Polygenic Score (PGS) ID: PGS002087

Predicted Trait
Reported Trait Sebaceous cyst
Mapped Trait(s) Epidermal Inclusion Cyst (EFO_1000243)
Additional Trait Information dermatologic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_706.2
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 206,669
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
PPM011556 PSS009351|
European Ancestry|
19,952 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0513 [0.0374, 0.0651] sex, age, birth date, deprivation index, 16 PCs —
PPM011557 PSS009125|
European Ancestry|
4,124 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0734 [0.0429, 0.1037] sex, age, birth date, deprivation index, 16 PCs —
PPM011558 PSS008679|
European Ancestry|
6,646 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0454 [0.0214, 0.0694] sex, age, birth date, deprivation index, 16 PCs —
PPM011559 PSS008453|
Greater Middle Eastern Ancestry|
1,194 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0444 [-0.0128, 0.1014] sex, age, birth date, deprivation index, 16 PCs —
PPM011560 PSS008233|
South Asian Ancestry|
6,311 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0351 [0.0103, 0.0597] sex, age, birth date, deprivation index, 16 PCs —
PPM011561 PSS008013|
East Asian Ancestry|
1,807 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): -0.0299 [-0.0762, 0.0165] sex, age, birth date, deprivation index, 16 PCs —
PPM011562 PSS007798|
African Ancestry|
2,471 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): -0.0274 [-0.067, 0.0122] sex, age, birth date, deprivation index, 16 PCs —
PPM011563 PSS008902|
African Ancestry|
3,913 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sebaceous cyst — — Partial Correlation (partial-r): 0.0023 [-0.0291, 0.0338] 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
PSS009125 — — 4,124 individuals — European Poland (NE Europe) UKB —
PSS008453 — — 1,194 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008679 — — 6,646 individuals — European Italy (South Europe) UKB —
PSS009351 — — 19,952 individuals — European UK (+ Ireland) UKB —
PSS008233 — — 6,311 individuals — South Asian India (South Asia) UKB —
PSS008902 — — 3,913 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008013 — — 1,807 individuals — East Asian China (East Asia) UKB —
PSS007798 — — 2,471 individuals — African American or Afro-Caribbean Carribean UKB —