Polygenic Score (PGS) ID: PGS002084

Predicted Trait
Reported Trait Sarcoidosis
Mapped Trait(s) skin sarcoidosis (EFO_1000767)
Additional Trait Information dermatologic
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_697
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 403,417
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: 42.9%
African: 28.6%
Greater Middle Eastern: 14.3%
South Asian: 14.3%
7 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
PPM011533 PSS009348|
European Ancestry|
19,670 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0184 [0.0044, 0.0324] sex, age, birth date, deprivation index, 16 PCs —
PPM011534 PSS009122|
European Ancestry|
4,059 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0038 [-0.0271, 0.0346] sex, age, birth date, deprivation index, 16 PCs —
PPM011535 PSS008676|
European Ancestry|
6,565 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0103 [-0.0139, 0.0345] sex, age, birth date, deprivation index, 16 PCs —
PPM011536 PSS008450|
Greater Middle Eastern Ancestry|
1,186 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0603 [0.0029, 0.1173] sex, age, birth date, deprivation index, 16 PCs —
PPM011537 PSS008230|
South Asian Ancestry|
6,194 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0182 [-0.0067, 0.0432] sex, age, birth date, deprivation index, 16 PCs —
PPM011538 PSS007795|
African Ancestry|
2,441 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0131 [-0.0268, 0.0529] sex, age, birth date, deprivation index, 16 PCs —
PPM011539 PSS008899|
African Ancestry|
3,882 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Sarcoidosis — — Partial Correlation (partial-r): 0.0187 [-0.0128, 0.0502] 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
PSS009348 — — 19,670 individuals — European UK (+ Ireland) UKB —
PSS008676 — — 6,565 individuals — European Italy (South Europe) UKB —
PSS008230 — — 6,194 individuals — South Asian India (South Asia) UKB —
PSS008450 — — 1,186 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS007795 — — 2,441 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009122 — — 4,059 individuals — European Poland (NE Europe) UKB —
PSS008899 — — 3,882 individuals — African unspecified Nigeria (West Africa) UKB —