Polygenic Score (PGS) ID: PGS000113

Predicted Trait
Reported Trait White blood cell count
Mapped Trait(s) leukocyte count (EFO_0004308)
Additional Trait Information WBC#
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name wbc
Development Method
Name Regularized Regression (Elastic Net)
Parameters Bi-allelic variants (MAF > 0.01, INFO > 0.4, missingness rate < 0.1) with LD thinning (r2 threshold = 0.5)
Variants
Original Genome Build GRCh37
Number of Variants 28,383
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000051
Citation (link to publication) Xu Y et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
408,032 individuals (100%)
Score Development/Training
European: 100%
326,426 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 408,032 individuals,
46.0 % Male samples
 European UKB
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
— 326,426 individuals,
46.0 % Male samples
 European UKB — Mean = 57.23 years
Range = [39.66, 72.91] years		 — — —

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
PPM000258 PSS000178|
European Ancestry|
81,606 individuals
 PGP000051 |
Xu Y et al. Cell Genom (2022)
 Reported Trait: White blood cell count — — Pearson correlation coefficent (r): 0.39876 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)
PPM000259 PSS000152|
European Ancestry|
40,466 individuals
 PGP000051 |
Xu Y et al. Cell Genom (2022)
 Reported Trait: White blood cell count — — Pearson correlation coefficent (r): 0.38866 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
PSS000152 — — 40,466 individuals,
49.0 % Male samples
 Mean = 43.84 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS000178 — — 81,606 individuals,
46.0 % Male samples
 Mean = 57.23 years
Range = [38.87, 70.97] years		 European — UKB —