Polygenic Score (PGS) ID: PGS000089

Predicted Trait
Reported Trait Basophil percentage of white cells
Mapped Trait(s) basophil percentage of leukocytes (EFO_0007992)
Additional Trait Information BASO%
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name baso_p
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 5,248
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%
404,532 individuals (100%)
Score Development/Training
European: 100%
323,626 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 404,532 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
— 323,626 individuals,
46.0 % Male samples
 European UKB — Mean = 57.23 years
Range = [38.87, 72.44] 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
PPM000210 PSS000154|
European Ancestry|
80,906 individuals
 PGP000051 |
Xu Y et al. Cell Genom (2022)
 Reported Trait: Basophil percentage of white cells — — Pearson correlation coefficent (r): 0.18838 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)
PPM000211 PSS000128|
European Ancestry|
40,133 individuals
 PGP000051 |
Xu Y et al. Cell Genom (2022)
 Reported Trait: Basophil percentage of white cells — — Pearson correlation coefficent (r): 0.17123 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
PSS000128 — — 40,133 individuals,
50.0 % Male samples
 Mean = 43.92 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS000154 — — 80,906 individuals,
46.0 % Male samples
 Mean = 57.2 years
Range = [40.18, 72.91] years		 European — UKB —