Polygenic Score (PGS) ID: PGS003947

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information http://ipgs.mit.edu/tanigawakellis2023/INI30250
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 INI30250
Development Method
Name snpnet
Parameters inclusive PGS
Variants
Original Genome Build GRCh37
Number of Variants 9,558
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
310,916 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
— 310,916 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
PPM019054 PSS011140|
European Ancestry|
64,861 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Reticulocyte count — — R²: 0.0537 [0.0504, 0.057]
PGS R2 (no covariates): 0.04073 [0.03782, 0.04365]
Incremental R2 (full-covars): 0.04072		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019056 PSS011111|
South Asian Ancestry|
1,393 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Reticulocyte count — — R²: 0.09735 [0.06879, 0.12592]
PGS R2 (no covariates): 0.07127 [0.04612, 0.09641]
Incremental R2 (full-covars): 0.06906		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019057 PSS011153|
African Ancestry|
1,125 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Reticulocyte count — — R²: 0.02713 [0.00914, 0.04511]
PGS R2 (no covariates): 0.01461 [0.00124, 0.02797]
Incremental R2 (full-covars): 0.01527		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019058 PSS011169|
Multi-ancestry (excluding European)|
7,578 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Reticulocyte count — — R²: 0.05468 [0.045, 0.06436]
PGS R2 (no covariates): 0.03553 [0.02757, 0.04349]
Incremental R2 (full-covars): 0.03303		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019055 PSS011099|
European Ancestry|
2,770 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Reticulocyte count — — R²: 0.10144 [0.08061, 0.12226]
PGS R2 (no covariates): 0.07084 [0.05284, 0.08884]
Incremental R2 (full-covars): 0.07225		 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
PSS011140 — — 64,861 individuals — European
(white British ancestry)		 — UKB —
PSS011111 — — 1,393 individuals — South Asian — UKB —
PSS011153 — — 1,125 individuals — African unspecified — UKB —
PSS011099 — — 2,770 individuals — European
(non-white British ancestry)		 — UKB —
PSS011169 — — 7,578 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —