PGS Catalog - PGS003544 / Monocyte count (Polygenic Score)

Polygenic Score (PGS) ID: PGS003544

Predicted Trait
Reported Trait	Monocyte count
Mapped Trait(s)	monocyte count (EFO_0005091)

Released in PGS Catalog: April 12, 2023

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Terms and Licenses

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	cont-decay-log_monocyte
Development Method
Name	LDpred2-auto
Parameters	vec_p_init = seq_log(1e^-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build	GRCh37
Number of Variants	979,739
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000457
Citation (link to publication)	Ding Y et al. bioRxiv (2022) Preprint

Ancestry Distribution
Score Development/Training	European: 100% 359,067 individuals (100%)
PGS Evaluation	European: 44.4% African: 22.2% East Asian: 11.1% Greater Middle Eastern: 11.1% South Asian: 11.1% 9 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
—	359,067 individuals, 0.46 % Male samples	European	UKB	—	Mean = 56.9 years Sd = 8.0 years	—	white British	—

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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
PPM017472	PSS010909\| European Ancestry\| 19,376 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.15	sex, age, deprivation index, PC1-16	—
PPM017556	PSS010825\| European Ancestry\| 3,982 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.14	sex, age, deprivation index, PC1-16	—
PPM017640	PSS010657\| European Ancestry\| 6,264 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.13	sex, age, deprivation index, PC1-16	—
PPM017724	PSS010573\| Greater Middle Eastern Ancestry\| 1,121 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.14	sex, age, deprivation index, PC1-16	—
PPM017808	PSS010237\| European Ancestry\| 2,256 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.14	sex, age, deprivation index, PC1-16	—
PPM017892	PSS010489\| South Asian Ancestry\| 6,008 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.1	sex, age, deprivation index, PC1-16	—
PPM017976	PSS010405\| East Asian Ancestry\| 1,748 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.07	sex, age, deprivation index, PC1-16	—
PPM018060	PSS010321\| African Ancestry\| 2,323 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.04	sex, age, deprivation index, PC1-16	—
PPM018144	PSS010741\| African Ancestry\| 3,670 individuals	PGP000457 \| Ding Y et al. bioRxiv (2022) \|Pre	Reported Trait: Monocyte count	—	—	partial-R2: 0.03	sex, age, deprivation index, PC1-16	—

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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
PSS010237	—	—	2,256 individuals, 45.0 % Male samples	Mean = 58.0 years Sd = 7.1 years	European	Ashkenazi	UKB	—
PSS010321	—	—	2,323 individuals, 36.0 % Male samples	Mean = 52.4 years Sd = 8.0 years	African American or Afro-Caribbean	Caribbean	UKB	—
PSS010405	—	—	1,748 individuals, 33.0 % Male samples	Mean = 52.5 years Sd = 7.8 years	East Asian	Chinese	UKB	—
PSS010489	—	—	6,008 individuals, 55.0 % Male samples	Mean = 53.3 years Sd = 8.4 years	South Asian	Indian	UKB	—
PSS010573	—	—	1,121 individuals, 60.0 % Male samples	Mean = 52.0 years Sd = 8.0 years	Greater Middle Eastern (Middle Eastern, North African or Persian)	Iranian	UKB	—
PSS010657	—	—	6,264 individuals, 45.0 % Male samples	Mean = 54.5 years Sd = 8.4 years	European	Italian	UKB	—
PSS010741	—	—	3,670 individuals, 47.0 % Male samples	Mean = 51.9 years Sd = 8.1 years	African unspecified	Nigerian	UKB	—
PSS010825	—	—	3,982 individuals, 38.0 % Male samples	Mean = 54.3 years Sd = 7.5 years	European	Polish	UKB	—
PSS010909	—	—	19,376 individuals, 46.0 % Male samples	Mean = 56.9 years Sd = 7.9 years	European	white British	UKB	—

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