Polygenic Score (PGS) ID: PGS000094

Predicted Trait
Reported Trait High light scatter reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information HLSR#
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name hlr
Variants
Original Genome Build GRCh37
Number of Variants 605
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) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
400,334 individuals (100%)
Score Development/Training
European: 100%
320,267 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
400,334 individuals,
46.0 % Male samples
European
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
320,267 individuals,
46.0 % Male samples
Mean = 57.23 years
Range = [38.87, 72.91] 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)
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
PPM000220 PSS000159|
European Ancestry|
80,067 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte count Pearson correlation coefficent (r): 0.4294 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)
PPM000221 PSS000133|
European Ancestry|
40,244 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: High light scatter reticulocyte count Pearson correlation coefficent (r): 0.363 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)

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
PSS000133 40,244 individuals,
49.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000159 80,067 individuals,
46.0 % Male samples
Mean = 57.2 years
Range = [39.91, 70.52] years
European UKB