Polygenic Score (PGS) ID: PGS003546

Predicted Trait
Reported Trait Platelet count
Mapped Trait(s) platelet count (EFO_0004309)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_platelet
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%
359,792 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
— 359,792 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
PPM017474 PSS010911|
European Ancestry|
19,418 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.23 sex, age, deprivation index, PC1-16 —
PPM017558 PSS010827|
European Ancestry|
3,991 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.22 sex, age, deprivation index, PC1-16 —
PPM017642 PSS010659|
European Ancestry|
6,277 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.21 sex, age, deprivation index, PC1-16 —
PPM017726 PSS010575|
Greater Middle Eastern Ancestry|
1,123 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.22 sex, age, deprivation index, PC1-16 —
PPM017810 PSS010239|
European Ancestry|
2,263 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017894 PSS010491|
South Asian Ancestry|
6,024 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.17 sex, age, deprivation index, PC1-16 —
PPM017978 PSS010407|
East Asian Ancestry|
1,750 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM018062 PSS010323|
African Ancestry|
2,330 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM018146 PSS010743|
African Ancestry|
3,682 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Platelet count — — partial-R2: 0.06 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
PSS010911 — — 19,418 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS010239 — — 2,263 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010659 — — 6,277 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS010407 — — 1,750 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010827 — — 3,991 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS010575 — — 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 —
PSS010323 — — 2,330 individuals,
37.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS010743 — — 3,682 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010491 — — 6,024 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —