Polygenic Score (PGS) ID: PGS003557

Predicted Trait
Reported Trait Lymphocyte percentage
Mapped Trait(s) lymphocyte percentage of leukocytes (EFO_0007993)
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-lymphocyte_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%
358,940 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
— 358,940 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
PPM017905 PSS010503|
South Asian Ancestry|
6,004 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017485 PSS010923|
European Ancestry|
19,370 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017569 PSS010839|
European Ancestry|
3,981 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017737 PSS010587|
Greater Middle Eastern Ancestry|
1,120 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017821 PSS010251|
European Ancestry|
2,258 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017989 PSS010419|
East Asian Ancestry|
1,749 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018073 PSS010335|
African Ancestry|
2,324 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018157 PSS010755|
African Ancestry|
3,666 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017653 PSS010671|
European Ancestry|
6,258 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte 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
PSS010335 — — 2,324 individuals,
36.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010755 — — 3,666 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010503 — — 6,004 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010251 — — 2,258 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010923 — — 19,370 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010671 — — 6,258 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010419 — — 1,749 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010839 — — 3,981 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010587 — — 1,120 individuals,
59.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —