PGS Catalog - PGS001968 / Monocyte count (Polygenic Score)

Polygenic Score (PGS) ID: PGS001968

Predicted Trait
Reported Trait	Monocyte count
Mapped Trait(s)	monocyte count (EFO_0005091)
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_monocyte
Development Method
Name	Penalized regression (bigstatsr)
Parameters	HapMap3 variants
Variants
Original Genome Build	GRCh37
Number of Variants	46,673
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
PPM010619	PSS009457\| European Ancestry\| 19,384 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.4056 [0.3937, 0.4173]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010620	PSS009231\| European Ancestry\| 3,993 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.3829 [0.3561, 0.4091]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010621	PSS008785\| European Ancestry\| 6,423 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.3731 [0.3518, 0.394]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010622	PSS008559\| Greater Middle Eastern Ancestry\| 1,151 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.3791 [0.328, 0.4279]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010623	PSS008337\| South Asian Ancestry\| 6,060 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.3366 [0.314, 0.3588]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010624	PSS008114\| East Asian Ancestry\| 1,760 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.2771 [0.2332, 0.3199]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010625	PSS007901\| African Ancestry\| 2,336 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.2104 [0.1711, 0.249]	sex, age, birth date, deprivation index, 16 PCs	—
PPM010626	PSS009005\| African Ancestry\| 3,699 individuals	PGP000263 \| Privé F et al. Am J Hum Genet (2022)	Reported Trait: Monocyte count	—	—	Partial Correlation (partial-r): 0.1892 [0.1579, 0.2202]	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
PSS007901	—	—	2,336 individuals	—	African American or Afro-Caribbean	Carribean	UKB	—
PSS008114	—	—	1,760 individuals	—	East Asian	China (East Asia)	UKB	—
PSS008337	—	—	6,060 individuals	—	South Asian	India (South Asia)	UKB	—
PSS008559	—	—	1,151 individuals	—	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iran (Middle East)	UKB	—
PSS008785	—	—	6,423 individuals	—	European	Italy (South Europe)	UKB	—
PSS009005	—	—	3,699 individuals	—	African unspecified	Nigeria (West Africa)	UKB	—
PSS009231	—	—	3,993 individuals	—	European	Poland (NE Europe)	UKB	—
PSS009457	—	—	19,384 individuals	—	European	UK (+ Ireland)	UKB	—

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