Polygenic Score (PGS) ID: PGS000104

Predicted Trait
Reported Trait Mean platelet volume
Mapped Trait(s) mean platelet volume (EFO_0004584)
Additional Trait Information MPV
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name mpv
Variants
Original Genome Build GRCh37
Number of Variants 681
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%
391,598 individuals (100%)
Score Development/Training
European: 100%
313,278 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
391,598 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
313,278 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [39.66, 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
PPM000240 PSS000169|
European Ancestry|
78,320 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Mean platelet volume Pearson correlation coefficent (r): 0.5811 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)
PPM000241 PSS000143|
European Ancestry|
37,224 individuals
PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre
Reported Trait: Mean platelet volume Pearson correlation coefficent (r): 0.5759 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
PSS000143 37,224 individuals,
50.0 % Male samples
Mean = 43.8 years
Range = [18.0, 75.7] years
European INTERVAL
PSS000169 78,320 individuals,
46.0 % Male samples
Mean = 57.26 years
Range = [38.87, 70.99] years
European UKB