PGS Catalog - PGS002183 / Lymphocyte count (Polygenic Score)

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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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

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

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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)	—

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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.

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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	—
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	—
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	—

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Evaluated Samples

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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
PSS007898	—	—	2,337 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS008111	—	—	1,761 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008334	—	—	6,058 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008556	—	—	1,150 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008782	—	—	6,421 individuals	—	European	Italy (South Europe)	UKB	—
PSS009002	—	—	3,699 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009228	—	—	3,993 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009454	—	—	19,387 individuals	—	European	UK (+ Ireland)	UKB	—

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