0.56491, 0.60938] R²: 0.01786
Incremental AUROC (full-covars): 0.00082
PGS R2 (no covariates): 0.00162
PGS AUROC (no covariates): 0.52504 [0.50255, 0.54753]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008775 PSS003756|
East Asian Ancestry|
1,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62831 [0.58912, 0.6675] R²: 0.04992
Incremental AUROC (full-covars): 0.00338
PGS R2 (no covariates): 0.003
PGS AUROC (no covariates): 0.53605 [0.49383, 0.57827]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008776 PSS003757|
European Ancestry|
23,689 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62276 [0.6147, 0.63082] R²: 0.0516
Incremental AUROC (full-covars): 0.00532
PGS R2 (no covariates): 0.00515
PGS AUROC (no covariates): 0.53825 [0.52992, 0.54658]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008777 PSS003758|
South Asian Ancestry|
7,257 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.61668 [0.60019, 0.63317] R²: 0.04334
Incremental AUROC (full-covars): 0.00291
PGS R2 (no covariates): 0.00324
PGS AUROC (no covariates): 0.53126 [0.51459, 0.54793]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008778 PSS003759|
European Ancestry|
65,054 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty — AUROC: 0.62552 [0.62077, 0.63026] R²: 0.05561
Incremental AUROC (full-covars): 0.00726
PGS R2 (no covariates): 0.00632
PGS AUROC (no covariates): 0.54175 [0.53682, 0.54668]		 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
PSS003755 — —
[
  • 697 cases
  • , 5,424 controls
]
 — African unspecified — UKB —
PSS003756 — —
[
  • 214 cases
  • , 1,354 controls
]
 — East Asian — UKB —
PSS003757 — —
[
  • 6,205 cases
  • , 17,484 controls
]
 — European non-white British ancestry UKB —
PSS003758 — —
[
  • 1,416 cases
  • , 5,841 controls
]
 — South Asian — UKB —
PSS003759 — —
[
  • 18,220 cases
  • , 46,834 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)