Polygenic Score (PGS) ID: PGS003934

Predicted Trait
Reported Trait Mean platelet (thrombocyte) volume
Mapped Trait(s) mean platelet volume (EFO_0004584)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30100
Released in PGS Catalog: Nov. 1, 2023
Download Score FTP directory
Terms and Licenses
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 INI30100
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 31,032
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000502
Citation (link to publication) Tanigawa Y et al. AJHG (2023)
Ancestry Distribution
Score Development/Training
Multi-ancestry (including European): 100%
  • European
  • South Asian
  • African
  • Additional Diverse Ancestries
316,082 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
Multi-ancestry (excluding European): 20%
  • East Asian
  • Additional Diverse Ancestries
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
— 316,082 individuals European, South Asian, African unspecified, Other admixed ancestry UKB — — — European, South Asian, African unspecified, Other admixed 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
PPM018989 PSS011144|
European Ancestry|
65,930 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Mean platelet (thrombocyte) volume — — R²: 0.36086 [0.35507, 0.36664]
PGS R2 (no covariates): 0.35829 [0.35251, 0.36408]
Incremental R2 (full-covars): 0.35783		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018990 PSS011109|
European Ancestry|
2,813 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Mean platelet (thrombocyte) volume — — R²: 0.36427 [0.33635, 0.3922]
PGS R2 (no covariates): 0.35942 [0.33147, 0.38737]
Incremental R2 (full-covars): 0.35587		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018991 PSS011113|
South Asian Ancestry|
1,433 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Mean platelet (thrombocyte) volume — — R²: 0.2322 [0.19468, 0.26972]
PGS R2 (no covariates): 0.23172 [0.19421, 0.26922]
Incremental R2 (full-covars): 0.22951		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018993 PSS011166|
Multi-ancestry (excluding European)|
7,746 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Mean platelet (thrombocyte) volume — — R²: 0.30944 [0.29261, 0.32626]
PGS R2 (no covariates): 0.31539 [0.29855, 0.33222]
Incremental R2 (full-covars): 0.2903		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018992 PSS011155|
African Ancestry|
1,157 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Mean platelet (thrombocyte) volume — — R²: 0.10997 [0.07685, 0.1431]
PGS R2 (no covariates): 0.10936 [0.0763, 0.14241]
Incremental R2 (full-covars): 0.10916		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —

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
PSS011109 — — 2,813 individuals — European
(non-white British ancestry)		 — UKB —
PSS011144 — — 65,930 individuals — European
(white British ancestry)		 — UKB —
PSS011113 — — 1,433 individuals — South Asian — UKB —
PSS011155 — — 1,157 individuals — African unspecified — UKB —
PSS011166 — — 7,746 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —