Polygenic Score (PGS) ID: PGS001517

Predicted Trait
Reported Trait Platelet crit
Mapped Trait(s) platelet crit (EFO_0007985)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30090
Released in PGS Catalog: Nov. 25, 2021
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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 GBE_INI30090
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 20,910
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
262,211 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
— 262,211 individuals European UKB — — — white British ancestry Training + validation cohort (train_val)

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
PPM007040 PSS006951|
African Ancestry|
6,139 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Platelet crit — — R²: 0.1382 [0.12263, 0.15377]
Incremental R2 (full-covars): 0.02064
PGS R2 (no covariates): 0.0286 [0.02062, 0.03659]		 age, sex, UKB array type, Genotype PCs —
PPM007041 PSS006952|
East Asian Ancestry|
1,655 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Platelet crit — — R²: 0.15738 [0.1257, 0.18906]
Incremental R2 (full-covars): 0.08366
PGS R2 (no covariates): 0.07725 [0.05295, 0.10155]		 age, sex, UKB array type, Genotype PCs —
PPM007042 PSS006953|
European Ancestry|
24,171 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Platelet crit — — R²: 0.23874 [0.2295, 0.24797]
Incremental R2 (full-covars): 0.16467
PGS R2 (no covariates): 0.16697 [0.15852, 0.17543]		 age, sex, UKB array type, Genotype PCs —
PPM007043 PSS006954|
South Asian Ancestry|
7,519 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Platelet crit — — R²: 0.23898 [0.2225, 0.25545]
Incremental R2 (full-covars): 0.10472
PGS R2 (no covariates): 0.10873 [0.09572, 0.12174]		 age, sex, UKB array type, Genotype PCs —
PPM007044 PSS006955|
European Ancestry|
65,601 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Platelet crit — — R²: 0.24748 [0.24183, 0.25313]
Incremental R2 (full-covars): 0.16016
PGS R2 (no covariates): 0.16141 [0.15632, 0.16649]		 age, sex, UKB array type, Genotype PCs —

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
PSS006951 — — 6,139 individuals — African unspecified — UKB —
PSS006952 — — 1,655 individuals — East Asian — UKB —
PSS006953 — — 24,171 individuals — European non-white British ancestry UKB —
PSS006954 — — 7,519 individuals — South Asian — UKB —
PSS006955 — — 65,601 individuals — European white British ancestry UKB Testing cohort (heldout set)