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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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 —