Polygenic Score (PGS) ID: PGS002014

Predicted Trait
Reported Trait Skin cancer
Mapped Trait(s) skin carcinoma (EFO_0009259)
Additional Trait Information neoplasms
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_172
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 534,399
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
PPM010986 PSS009273|
European Ancestry|
19,990 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): 0.1242 [0.1105, 0.1378] sex, age, birth date, deprivation index, 16 PCs —
PPM010990 PSS008155|
South Asian Ancestry|
6,328 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): -0.0147 [-0.0394, 0.01] sex, age, birth date, deprivation index, 16 PCs —
PPM010991 PSS007943|
East Asian Ancestry|
1,810 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): -0.0041 [-0.0504, 0.0423] sex, age, birth date, deprivation index, 16 PCs —
PPM010992 PSS007725|
African Ancestry|
2,483 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): -0.0062 [-0.0457, 0.0333] sex, age, birth date, deprivation index, 16 PCs —
PPM010993 PSS008827|
African Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): 0.0146 [-0.0168, 0.0459] sex, age, birth date, deprivation index, 16 PCs —
PPM010987 PSS009047|
European Ancestry|
4,134 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): 0.0876 [0.0572, 0.1178] sex, age, birth date, deprivation index, 16 PCs —
PPM010988 PSS008601|
European Ancestry|
6,656 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): 0.076 [0.0521, 0.0999] sex, age, birth date, deprivation index, 16 PCs —
PPM010989 PSS008379|
Greater Middle Eastern Ancestry|
1,200 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin cancer — — Partial Correlation (partial-r): 0.0717 [0.0147, 0.1282] 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
PSS007943 — — 1,810 individuals — East Asian China (East Asia) UKB —
PSS007725 — — 2,483 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009047 — — 4,134 individuals — European Poland (NE Europe) UKB —
PSS008155 — — 6,328 individuals — South Asian India (South Asia) UKB —
PSS009273 — — 19,990 individuals — European UK (+ Ireland) UKB —
PSS008601 — — 6,656 individuals — European Italy (South Europe) UKB —
PSS008827 — — 3,924 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008379 — — 1,200 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —