Polygenic Score (PGS) ID: PGS001255

Predicted Trait
Reported Trait Otosclerosis (time-to-event)
Mapped Trait(s) otosclerosis (EFO_0004213)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC914
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_HC914
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 213
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: 50%
African: 25%
South Asian: 25%
4 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
—
[
  • 555 cases
  • , 269,149 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
PPM008781 PSS004702|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE otosclerosis — AUROC: 0.91156 [0.77281, 1.0] R²: 0.29139
Incremental AUROC (full-covars): 0.03981
PGS R2 (no covariates): 0.06779
PGS AUROC (no covariates): 0.7376 [0.46621, 1.0]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008782 PSS004703|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE otosclerosis — AUROC: 0.66807 [0.58985, 0.74629] R²: 0.03365
Incremental AUROC (full-covars): 0.05467
PGS R2 (no covariates): 0.01522
PGS AUROC (no covariates): 0.62631 [0.54794, 0.70468]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008783 PSS004704|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE otosclerosis — AUROC: 0.71231 [0.61511, 0.80951] R²: 0.04349
Incremental AUROC (full-covars): 0.03275
PGS R2 (no covariates): 0.00824
PGS AUROC (no covariates): 0.59763 [0.48884, 0.70642]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008784 PSS004705|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE otosclerosis — AUROC: 0.6532 [0.60975, 0.69665] R²: 0.02085
Incremental AUROC (full-covars): 0.05946
PGS R2 (no covariates): 0.01341
PGS AUROC (no covariates): 0.6319 [0.58724, 0.67656]		 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
PSS004702 — —
[
  • 4 cases
  • , 6,493 controls
]
 — African unspecified — UKB —
PSS004703 — —
[
  • 53 cases
  • , 24,852 controls
]
 — European non-white British ancestry UKB —
PSS004704 — —
[
  • 20 cases
  • , 7,811 controls
]
 — South Asian — UKB —
PSS004705 — —
[
  • 156 cases
  • , 67,269 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)