Polygenic Score (PGS) ID: PGS003933

Predicted Trait
Reported Trait Platelet crit
Mapped Trait(s) platelet crit (EFO_0007985)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30090
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI30090
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 27,034
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
315,950 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
— 315,950 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
PPM018984 PSS011138|
European Ancestry|
65,896 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Platelet crit — — R²: 0.25161 [0.24596, 0.25727]
PGS R2 (no covariates): 0.16315 [0.15806, 0.16824]
Incremental R2 (full-covars): 0.16228		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018985 PSS011109|
European Ancestry|
2,813 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Platelet crit — — R²: 0.24843 [0.22117, 0.27569]
PGS R2 (no covariates): 0.17673 [0.15154, 0.20191]
Incremental R2 (full-covars): 0.17323		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018986 PSS011113|
South Asian Ancestry|
1,433 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Platelet crit — — R²: 0.24781 [0.20983, 0.28578]
PGS R2 (no covariates): 0.11999 [0.08908, 0.1509]
Incremental R2 (full-covars): 0.10886		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018987 PSS011155|
African Ancestry|
1,157 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Platelet crit — — R²: 0.1523 [0.11518, 0.18943]
PGS R2 (no covariates): 0.04384 [0.02137, 0.06631]
Incremental R2 (full-covars): 0.02917		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM018988 PSS011167|
Multi-ancestry (excluding European)|
7,743 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Platelet crit — — R²: 0.22916 [0.213, 0.24532]
PGS R2 (no covariates): 0.13828 [0.12425, 0.15231]
Incremental R2 (full-covars): 0.13431		 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 —
PSS011113 — — 1,433 individuals — South Asian — UKB —
PSS011155 — — 1,157 individuals — African unspecified — UKB —
PSS011167 — — 7,743 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS011138 — — 65,896 individuals — European
(white British ancestry)		 — UKB —