Polygenic Score (PGS) ID: PGS000111

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information RET#
Released in PGS: Feb. 19, 2020

Score Details

Score Construction
PGS Name ret
Variants
Original Genome Build GRCh37
Number of Variants 590
Development Method
Name Regularized Regression (Elastic Net)
Parameters Variants included in the regression were selected according to their GWAS significance (p < 8.31e-9) and a subsequent conditional analysis (r2 threshold = 0.9); effect sizes of variants are estimated by regularized regression
PGS Source
PGS Catalog Publication (PGP) ID PGP000051
Citation (link to publication) Xu Y et al. bioRxiv (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
396,720 individuals,
46.0 % Male samples
European
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
317,376 individuals,
46.0 % Male samples
Mean = 57.21 years
Range = [38.87, 72.44] years
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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000255 PSS000150 PGP000051
Xu Y et al. (2020)
Reported Trait: Reticulocyte count Pearson correlation coefficent (r): 0.4069 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)
PPM000254 PSS000176 PGP000051
Xu Y et al. (2020)
Reported Trait: Reticulocyte count Pearson correlation coefficent (r): 0.4241 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) UKB Testing Set - these samples were held out from Score Development (regression training) but overlap with the samples used for variant selection (GWAS)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000150 40,253 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000176 79,344 individuals,
46.0 % Male samples
Mean = 57.29 years
Range = [39.66, 72.91] years
European UKB