Polygenic Score (PGS) ID: PGS001302

Predicted Trait
Reported Trait Cataract
Mapped Trait(s) cataract (EFO_0001059)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC25
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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Score Details

Score Construction
PGS Name GBE_HC25
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,214
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 20,429 cases
  • , 249,275 controls
]
European white British ancestry UKB

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
PPM009005 PSS004379|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81842 [0.80148, 0.83536] : 0.25176
Incremental AUROC (full-covars): -0.00057
PGS R2 (no covariates): 0.00041
PGS AUROC (no covariates): 0.51203 [0.48858, 0.53548]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009006 PSS004380|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81531 [0.78353, 0.84709] : 0.22081
Incremental AUROC (full-covars): 0.00025
PGS R2 (no covariates): 0.00037
PGS AUROC (no covariates): 0.48894 [0.43818, 0.53971]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009007 PSS004381|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.76448 [0.75374, 0.77523] : 0.14636
Incremental AUROC (full-covars): 0.00517
PGS R2 (no covariates): 0.00768
PGS AUROC (no covariates): 0.56031 [0.5466, 0.57402]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009008 PSS004382|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.81674 [0.80411, 0.82937] : 0.28207
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00627
PGS AUROC (no covariates): 0.54731 [0.52945, 0.56518]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009009 PSS004383|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Cataract AUROC: 0.73692 [0.73039, 0.74345] : 0.12068
Incremental AUROC (full-covars): 0.00566
PGS R2 (no covariates): 0.00657
PGS AUROC (no covariates): 0.55468 [0.5465, 0.56286]
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
PSS004380
[
  • 140 cases
  • , 1,564 controls
]
East Asian UKB
PSS004381
[
  • 1,738 cases
  • , 23,167 controls
]
European non-white British ancestry UKB
PSS004382
[
  • 1,165 cases
  • , 6,666 controls
]
South Asian UKB
PSS004383
[
  • 5,153 cases
  • , 62,272 controls
]
European white British ancestry UKB Testing cohort (heldout set)
PSS004379
[
  • 637 cases
  • , 5,860 controls
]
African unspecified UKB