Polygenic Score (PGS) ID: PGS001252

Predicted Trait
Reported Trait Hearing difficulty and deafness
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC3002247
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_BIN_FC3002247
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,731
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%
260,368 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
—
[
  • 72,887 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
PPM008769 PSS003899|
African Ancestry|
6,123 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.58635 [0.56411, 0.60859] R²: 0.01752
Incremental AUROC (full-covars): -0.00041
PGS R2 (no covariates): 0.00138
PGS AUROC (no covariates): 0.52307 [0.50054, 0.54561]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008770 PSS003900|
East Asian Ancestry|
1,568 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62777 [0.58865, 0.66688] R²: 0.04973
Incremental AUROC (full-covars): 0.00284
PGS R2 (no covariates): 0.00305
PGS AUROC (no covariates): 0.53516 [0.49316, 0.57716]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008771 PSS003901|
European Ancestry|
23,697 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62252 [0.61446, 0.63058] R²: 0.05132
Incremental AUROC (full-covars): 0.00531
PGS R2 (no covariates): 0.00527
PGS AUROC (no covariates): 0.53867 [0.53034, 0.54699]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008772 PSS003902|
South Asian Ancestry|
7,266 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.61586 [0.5994, 0.63232] R²: 0.04282
Incremental AUROC (full-covars): 0.00304
PGS R2 (no covariates): 0.00345
PGS AUROC (no covariates): 0.53204 [0.5154, 0.54867]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008773 PSS003903|
European Ancestry|
65,065 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Hearing difficulty and Deafness — AUROC: 0.62548 [0.62074, 0.63023] R²: 0.05558
Incremental AUROC (full-covars): 0.00728
PGS R2 (no covariates): 0.00646
PGS AUROC (no covariates): 0.54216 [0.53723, 0.54709]		 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
PSS003900 — —
[
  • 214 cases
  • , 1,354 controls
]
 — East Asian — UKB —
PSS003901 — —
[
  • 6,214 cases
  • , 17,483 controls
]
 — European non-white British ancestry UKB —
PSS003902 — —
[
  • 1,425 cases
  • , 5,841 controls
]
 — South Asian — UKB —
PSS003903 — —
[
  • 18,231 cases
  • , 46,834 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003899 — —
[
  • 699 cases
  • , 5,424 controls
]
 — African unspecified — UKB —