Polygenic Score (PGS) ID: PGS002650

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.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 406,785
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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 321,608 individuals European UKB

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
PPM014513 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 when combined with BOLT-LMM vs. covariates alone): 0.1032 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_HIGH_LIGHT_SCATTER_RETICULOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014366 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 when combined with BOLT-LMM vs. covariates alone): 0.0563 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_HIGH_LIGHT_SCATTER_RETICULOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014415 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 when combined with BOLT-LMM vs. covariates alone): 0.1068 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_HIGH_LIGHT_SCATTER_RETICULOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014464 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 when combined with BOLT-LMM vs. covariates alone): 0.1606 age, sex, age*sex, assessment center, genotyping array, 10 PCs See blood_HIGH_LIGHT_SCATTER_RETICULOCYTE_COUNT.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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
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 —