Polygenic Score (PGS) ID: PGS000098

Predicted Trait
Reported Trait Lymphocyte percentage of white cells
Mapped Trait(s) lymphocyte percentage of leukocytes (EFO_0007993)
Additional Trait Information LYMPH%
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name lymph_p
Variants
Original Genome Build GRCh37
Number of Variants 489
Development Method
Name Regularized Regression (Elastic Net)
Parameters Variants included in the regression were selected according to their GWAS significance (p < 8.31e-9) and a subsequent conditional analysis (r2 threshold = 0.9); effect sizes of variants are estimated by regularized regression
PGS Source
PGS Catalog Publication (PGP) ID PGP000051
Citation (link to publication) Xu Y et al. bioRxiv (2020) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
407,319 individuals (100%)
Score Development/Training
European: 100%
325,855 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
407,319 individuals,
46.0 % Male samples
European
Score Development/Training
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
325,855 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [38.87, 72.91] years
European UKB

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
PPM000228 PSS000163|
European Ancestry|
81,464 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Lymphocyte percentage of white cells Pearson correlation coefficent (r): 0.3046 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) UKB Testing Set - these samples were held out from Score Development (regression training) but overlap with the samples used for variant selection (GWAS)
PPM000229 PSS000137|
European Ancestry|
39,178 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Lymphocyte percentage of white cells Pearson correlation coefficent (r): 0.2817 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)

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
PSS000137 39,178 individuals,
50.0 % Male samples
Mean = 43.82 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000163 81,464 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [40.17, 71.1] years
European UKB