PGS Catalog - PGS001408 / Immature reticulocyte fraction (Polygenic Score)

Polygenic Score (PGS) ID: PGS001408

Predicted Trait
Reported Trait	Immature reticulocyte fraction
Mapped Trait(s)	Immature Reticulocyte Fraction Measurement (EFO_0009253)
Additional Trait Information	https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30280

Released in PGS Catalog: Nov. 25, 2021

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Score Details

Score Construction
PGS Name	GBE_INI30280
Development Method
Name	snpnet
Parameters	NR
Variants
Original Genome Build	GRCh37
Number of Variants	10,871
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
PPM007065	PSS007031\| African Ancestry\| 5,973 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Immature reticulocyte fraction	—	—	R²: 0.03195 [0.02354, 0.04036] Incremental R2 (full-covars): 0.01989 PGS R2 (no covariates): 0.01953 [0.01287, 0.02619]	age, sex, UKB array type, Genotype PCs	—
PPM007066	PSS007032\| East Asian Ancestry\| 1,623 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Immature reticulocyte fraction	—	—	R²: 0.04983 [0.02973, 0.06992] Incremental R2 (full-covars): 0.02998 PGS R2 (no covariates): 0.03394 [0.01708, 0.05081]	age, sex, UKB array type, Genotype PCs	—
PPM007067	PSS007033\| European Ancestry\| 23,680 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Immature reticulocyte fraction	—	—	R²: 0.10073 [0.09364, 0.10782] Incremental R2 (full-covars): 0.08989 PGS R2 (no covariates): 0.09045 [0.08366, 0.09725]	age, sex, UKB array type, Genotype PCs	—
PPM007068	PSS007034\| South Asian Ancestry\| 7,321 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Immature reticulocyte fraction	—	—	R²: 0.07122 [0.06025, 0.0822] Incremental R2 (full-covars): 0.05964 PGS R2 (no covariates): 0.06252 [0.05214, 0.0729]	age, sex, UKB array type, Genotype PCs	—
PPM007069	PSS007035\| European Ancestry\| 64,524 individuals	PGP000244 \| Tanigawa Y et al. PLoS Genet (2022)	Reported Trait: Immature reticulocyte fraction	—	—	R²: 0.09976 [0.09547, 0.10405] Incremental R2 (full-covars): 0.0902 PGS R2 (no covariates): 0.09063 [0.0865, 0.09477]	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
PSS007031	—	—	5,973 individuals	—	African unspecified	—	UKB	—
PSS007032	—	—	1,623 individuals	—	East Asian	—	UKB	—
PSS007033	—	—	23,680 individuals	—	European	non-white British ancestry	UKB	—
PSS007034	—	—	7,321 individuals	—	South Asian	—	UKB	—
PSS007035	—	—	64,524 individuals	—	European	white British ancestry	UKB	Testing cohort (heldout set)