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
Download Score FTP directory
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_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
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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
]
EuropeanUKB———white British ancestry—
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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.

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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
PPM008774PSS003755|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008775PSS003756|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008776PSS003757|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008777PSS003758|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM008778PSS003759|
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 PCsFull Model & PGS R2 is estimated using Nagelkerke's method
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Evaluated Samples

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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
]
—Europeannon-white British ancestryUKB—
PSS003758——
[
  • 1,416 cases
  • , 5,841 controls
]
—South Asian—UKB—
PSS003759——
[
  • 18,220 cases
  • , 46,834 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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