Polygenic Score (PGS) ID: PGS003549

Predicted Trait
Reported Trait Platelet distribution width
Mapped Trait(s) platelet component distribution width (EFO_0007984)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_platelet_width
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
PPM017477 PSS010915|
European Ancestry|
19,418 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.21 sex, age, deprivation index, PC1-16 —
PPM017561 PSS010831|
European Ancestry|
3,991 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.21 sex, age, deprivation index, PC1-16 —
PPM017645 PSS010663|
European Ancestry|
6,278 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.19 sex, age, deprivation index, PC1-16 —
PPM017729 PSS010579|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017897 PSS010495|
South Asian Ancestry|
6,026 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.18 sex, age, deprivation index, PC1-16 —
PPM017981 PSS010411|
East Asian Ancestry|
1,750 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM018065 PSS010327|
African Ancestry|
2,330 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM018149 PSS010747|
African Ancestry|
3,682 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017813 PSS010243|
European Ancestry|
2,264 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet distribution width — — partial-R2: 0.16 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
PSS010495 — — 6,026 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010915 — — 19,418 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010243 — — 2,264 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010663 — — 6,278 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010411 — — 1,750 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010831 — — 3,991 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010579 — — 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 —
PSS010327 — — 2,330 individuals,
37.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010747 — — 3,682 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —