Polygenic Score (PGS) ID: PGS003940

Predicted Trait
Reported Trait Basophil count
Mapped Trait(s) basophil count (EFO_0005090)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30160
Released in PGS Catalog: Nov. 1, 2023
Download Score FTP directory
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 INI30160
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 4,184
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
315,523 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
— 315,523 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
PPM019019 PSS011139|
European Ancestry|
65,814 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.01943 [0.01737, 0.02149]
PGS R2 (no covariates): 0.01516 [0.01334, 0.01699]
Incremental R2 (full-covars): 0.01498		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019021 PSS011112|
South Asian Ancestry|
1,428 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.00683 [-0.00149, 0.01515]
PGS R2 (no covariates): 0.00551 [-0.00198, 0.013]
Incremental R2 (full-covars): 0.00504		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019020 PSS011110|
European Ancestry|
2,810 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.02167 [0.01119, 0.03216]
PGS R2 (no covariates): 0.01847 [0.00876, 0.02818]
Incremental R2 (full-covars): 0.01766		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019022 PSS011154|
African Ancestry|
1,154 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.00981 [-0.00119, 0.02082]
PGS R2 (no covariates): 0.00446 [-0.003, 0.01192]
Incremental R2 (full-covars): 0.00447		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019023 PSS011168|
Multi-ancestry (excluding European)|
7,732 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Basophil count — — R²: 0.02131 [0.01506, 0.02757]
PGS R2 (no covariates): 0.01354 [0.00851, 0.01856]
Incremental R2 (full-covars): 0.01229		 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
PSS011110 — — 2,810 individuals — European
(non-white British ancestry)		 — UKB —
PSS011112 — — 1,428 individuals — South Asian — UKB —
PSS011154 — — 1,154 individuals — African unspecified — UKB —
PSS011168 — — 7,732 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011139 — — 65,814 individuals — European
(white British ancestry)		 — UKB —