Polygenic Score (PGS) ID: PGS001962

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-PLR_log_leukocyte
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 80,228
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010571 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): 0.3641 [0.3518, 0.3762] sex, age, birth date, deprivation index, 16 PCs
PPM010572 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): 0.3304 [0.3024, 0.3578] sex, age, birth date, deprivation index, 16 PCs
PPM010574 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): 0.2724 [0.2177, 0.3255] sex, age, birth date, deprivation index, 16 PCs
PPM010575 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): 0.3155 [0.2926, 0.338] sex, age, birth date, deprivation index, 16 PCs
PPM010576 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): 0.2467 [0.2021, 0.2903] sex, age, birth date, deprivation index, 16 PCs
PPM010577 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): 0.1956 [0.1562, 0.2344] sex, age, birth date, deprivation index, 16 PCs
PPM010578 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): 0.1532 [0.1215, 0.1845] sex, age, birth date, deprivation index, 16 PCs
PPM010573 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): 0.3374 [0.3155, 0.3589] 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
PSS008331 6,078 individuals South Asian India (South Asia) UKB
PSS008108 1,762 individuals East Asian China (East Asia) UKB
PSS009451 19,419 individuals European UK (+ Ireland) UKB
PSS008779 6,437 individuals European Italy (South Europe) UKB
PSS007895 2,343 individuals African American or Afro-Caribbean Carribean UKB