Polygenic Score (PGS) ID: PGS002221

Predicted Trait
Reported Trait Mean reticulocyte volume
Mapped Trait(s) mean reticulocyte volume (EFO_0010701)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_reticulocyte_volume
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 523,074
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012614 PSS009487|
European Ancestry|
19,120 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.3894 [0.3773, 0.4014] sex, age, birth date, deprivation index, 16 PCs —
PPM012615 PSS009261|
European Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.3877 [0.3608, 0.4141] sex, age, birth date, deprivation index, 16 PCs —
PPM012616 PSS008815|
European Ancestry|
6,298 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.3736 [0.3521, 0.3947] sex, age, birth date, deprivation index, 16 PCs —
PPM012617 PSS008589|
Greater Middle Eastern Ancestry|
1,127 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.3308 [0.2773, 0.3823] sex, age, birth date, deprivation index, 16 PCs —
PPM012618 PSS008367|
South Asian Ancestry|
5,935 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.3152 [0.2921, 0.338] sex, age, birth date, deprivation index, 16 PCs —
PPM012619 PSS008143|
East Asian Ancestry|
1,722 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.2541 [0.2091, 0.298] sex, age, birth date, deprivation index, 16 PCs —
PPM012620 PSS007931|
African Ancestry|
2,293 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.2118 [0.1722, 0.2507] sex, age, birth date, deprivation index, 16 PCs —
PPM012621 PSS009035|
African Ancestry|
3,602 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Mean reticulocyte volume — — Partial Correlation (partial-r): 0.1834 [0.1516, 0.2149] sex, age, birth date, deprivation index, 16 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
PSS009035 — — 3,602 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009261 — — 3,924 individuals — European Poland (NE Europe) UKB —
PSS008589 — — 1,127 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009487 — — 19,120 individuals — European UK (+ Ireland) UKB —
PSS008815 — — 6,298 individuals — European Italy (South Europe) UKB —
PSS008367 — — 5,935 individuals — South Asian India (South Asia) UKB —
PSS008143 — — 1,722 individuals — East Asian China (East Asia) UKB —
PSS007931 — — 2,293 individuals — African American or Afro-Caribbean Carribean UKB —