Polygenic Score (PGS) ID: PGS000963

Predicted Trait
Reported Trait Follicular cysts of skin and subcutaneous tissue (time-to-event)
Mapped Trait(s) Follicular Cyst (EFO_1001329)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1184
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_HC1184
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 264
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
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
—
[
  • 8,049 cases
  • , 261,655 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
PPM007639 PSS004168|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE follicular cysts of skin and subcutaneous tissue — AUROC: 0.56399 [0.51489, 0.61308] R²: 0.01027
Incremental AUROC (full-covars): -0.00108
PGS R2 (no covariates): 0.00011
PGS AUROC (no covariates): 0.51899 [0.4747, 0.56328]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007640 PSS004169|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE follicular cysts of skin and subcutaneous tissue — AUROC: 0.64299 [0.54406, 0.74191] R²: 0.02377
Incremental AUROC (full-covars): 0.01591
PGS R2 (no covariates): 0.00898
PGS AUROC (no covariates): 0.60189 [0.51478, 0.689]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007641 PSS004170|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE follicular cysts of skin and subcutaneous tissue — AUROC: 0.61353 [0.59056, 0.63651] R²: 0.02635
Incremental AUROC (full-covars): 0.0691
PGS R2 (no covariates): 0.02281
PGS AUROC (no covariates): 0.59346 [0.56998, 0.61695]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007642 PSS004171|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE follicular cysts of skin and subcutaneous tissue — AUROC: 0.64204 [0.6008, 0.68328] R²: 0.03504
Incremental AUROC (full-covars): 0.04562
PGS R2 (no covariates): 0.02125
PGS AUROC (no covariates): 0.56287 [0.51348, 0.61226]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007643 PSS004172|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE follicular cysts of skin and subcutaneous tissue — AUROC: 0.6146 [0.60131, 0.6279] R²: 0.02902
Incremental AUROC (full-covars): 0.06632
PGS R2 (no covariates): 0.02439
PGS AUROC (no covariates): 0.58761 [0.57398, 0.60124]		 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
PSS004168 — —
[
  • 141 cases
  • , 6,356 controls
]
 — African unspecified — UKB —
PSS004169 — —
[
  • 29 cases
  • , 1,675 controls
]
 — East Asian — UKB —
PSS004170 — —
[
  • 668 cases
  • , 24,237 controls
]
 — European non-white British ancestry UKB —
PSS004171 — —
[
  • 180 cases
  • , 7,651 controls
]
 — South Asian — UKB —
PSS004172 — —
[
  • 1,995 cases
  • , 65,430 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)