Polygenic Score (PGS) ID: PGS001200

Predicted Trait
Reported Trait Mean platelet volume
Mapped Trait(s) mean platelet volume (EFO_0004584)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI30100
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_INI30100
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 24,114
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%
262,322 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
— 262,322 individuals European UKB — — — white British ancestry —

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
PPM008619 PSS006956|
African Ancestry|
6,139 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean platelet volume — — R²: 0.11523 [0.10064, 0.12983]
Incremental R2 (full-covars): 0.10713
PGS R2 (no covariates): 0.10764 [0.09341, 0.12187]		 age, sex, UKB array type, Genotype PCs —
PPM008620 PSS006957|
East Asian Ancestry|
1,655 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean platelet volume — — R²: 0.22982 [0.19483, 0.26481]
Incremental R2 (full-covars): 0.1912
PGS R2 (no covariates): 0.20572 [0.17158, 0.23986]		 age, sex, UKB array type, Genotype PCs —
PPM008621 PSS006958|
European Ancestry|
24,175 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean platelet volume — — R²: 0.36048 [0.35094, 0.37001]
Incremental R2 (full-covars): 0.35332
PGS R2 (no covariates): 0.3577 [0.34816, 0.36724]		 age, sex, UKB array type, Genotype PCs —
PPM008622 PSS006959|
South Asian Ancestry|
7,520 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean platelet volume — — R²: 0.26489 [0.24813, 0.28164]
Incremental R2 (full-covars): 0.25606
PGS R2 (no covariates): 0.25974 [0.24303, 0.27644]		 age, sex, UKB array type, Genotype PCs —
PPM008623 PSS006960|
European Ancestry|
65,636 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Mean platelet volume — — R²: 0.36177 [0.35598, 0.36757]
Incremental R2 (full-covars): 0.35994
PGS R2 (no covariates): 0.36024 [0.35444, 0.36603]		 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
PSS006956 — — 6,139 individuals — African unspecified — UKB —
PSS006957 — — 1,655 individuals — East Asian — UKB —
PSS006958 — — 24,175 individuals — European non-white British ancestry UKB —
PSS006959 — — 7,520 individuals — South Asian — UKB —
PSS006960 — — 65,636 individuals — European white British ancestry UKB Testing cohort (heldout set)