Polygenic Score (PGS) ID: PGS003924

Predicted Trait
Reported Trait White blood cell (leukocyte) count
Mapped Trait(s) leukocyte count (EFO_0004308)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30000
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI30000
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 17,890
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000502
Citation (link to publication) Tanigawa Y et al. AJHG (2023)
Ancestry Distribution
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • South Asian
  • African
  • Additional Diverse Ancestries
316,081 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • Additional Diverse Ancestries
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
— 316,081 individuals European, South Asian, African unspecified, Other admixed ancestry UKB — — — European, South Asian, African unspecified, Other admixed 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
PPM018940 PSS011109|
European Ancestry|
2,813 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: White blood cell (leukocyte) count — — R²: 0.09098 [0.07103, 0.11094]
PGS R2 (no covariates): 0.07615 [0.05759, 0.0947]
Incremental R2 (full-covars): 0.07328		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018941 PSS011113|
South Asian Ancestry|
1,433 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: White blood cell (leukocyte) count — — R²: 0.09373 [0.06559, 0.12186]
PGS R2 (no covariates): 0.08974 [0.06208, 0.11739]
Incremental R2 (full-covars): 0.08665		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018942 PSS011155|
African Ancestry|
1,157 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: White blood cell (leukocyte) count — — R²: 0.05083 [0.02681, 0.07484]
PGS R2 (no covariates): 0.04407 [0.02155, 0.06659]
Incremental R2 (full-covars): 0.04309		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018943 PSS011166|
Multi-ancestry (excluding European)|
7,746 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: White blood cell (leukocyte) count — — R²: 0.09843 [0.08604, 0.11081]
PGS R2 (no covariates): 0.08243 [0.0709, 0.09397]
Incremental R2 (full-covars): 0.07062		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018939 PSS011136|
European Ancestry|
65,932 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: White blood cell (leukocyte) count — — R²: 0.08905 [0.08496, 0.09315]
PGS R2 (no covariates): 0.07643 [0.07259, 0.08028]
Incremental R2 (full-covars): 0.07561		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —

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
PSS011109 — — 2,813 individuals — European
(non-white British ancestry)		 — UKB —
PSS011113 — — 1,433 individuals — South Asian — UKB —
PSS011155 — — 1,157 individuals — African unspecified — UKB —
PSS011166 — — 7,746 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011136 — — 65,932 individuals — European
(white British ancestry)		 — UKB —