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. medRxiv (2021) Preprint
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
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
258,164 individuals European white British ancestry UKB 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. medRxiv (2021)
|Pre
Reported Trait: Immature reticulocyte fraction : 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. medRxiv (2021)
|Pre
Reported Trait: Immature reticulocyte fraction : 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. medRxiv (2021)
|Pre
Reported Trait: Immature reticulocyte fraction : 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. medRxiv (2021)
|Pre
Reported Trait: Immature reticulocyte fraction : 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. medRxiv (2021)
|Pre
Reported Trait: Immature reticulocyte fraction : 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)