Polygenic Score (PGS) ID: PGS001528

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30250
Released in PGS Catalog: Nov. 25, 2021
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 GBE_INI30250
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,262
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%
258,297 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
— 258,297 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM007061 PSS007022|
East Asian Ancestry|
1,623 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte count — — R²: 0.07592 [0.05179, 0.10005]
Incremental R2 (full-covars): 0.04581
PGS R2 (no covariates): 0.04535 [0.02608, 0.06461]		 age, sex, UKB array type, Genotype PCs —
PPM007062 PSS007023|
European Ancestry|
23,688 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte count — — R²: 0.04398 [0.039, 0.04896]
Incremental R2 (full-covars): 0.0298
PGS R2 (no covariates): 0.03007 [0.02589, 0.03425]		 age, sex, UKB array type, Genotype PCs —
PPM007063 PSS007024|
South Asian Ancestry|
7,323 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte count — — R²: 0.05148 [0.04195, 0.06101]
Incremental R2 (full-covars): 0.03077
PGS R2 (no covariates): 0.03212 [0.02444, 0.0398]		 age, sex, UKB array type, Genotype PCs —
PPM007060 PSS007021|
African Ancestry|
5,974 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte count — — R²: 0.03089 [0.02261, 0.03917]
Incremental R2 (full-covars): 0.01205
PGS R2 (no covariates): 0.01388 [0.00823, 0.01953]		 age, sex, UKB array type, Genotype PCs —
PPM007064 PSS007025|
European Ancestry|
64,570 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte count — — R²: 0.0518 [0.04854, 0.05506]
Incremental R2 (full-covars): 0.03968
PGS R2 (no covariates): 0.03966 [0.03677, 0.04254]		 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
PSS007021 — — 5,974 individuals — African unspecified — UKB —
PSS007022 — — 1,623 individuals — East Asian — UKB —
PSS007023 — — 23,688 individuals — European non-white British ancestry UKB —
PSS007024 — — 7,323 individuals — South Asian — UKB —
PSS007025 — — 64,570 individuals — European white British ancestry UKB Testing cohort (heldout set)