Polygenic Score (PGS) ID: PGS003562

Predicted Trait
Reported Trait Monocyte percentage
Mapped Trait(s) monocyte percentage of leukocytes (EFO_0007989)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-monocyte_perc
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%
356,386 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
— 356,386 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
PPM017574 PSS010845|
European Ancestry|
3,952 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017658 PSS010677|
European Ancestry|
6,213 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017826 PSS010257|
European Ancestry|
2,241 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.15 sex, age, deprivation index, PC1-16 —
PPM017910 PSS010509|
South Asian Ancestry|
5,958 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017994 PSS010425|
East Asian Ancestry|
1,732 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM018078 PSS010341|
African Ancestry|
2,285 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM018162 PSS010761|
African Ancestry|
3,634 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017490 PSS010929|
European Ancestry|
19,237 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.16 sex, age, deprivation index, PC1-16 —
PPM017742 PSS010593|
Greater Middle Eastern Ancestry|
1,114 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Monocyte percentage — — partial-R2: 0.16 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
PSS010593 — — 1,114 individuals,
60.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010341 — — 2,285 individuals,
37.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010761 — — 3,634 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010509 — — 5,958 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010257 — — 2,241 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010929 — — 19,237 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010677 — — 6,213 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010425 — — 1,732 individuals,
34.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010845 — — 3,952 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —