Polygenic Score (PGS) ID: PGS002180

Predicted Trait
Reported Trait White blood cell (leukocyte) count
Mapped Trait(s) leukocyte count (EFO_0004308)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_leukocyte
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 846,337
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
PPM012287 PSS009451|
European Ancestry|
19,419 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.3596 [0.3473, 0.3718] sex, age, birth date, deprivation index, 16 PCs —
PPM012288 PSS009225|
European Ancestry|
4,002 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.3332 [0.3053, 0.3605] sex, age, birth date, deprivation index, 16 PCs —
PPM012289 PSS008779|
European Ancestry|
6,437 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.3368 [0.3149, 0.3583] sex, age, birth date, deprivation index, 16 PCs —
PPM012290 PSS008553|
Greater Middle Eastern Ancestry|
1,153 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.2706 [0.2158, 0.3237] sex, age, birth date, deprivation index, 16 PCs —
PPM012291 PSS008331|
South Asian Ancestry|
6,078 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.3147 [0.2919, 0.3372] sex, age, birth date, deprivation index, 16 PCs —
PPM012292 PSS008108|
East Asian Ancestry|
1,762 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.2454 [0.2007, 0.289] sex, age, birth date, deprivation index, 16 PCs —
PPM012293 PSS007895|
African Ancestry|
2,343 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.1863 [0.1467, 0.2253] sex, age, birth date, deprivation index, 16 PCs —
PPM012294 PSS008999|
African Ancestry|
3,711 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: White blood cell (leukocyte) count — — Partial Correlation (partial-r): 0.1563 [0.1247, 0.1876] 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
PSS008999 — — 3,711 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008553 — — 1,153 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009225 — — 4,002 individuals — European Poland (NE Europe) UKB —
PSS008779 — — 6,437 individuals — European Italy (South Europe) UKB —
PSS008331 — — 6,078 individuals — South Asian India (South Asia) UKB —
PSS009451 — — 19,419 individuals — European UK (+ Ireland) UKB —
PSS008108 — — 1,762 individuals — East Asian China (East Asia) UKB —
PSS007895 — — 2,343 individuals — African American or Afro-Caribbean Carribean UKB —