Polygenic Score (PGS) ID: PGS001239

Predicted Trait
Reported Trait White blood cell count
Mapped Trait(s) leukocyte count (EFO_0004308)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30000
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name GBE_INI30000
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 13,785
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
262,322 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
— 262,322 individuals European UKB — — — white British ancestry —

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
PPM008704 PSS006891|
African Ancestry|
6,139 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: White blood cell count — — R²: 0.05282 [0.04224, 0.0634]
Incremental R2 (full-covars): 0.00963
PGS R2 (no covariates): 0.01451 [0.00874, 0.02028]		 age, sex, UKB array type, Genotype PCs —
PPM008705 PSS006892|
East Asian Ancestry|
1,655 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: White blood cell count — — R²: 0.07596 [0.05182, 0.10009]
Incremental R2 (full-covars): 0.0496
PGS R2 (no covariates): 0.05069 [0.03044, 0.07095]		 age, sex, UKB array type, Genotype PCs —
PPM008706 PSS006893|
European Ancestry|
24,174 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: White blood cell count — — R²: 0.08839 [0.08166, 0.09513]
Incremental R2 (full-covars): 0.07763
PGS R2 (no covariates): 0.08212 [0.07559, 0.08865]		 age, sex, UKB array type, Genotype PCs —
PPM008707 PSS006894|
South Asian Ancestry|
7,520 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: White blood cell count — — R²: 0.07166 [0.06066, 0.08267]
Incremental R2 (full-covars): 0.06404
PGS R2 (no covariates): 0.06438 [0.05387, 0.07489]		 age, sex, UKB array type, Genotype PCs —
PPM008708 PSS006895|
European Ancestry|
65,638 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: White blood cell count — — R²: 0.0777 [0.07382, 0.08158]
Incremental R2 (full-covars): 0.07177
PGS R2 (no covariates): 0.07264 [0.06887, 0.07641]		 age, sex, UKB array type, Genotype PCs —

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
PSS006891 — — 6,139 individuals — African unspecified — UKB —
PSS006892 — — 1,655 individuals — East Asian — UKB —
PSS006893 — — 24,174 individuals — European non-white British ancestry UKB —
PSS006894 — — 7,520 individuals — South Asian — UKB —
PSS006895 — — 65,638 individuals — European white British ancestry UKB Testing cohort (heldout set)