| Predicted Trait | |
| Reported Trait | Reticulocyte fraction of red cells |
| Mapped Trait(s) | reticulocyte count (EFO_0007986) |
| Additional Trait Information | RET% |
| Score Construction | |
| PGS Name | ret_p |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 572 |
| 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 |
| Study Identifiers | Sample Numbers | Sample Ancestry |
|---|---|---|
| 396,811 individuals, 46.0 % Male samples |
European |
| Detailed Phenotype Description | Participant Follow-up Time | Sample Numbers | Age of Study Participants | Sample Ancestry | Additional Ancestry Description | Cohort(s) | Additional Sample/Cohort Information |
|---|---|---|---|---|---|---|---|
| — | — | 317,449 individuals, 46.0 % Male samples |
Mean = 57.23 years Range = [38.87, 72.44] years |
European | — | UKB | — |
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 the Model | PGS Performance: Other Relevant Information |
|---|---|---|---|---|---|---|---|---|
| PPM000257 | PSS000151 | PGP000051 Xu Y et al. (2020) Pre |
Reported Trait: Reticulocyte fraction of red cells | — | — | Pearson correlation coefficent (r): 0.423 | 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) | — |
| PPM000256 | PSS000177 | PGP000051 Xu Y et al. (2020) Pre |
Reported Trait: Reticulocyte fraction of red cells | — | — | Pearson correlation coefficent (r): 0.4316 | 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) |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000151 | — | — | 40,286 individuals, 49.0 % Male samples |
Mean = 43.84 years Range = [18.0, 76.4] years |
European | — | INTERVAL | — |
| PSS000177 | — | — | 79,362 individuals, 46.0 % Male samples |
Mean = 57.22 years Range = [39.66, 72.91] years |
European | — | UKB | — |