PGS Catalog - PGS002014 / Skin cancer (Polygenic Score)

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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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_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

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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
—	391,124 individuals	European	UKB	—	—	—	UK (+ Ireland)	—

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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
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	—
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	—
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	—

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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
PSS007725	—	—	2,483 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS007943	—	—	1,810 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008155	—	—	6,328 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008379	—	—	1,200 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008601	—	—	6,656 individuals	—	European	Italy (South Europe)	UKB	—
PSS008827	—	—	3,924 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009047	—	—	4,134 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009273	—	—	19,990 individuals	—	European	UK (+ Ireland)	UKB	—

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