Polygenic Score (PGS) ID: PGS000990

Predicted Trait
Reported Trait Retinal detachments and breaks (time-to-event)
Mapped Trait(s)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC878
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_HC878
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 237
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: 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
—
[
  • 3,438 cases
  • , 266,266 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
PPM007718PSS004682|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE retinal detachments and breaks—AUROC: 0.61927 [0.54935, 0.68918]R²: 0.0247
Incremental AUROC (full-covars): -0.01882
PGS R2 (no covariates): 0.00198
PGS AUROC (no covariates): 0.46633 [0.38893, 0.54373]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007719PSS004683|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE retinal detachments and breaks—AUROC: 0.75788 [0.63933, 0.87643]R²: 0.10693
Incremental AUROC (full-covars): 0.0196
PGS R2 (no covariates): 0.01417
PGS AUROC (no covariates): 0.5954 [0.44975, 0.74105]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007720PSS004684|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE retinal detachments and breaks—AUROC: 0.64308 [0.61279, 0.67337]R²: 0.02565
Incremental AUROC (full-covars): 0.00606
PGS R2 (no covariates): 0.00213
PGS AUROC (no covariates): 0.54152 [0.50847, 0.57457]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007721PSS004685|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE retinal detachments and breaks—AUROC: 0.71433 [0.66221, 0.76646]R²: 0.05371
Incremental AUROC (full-covars): 0.0098
PGS R2 (no covariates): 0.00492
PGS AUROC (no covariates): 0.56225 [0.49739, 0.62711]		age, sex, UKB array type, Genotype PCsFull Model & PGS R2 is estimated using Nagelkerke's method
PPM007722PSS004686|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: TTE retinal detachments and breaks—AUROC: 0.63532 [0.61784, 0.65279]R²: 0.02226
Incremental AUROC (full-covars): 0.00479
PGS R2 (no covariates): 0.00207
PGS AUROC (no covariates): 0.53945 [0.52027, 0.55863]		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
PSS004682——
[
  • 57 cases
  • , 6,440 controls
]
—African unspecified—UKB—
PSS004683——
[
  • 12 cases
  • , 1,692 controls
]
—East Asian—UKB—
PSS004684——
[
  • 296 cases
  • , 24,609 controls
]
—Europeannon-white British ancestryUKB—
PSS004685——
[
  • 76 cases
  • , 7,755 controls
]
—South Asian—UKB—
PSS004686——
[
  • 908 cases
  • , 66,517 controls
]
—Europeanwhite British ancestryUKBTesting cohort (heldout set)
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