Polygenic Score (PGS) ID: PGS002147

Predicted Trait
Reported Trait Immature reticulocyte fraction
Mapped Trait(s) reticulocyte amount (OBA_0002272)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_immature_reticulocyte_frac
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 664,696
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
PPM012023 PSS009417|
European Ancestry|
19,121 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.3135 [0.3007, 0.3263] sex, age, birth date, deprivation index, 16 PCs —
PPM012024 PSS009191|
European Ancestry|
3,924 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.3215 [0.2931, 0.3494] sex, age, birth date, deprivation index, 16 PCs —
PPM012025 PSS008745|
European Ancestry|
6,298 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.3195 [0.2971, 0.3416] sex, age, birth date, deprivation index, 16 PCs —
PPM012026 PSS008519|
Greater Middle Eastern Ancestry|
1,127 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.2889 [0.234, 0.342] sex, age, birth date, deprivation index, 16 PCs —
PPM012027 PSS008297|
South Asian Ancestry|
5,937 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.2624 [0.2385, 0.286] sex, age, birth date, deprivation index, 16 PCs —
PPM012028 PSS008074|
East Asian Ancestry|
1,722 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.2089 [0.163, 0.2539] sex, age, birth date, deprivation index, 16 PCs —
PPM012029 PSS007861|
African Ancestry|
2,294 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.1842 [0.1442, 0.2236] sex, age, birth date, deprivation index, 16 PCs —
PPM012030 PSS008965|
African Ancestry|
3,602 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Immature reticulocyte fraction — — Partial Correlation (partial-r): 0.174 [0.1421, 0.2056] 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
PSS008965 — — 3,602 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009191 — — 3,924 individuals — European Poland (NE Europe) UKB —
PSS008519 — — 1,127 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008297 — — 5,937 individuals — South Asian India (South Asia) UKB —
PSS009417 — — 19,121 individuals — European UK (+ Ireland) UKB —
PSS008745 — — 6,298 individuals — European Italy (South Europe) UKB —
PSS008074 — — 1,722 individuals — East Asian China (East Asia) UKB —
PSS007861 — — 2,294 individuals — African American or Afro-Caribbean Carribean UKB —