Polygenic Score (PGS) ID: PGS003548

Predicted Trait
Reported Trait Mean platelet (thrombocyte) volume
Mapped Trait(s) mean platelet volume (EFO_0004584)
Released in PGS Catalog: April 12, 2023
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name cont-decay-log_platelet_volume
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
359,833 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
359,833 individuals,
0.46 % Male samples
European UKB Mean = 56.9 years
Sd = 8.0 years
white British

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
PPM017560 PSS010829|
European Ancestry|
3,991 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.35 sex, age, deprivation index, PC1-16
PPM017644 PSS010661|
European Ancestry|
6,278 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.31 sex, age, deprivation index, PC1-16
PPM017812 PSS010241|
European Ancestry|
2,264 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.28 sex, age, deprivation index, PC1-16
PPM017896 PSS010493|
South Asian Ancestry|
6,026 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.26 sex, age, deprivation index, PC1-16
PPM017980 PSS010409|
East Asian Ancestry|
1,750 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.19 sex, age, deprivation index, PC1-16
PPM018064 PSS010325|
African Ancestry|
2,330 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.1 sex, age, deprivation index, PC1-16
PPM018148 PSS010745|
African Ancestry|
3,682 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.09 sex, age, deprivation index, PC1-16
PPM017476 PSS010913|
European Ancestry|
19,418 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.34 sex, age, deprivation index, PC1-16
PPM017728 PSS010577|
Greater Middle Eastern Ancestry|
1,123 individuals
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre
Reported Trait: Mean platelet (thrombocyte) volume partial-R2: 0.26 sex, age, deprivation index, PC1-16

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
PSS010241 2,264 individuals,
45.0 % Male samples
Mean = 58.0 years
Sd = 7.1 years
European Ashkenazi UKB
PSS010913 19,418 individuals,
46.0 % Male samples
Mean = 56.9 years
Sd = 7.9 years
European white British UKB
PSS010661 6,278 individuals,
45.0 % Male samples
Mean = 54.5 years
Sd = 8.4 years
European Italian UKB
PSS010409 1,750 individuals,
33.0 % Male samples
Mean = 52.5 years
Sd = 7.8 years
East Asian Chinese UKB
PSS010829 3,991 individuals,
38.0 % Male samples
Mean = 54.3 years
Sd = 7.5 years
European Polish UKB
PSS010577 1,123 individuals,
59.0 % Male samples
Mean = 52.0 years
Sd = 8.0 years
Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB
PSS010325 2,330 individuals,
37.0 % Male samples
Mean = 52.4 years
Sd = 8.0 years
African American or Afro-Caribbean Caribbean UKB
PSS010745 3,682 individuals,
47.0 % Male samples
Mean = 51.9 years
Sd = 8.1 years
African unspecified Nigerian UKB
PSS010493 6,026 individuals,
55.0 % Male samples
Mean = 53.3 years
Sd = 8.4 years
South Asian Indian UKB