PGS Catalog - PGS002405 / High light scatter reticulocyte count (Polygenic Score)

Polygenic Score (PGS) ID: PGS002405

Predicted Trait
Reported Trait	High light scatter reticulocyte count
Mapped Trait(s)	reticulocyte count (EFO_0007986)
Additional Trait Information	High Light Scatter Retic. Count

Released in PGS Catalog: June 9, 2022

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Score Details

Score Construction
PGS Name	blood_HIGH_LIGHT_SCATTER_RETICULOCYTE_COUNT.P+T.0.0001
Development Method
Name	Pruning and Thresholding (P+T)
Parameters	p < 0.0001
Variants
Original Genome Build	GRCh37
Number of Variants	16,031
Effect Weight Type	beta

PGS Source
PGS Catalog Publication (PGP) ID	PGP000332
Citation (link to publication)	Weissbrod O et al. Nat Genet (2022)

Ancestry Distribution
Source of Variant Associations (GWAS)	European: 100% 321,608 individuals (100%)
PGS Evaluation	African: 25% East Asian: 25% European: 25% South Asian: 25% 4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)

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Study Identifiers	Sample Numbers	Sample Ancestry	Cohort(s)
—	321,608 individuals	European	UKB

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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.

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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
PPM013386	PSS009775\| African Ancestry\| 5,976 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: High Light Scatter Reticulocyte Count	—	—	Incremental R2 (full model vs. covariates alone): 0.0037	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013435	PSS009776\| East Asian Ancestry\| 881 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: High Light Scatter Reticulocyte Count	—	—	Incremental R2 (full model vs. covariates alone): 0.055	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013484	PSS009777\| European Ancestry\| 41,231 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: High Light Scatter Reticulocyte Count	—	—	Incremental R2 (full model vs. covariates alone): 0.0785	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—
PPM013533	PSS009778\| South Asian Ancestry\| 7,560 individuals	PGP000332 \| Weissbrod O et al. Nat Genet (2022)	Reported Trait: High Light Scatter Reticulocyte Count	—	—	Incremental R2 (full model vs. covariates alone): 0.05	age, sex, age*sex, assessment center, genotyping array, 10 PCs	—

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Evaluated Samples

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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
PSS009775	—	—	5,976 individuals	—	African unspecified	—	UKB	—
PSS009776	—	—	881 individuals	—	East Asian	—	UKB	—
PSS009777	—	—	41,231 individuals	—	European	Non-British European	UKB	—
PSS009778	—	—	7,560 individuals	—	South Asian	—	UKB	—

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