Polygenic Score (PGS) ID: PGS003566

Predicted Trait
Reported Trait Neutrophil percentage
Mapped Trait(s) neutrophil percentage of leukocytes (EFO_0007990)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name cont-decay-neutrophil_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%
358,504 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
— 358,504 individuals,
0.46 % Male samples
 European UKB — Mean = 56.8 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
PPM017494 PSS010933|
European Ancestry|
19,342 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017662 PSS010681|
European Ancestry|
6,254 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017746 PSS010597|
Greater Middle Eastern Ancestry|
1,117 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017830 PSS010261|
European Ancestry|
2,256 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017914 PSS010513|
South Asian Ancestry|
6,003 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017998 PSS010429|
East Asian Ancestry|
1,748 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018082 PSS010345|
African Ancestry|
2,321 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM018166 PSS010765|
African Ancestry|
3,652 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017578 PSS010849|
European Ancestry|
3,977 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Neutrophil percentage — — partial-R2: 0.09 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
PSS010849 — — 3,977 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010597 — — 1,117 individuals,
59.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010345 — — 2,321 individuals,
36.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010933 — — 19,342 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010765 — — 3,652 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010513 — — 6,003 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010261 — — 2,256 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010681 — — 6,254 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010429 — — 1,748 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —