Polygenic Score (PGS) ID: PGS001406

Predicted Trait
Reported Trait High light scatter reticulocyte count
Mapped Trait(s) reticulocyte measurement (EFO_0010700)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30300
Released in PGS Catalog: Nov. 25, 2021
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Score Details

Score Construction
PGS Name GBE_INI30300
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 15,856
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 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
PPM007070 PSS007041|
African Ancestry|
5,974 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.03376 [0.02514, 0.04239]
Incremental R2 (full-covars): 0.02097
PGS R2 (no covariates): 0.02166 [0.01466, 0.02866]		 age, sex, UKB array type, Genotype PCs —
PPM007071 PSS007042|
East Asian Ancestry|
1,623 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.08784 [0.06222, 0.11346]
Incremental R2 (full-covars): 0.06019
PGS R2 (no covariates): 0.06306 [0.04077, 0.08536]		 age, sex, UKB array type, Genotype PCs —
PPM007072 PSS007043|
European Ancestry|
23,681 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.116 [0.10853, 0.12348]
Incremental R2 (full-covars): 0.09413
PGS R2 (no covariates): 0.09553 [0.08859, 0.10247]		 age, sex, UKB array type, Genotype PCs —
PPM007073 PSS007044|
South Asian Ancestry|
7,321 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.09799 [0.08549, 0.1105]
Incremental R2 (full-covars): 0.07113
PGS R2 (no covariates): 0.07659 [0.06528, 0.08791]		 age, sex, UKB array type, Genotype PCs —
PPM007074 PSS007045|
European Ancestry|
64,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.12733 [0.12263, 0.13203]
Incremental R2 (full-covars): 0.11178
PGS R2 (no covariates): 0.1113 [0.10683, 0.11578]		 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
PSS007041 — — 5,974 individuals — African unspecified — UKB —
PSS007042 — — 1,623 individuals — East Asian — UKB —
PSS007043 — — 23,681 individuals — European non-white British ancestry UKB —
PSS007044 — — 7,321 individuals — South Asian — UKB —
PSS007045 — — 64,524 individuals — European white British ancestry UKB Testing cohort (heldout set)