Polygenic Score (PGS) ID: PGS001930

Predicted Trait
Reported Trait Immature reticulocyte fraction
Mapped Trait(s) Immature Reticulocyte Fraction Measurement (EFO_0009253)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_immature_reticulocyte_frac
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 39,162
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
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
391,124 individuals European UK (+ Ireland) UKB

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
PPM010315 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): 0.3146 [0.3017, 0.3273] sex, age, birth date, deprivation index, 16 PCs
PPM010316 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): 0.3213 [0.2928, 0.3491] sex, age, birth date, deprivation index, 16 PCs
PPM010317 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): 0.3224 [0.3, 0.3444] sex, age, birth date, deprivation index, 16 PCs
PPM010318 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): 0.2696 [0.214, 0.3234] sex, age, birth date, deprivation index, 16 PCs
PPM010319 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): 0.2631 [0.2392, 0.2867] sex, age, birth date, deprivation index, 16 PCs
PPM010320 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): 0.2154 [0.1696, 0.2602] sex, age, birth date, deprivation index, 16 PCs
PPM010321 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): 0.1811 [0.141, 0.2205] sex, age, birth date, deprivation index, 16 PCs
PPM010322 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): 0.1665 [0.1345, 0.1982] 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