Polygenic Score (PGS) ID: PGS002203

Predicted Trait
Reported Trait Lymphocyte percentage
Mapped Trait(s) lymphocyte percentage of leukocytes (EFO_0007993)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_lymphocyte_perc
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 775,312
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
PPM012471 PSS009473|
European Ancestry|
19,383 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.3116 [0.2989, 0.3243] sex, age, birth date, deprivation index, 16 PCs —
PPM012472 PSS009247|
European Ancestry|
3,992 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.2932 [0.2645, 0.3213] sex, age, birth date, deprivation index, 16 PCs —
PPM012473 PSS008801|
European Ancestry|
6,417 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.2976 [0.2751, 0.3198] sex, age, birth date, deprivation index, 16 PCs —
PPM012474 PSS008575|
Greater Middle Eastern Ancestry|
1,150 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.2842 [0.2297, 0.3369] sex, age, birth date, deprivation index, 16 PCs —
PPM012475 PSS008353|
South Asian Ancestry|
6,056 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.2664 [0.2428, 0.2897] sex, age, birth date, deprivation index, 16 PCs —
PPM012476 PSS008130|
East Asian Ancestry|
1,761 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.2567 [0.2122, 0.3] sex, age, birth date, deprivation index, 16 PCs —
PPM012477 PSS007917|
African Ancestry|
2,337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.1725 [0.1327, 0.2117] sex, age, birth date, deprivation index, 16 PCs —
PPM012478 PSS009021|
African Ancestry|
3,695 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.164 [0.1324, 0.1953] 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
PSS008801 — — 6,417 individuals — European Italy (South Europe) UKB —
PSS007917 — — 2,337 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008575 — — 1,150 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009473 — — 19,383 individuals — European UK (+ Ireland) UKB —
PSS009021 — — 3,695 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009247 — — 3,992 individuals — European Poland (NE Europe) UKB —
PSS008353 — — 6,056 individuals — South Asian India (South Asia) UKB —
PSS008130 — — 1,761 individuals — East Asian China (East Asia) UKB —