Polygenic Score (PGS) ID: PGS001965

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-PLR_log_lymphocyte
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 76,535
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
PPM010595 PSS009454|
European Ancestry|
19,387 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte count Partial Correlation (partial-r): 0.3636 [0.3514, 0.3758] sex, age, birth date, deprivation index, 16 PCs
PPM010596 PSS009228|
European Ancestry|
3,993 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte count Partial Correlation (partial-r): 0.3456 [0.3179, 0.3727] sex, age, birth date, deprivation index, 16 PCs
PPM010597 PSS008782|
European Ancestry|
6,421 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte count Partial Correlation (partial-r): 0.3335 [0.3115, 0.3551] sex, age, birth date, deprivation index, 16 PCs
PPM010598 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): 0.3153 [0.2618, 0.3669] sex, age, birth date, deprivation index, 16 PCs
PPM010599 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): 0.301 [0.2779, 0.3238] sex, age, birth date, deprivation index, 16 PCs
PPM010600 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): 0.2717 [0.2277, 0.3147] sex, age, birth date, deprivation index, 16 PCs
PPM010602 PSS009002|
African Ancestry|
3,699 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte count Partial Correlation (partial-r): 0.1702 [0.1386, 0.2014] sex, age, birth date, deprivation index, 16 PCs
PPM010601 PSS007898|
African Ancestry|
2,337 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte count Partial Correlation (partial-r): 0.167 [0.1271, 0.2063] 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
PSS008782 6,421 individuals European Italy (South Europe) UKB
PSS008111 1,761 individuals East Asian China (East Asia) UKB
PSS007898 2,337 individuals African American or Afro-Caribbean Carribean UKB