Polygenic Score (PGS) ID: PGS002183

Predicted Trait
Reported Trait Lymphocyte count
Mapped Trait(s) lymphocyte count (EFO_0004587)
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_lymphocyte
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 814,921
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
PPM012311 PSS009454|
European Ancestry|
19,387 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.3574 [0.3451, 0.3697] sex, age, birth date, deprivation index, 16 PCs —
PPM012312 PSS009228|
European Ancestry|
3,993 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.3369 [0.3091, 0.3642] sex, age, birth date, deprivation index, 16 PCs —
PPM012314 PSS008556|
Greater Middle Eastern Ancestry|
1,150 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.2968 [0.2427, 0.3491] sex, age, birth date, deprivation index, 16 PCs —
PPM012315 PSS008334|
South Asian Ancestry|
6,058 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.2945 [0.2713, 0.3173] sex, age, birth date, deprivation index, 16 PCs —
PPM012316 PSS008111|
East Asian Ancestry|
1,761 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.2745 [0.2305, 0.3174] sex, age, birth date, deprivation index, 16 PCs —
PPM012317 PSS007898|
African Ancestry|
2,337 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.1609 [0.121, 0.2003] sex, age, birth date, deprivation index, 16 PCs —
PPM012318 PSS009002|
African Ancestry|
3,699 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.1618 [0.1302, 0.1931] sex, age, birth date, deprivation index, 16 PCs —
PPM012313 PSS008782|
European Ancestry|
6,421 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte count — — Partial Correlation (partial-r): 0.3319 [0.31, 0.3536] 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
PSS009002 — — 3,699 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009228 — — 3,993 individuals — European Poland (NE Europe) UKB —
PSS008556 — — 1,150 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008334 — — 6,058 individuals — South Asian India (South Asia) UKB —
PSS009454 — — 19,387 individuals — European UK (+ Ireland) UKB —
PSS008111 — — 1,761 individuals — East Asian China (East Asia) UKB —
PSS008782 — — 6,421 individuals — European Italy (South Europe) UKB —
PSS007898 — — 2,337 individuals — African American or Afro-Caribbean Carribean UKB —