Polygenic Score (PGS) ID: PGS000988

Predicted Trait
Reported Trait High light scatter reticulocyte percentage
Mapped Trait(s) reticulocyte measurement (EFO_0010700)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30290
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_INI30290
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 7,184
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%
258,164 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
— 258,164 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
PPM007708 PSS007036|
African Ancestry|
5,974 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte % — — R²: 0.02767 [0.0198, 0.03553]
Incremental R2 (full-covars): 0.01965
PGS R2 (no covariates): 0.01997 [0.01324, 0.0267]		 age, sex, UKB array type, Genotype PCs —
PPM007709 PSS007037|
East Asian Ancestry|
1,623 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte % — — R²: 0.05671 [0.03542, 0.07799]
Incremental R2 (full-covars): 0.04573
PGS R2 (no covariates): 0.04876 [0.02885, 0.06866]		 age, sex, UKB array type, Genotype PCs —
PPM007710 PSS007038|
European Ancestry|
23,681 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte % — — R²: 0.08594 [0.07929, 0.0926]
Incremental R2 (full-covars): 0.07798
PGS R2 (no covariates): 0.07863 [0.07222, 0.08505]		 age, sex, UKB array type, Genotype PCs —
PPM007711 PSS007039|
South Asian Ancestry|
7,321 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte % — — R²: 0.07357 [0.06245, 0.0847]
Incremental R2 (full-covars): 0.06049
PGS R2 (no covariates): 0.06609 [0.05546, 0.07672]		 age, sex, UKB array type, Genotype PCs —
PPM007712 PSS007040|
European Ancestry|
64,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte % — — R²: 0.01671 [0.0148, 0.01863]
Incremental R2 (full-covars): 0.01605
PGS R2 (no covariates): 0.016 [0.01412, 0.01788]		 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
PSS007036 — — 5,974 individuals — African unspecified — UKB —
PSS007037 — — 1,623 individuals — East Asian — UKB —
PSS007038 — — 23,681 individuals — European non-white British ancestry UKB —
PSS007039 — — 7,321 individuals — South Asian — UKB —
PSS007040 — — 64,524 individuals — European white British ancestry UKB Testing cohort (heldout set)