Polygenic Score (PGS) ID: PGS001140

Predicted Trait
Reported Trait Seborrheic keratosis (time-to-event)
Mapped Trait(s) seborrheic keratosis (EFO_0005584)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC1190
Released in PGS Catalog: Oct. 21, 2021
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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_HC1190
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,368
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
—
[
  • 17,137 cases
  • , 252,567 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
PPM008427 PSS004178|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.69791 [0.62772, 0.7681] R²: 0.0531
Incremental AUROC (full-covars): 0.01676
PGS R2 (no covariates): 0.01004
PGS AUROC (no covariates): 0.5859 [0.50622, 0.66558]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008428 PSS004179|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.74674 [0.66312, 0.83035] R²: 0.10541
Incremental AUROC (full-covars): -0.00457
PGS R2 (no covariates): 0.01744
PGS AUROC (no covariates): 0.62007 [0.51848, 0.72165]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008429 PSS004180|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.63238 [0.61781, 0.64695] R²: 0.03162
Incremental AUROC (full-covars): 0.01328
PGS R2 (no covariates): 0.00595
PGS AUROC (no covariates): 0.55636 [0.54088, 0.57185]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008430 PSS004181|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.65125 [0.6056, 0.6969] Incremental AUROC (full-covars): 0.00972
R²: 0.03155
PGS R2 (no covariates): 0.00354
PGS AUROC (no covariates): 0.54802 [0.49607, 0.59996]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008431 PSS004182|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE seborrhoeic keratosis — AUROC: 0.62735 [0.61905, 0.63565] R²: 0.03214
Incremental AUROC (full-covars): 0.01502
PGS R2 (no covariates): 0.00744
PGS AUROC (no covariates): 0.56248 [0.55356, 0.57141]		 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
PSS004178 — —
[
  • 54 cases
  • , 6,443 controls
]
 — African unspecified — UKB —
PSS004179 — —
[
  • 37 cases
  • , 1,667 controls
]
 — East Asian — UKB —
PSS004180 — —
[
  • 1,295 cases
  • , 23,610 controls
]
 — European non-white British ancestry UKB —
PSS004181 — —
[
  • 113 cases
  • , 7,718 controls
]
 — South Asian — UKB —
PSS004182 — —
[
  • 4,266 cases
  • , 63,159 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)