Polygenic Score (PGS) ID: PGS002085

Predicted Trait
Reported Trait Seborrheic keratosis
Mapped Trait(s) seborrheic keratosis (EFO_0005584)
Additional Trait Information dermatologic
Released in PGS Catalog: Jan. 10, 2022
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 portability-ldpred2_702.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 481,233
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM011540 PSS009349|
European Ancestry|
19,837 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0237 [0.0098, 0.0376] sex, age, birth date, deprivation index, 16 PCs —
PPM011541 PSS009123|
European Ancestry|
4,111 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.03 sex, age, birth date, deprivation index, 16 PCs —
PPM011542 PSS008677|
European Ancestry|
6,626 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0128 [-0.0113, 0.0369] sex, age, birth date, deprivation index, 16 PCs —
PPM011543 PSS008451|
Greater Middle Eastern Ancestry|
1,197 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0512 [-0.006, 0.108] sex, age, birth date, deprivation index, 16 PCs —
PPM011544 PSS008231|
South Asian Ancestry|
6,321 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0097 [-0.0344, 0.015] sex, age, birth date, deprivation index, 16 PCs —
PPM011545 PSS008011|
East Asian Ancestry|
1,807 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0149 [-0.0612, 0.0315] sex, age, birth date, deprivation index, 16 PCs —
PPM011546 PSS007796|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): 0.0158 [-0.0237, 0.0553] sex, age, birth date, deprivation index, 16 PCs —
PPM011547 PSS008900|
African Ancestry|
3,922 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Seborrheic keratosis — — Partial Correlation (partial-r): -0.0283 [-0.0596, 0.0031] sex, age, birth date, deprivation index, 16 PCs —

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
PSS008900 — — 3,922 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009349 — — 19,837 individuals — European UK (+ Ireland) UKB —
PSS008677 — — 6,626 individuals — European Italy (South Europe) UKB —
PSS008231 — — 6,321 individuals — South Asian India (South Asia) UKB —
PSS008011 — — 1,807 individuals — East Asian China (East Asia) UKB —
PSS007796 — — 2,483 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009123 — — 4,111 individuals — European Poland (NE Europe) UKB —
PSS008451 — — 1,197 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —