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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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
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 —

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
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 —
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 —
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 —

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