Polygenic Score (PGS) ID: PGS000989

Predicted Trait
Reported Trait Reticulocyte percentage
Mapped Trait(s) reticulocyte measurement (EFO_0010700)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30240
Released in PGS Catalog: Oct. 21, 2021
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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_INI30240
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6,251
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 —

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
PPM007715 PSS007018|
European Ancestry|
23,688 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte % — — R²: 0.0318 [0.02751, 0.03609]
Incremental R2 (full-covars): 0.02883
PGS R2 (no covariates): 0.02905 [0.02494, 0.03316]		 age, sex, UKB array type, Genotype PCs —
PPM007713 PSS007016|
African Ancestry|
5,974 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte % — — R²: 0.01993 [0.01321, 0.02666]
Incremental R2 (full-covars): 0.01309
PGS R2 (no covariates): 0.01384 [0.0082, 0.01948]		 age, sex, UKB array type, Genotype PCs —
PPM007714 PSS007017|
East Asian Ancestry|
1,623 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte % — — R²: 0.05032 [0.03013, 0.0705]
Incremental R2 (full-covars): 0.03871
PGS R2 (no covariates): 0.03842 [0.02056, 0.05628]		 age, sex, UKB array type, Genotype PCs —
PPM007716 PSS007019|
South Asian Ancestry|
7,323 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte % — — R²: 0.03312 [0.02533, 0.04091]
Incremental R2 (full-covars): 0.02678
PGS R2 (no covariates): 0.02784 [0.02066, 0.03502]		 age, sex, UKB array type, Genotype PCs —
PPM007717 PSS007020|
European Ancestry|
64,569 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Reticulocyte % — — R²: 0.02928 [0.02677, 0.03179]
Incremental R2 (full-covars): 0.02823
PGS R2 (no covariates): 0.02826 [0.0258, 0.03073]		 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
PSS007016 — — 5,974 individuals — African unspecified — UKB —
PSS007017 — — 1,623 individuals — East Asian — UKB —
PSS007018 — — 23,688 individuals — European non-white British ancestry UKB —
PSS007019 — — 7,323 individuals — South Asian — UKB —
PSS007020 — — 64,569 individuals — European white British ancestry UKB Testing cohort (heldout set)