Polygenic Score (PGS) ID: PGS003952

Predicted Trait
Reported Trait High light scatter reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30300
Released in PGS Catalog: Nov. 1, 2023
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Score Details

Score Construction
PGS Name INI30300
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 19,565
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
310,755 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
— 310,755 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
PPM019079 PSS011143|
European Ancestry|
64,816 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.13075 [0.12601, 0.13548]
PGS R2 (no covariates): 0.11335 [0.10885, 0.11784]
Incremental R2 (full-covars): 0.11327		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019080 PSS011100|
European Ancestry|
2,768 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.14122 [0.11773, 0.16471]
PGS R2 (no covariates): 0.12176 [0.09946, 0.14407]
Incremental R2 (full-covars): 0.12235		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019081 PSS011111|
South Asian Ancestry|
1,393 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.11255 [0.08236, 0.14275]
PGS R2 (no covariates): 0.0909 [0.0631, 0.1187]
Incremental R2 (full-covars): 0.08654		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019082 PSS011153|
African Ancestry|
1,125 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.04777 [0.02441, 0.07112]
PGS R2 (no covariates): 0.04026 [0.01865, 0.06188]
Incremental R2 (full-covars): 0.04027		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019083 PSS011170|
Multi-ancestry (excluding European)|
7,574 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: High light scatter reticulocyte count — — R²: 0.12479 [0.11125, 0.13833]
PGS R2 (no covariates): 0.09343 [0.0813, 0.10557]
Incremental R2 (full-covars): 0.08525		 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
PSS011143 — — 64,816 individuals — European
(white British ancestry)		 — UKB —
PSS011111 — — 1,393 individuals — South Asian — UKB —
PSS011153 — — 1,125 individuals — African unspecified — UKB —
PSS011100 — — 2,768 individuals — European
(non-white British ancestry)		 — UKB —
PSS011170 — — 7,574 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —