Polygenic Score (PGS) ID: PGS001976

Predicted Trait
Reported Trait Reticulocyte count
Mapped Trait(s) reticulocyte count (EFO_0007986)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_log_reticulocyte
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 75,033
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
PPM010683 PSS009465|
European Ancestry|
19,117 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.3967 [0.3847, 0.4086] sex, age, birth date, deprivation index, 16 PCs
PPM010684 PSS009239|
European Ancestry|
3,923 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.3757 [0.3485, 0.4024] sex, age, birth date, deprivation index, 16 PCs
PPM010685 PSS008793|
European Ancestry|
6,297 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.3753 [0.3538, 0.3963] sex, age, birth date, deprivation index, 16 PCs
PPM010686 PSS008567|
Greater Middle Eastern Ancestry|
1,127 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.3116 [0.2574, 0.3638] sex, age, birth date, deprivation index, 16 PCs
PPM010688 PSS008122|
East Asian Ancestry|
1,722 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.2708 [0.2261, 0.3142] sex, age, birth date, deprivation index, 16 PCs
PPM010690 PSS009013|
African Ancestry|
3,602 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.1736 [0.1416, 0.2052] sex, age, birth date, deprivation index, 16 PCs
PPM010687 PSS008345|
South Asian Ancestry|
5,935 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.2981 [0.2747, 0.3211] sex, age, birth date, deprivation index, 16 PCs
PPM010689 PSS007909|
African Ancestry|
2,294 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Reticulocyte count Partial Correlation (partial-r): 0.1931 [0.1532, 0.2323] 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
PSS007909 2,294 individuals African American or Afro-Caribbean Carribean UKB
PSS009013 3,602 individuals African unspecified Nigeria (West Africa) UKB
PSS009239 3,923 individuals European Poland (NE Europe) UKB
PSS008567 1,127 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009465 19,117 individuals European UK (+ Ireland) UKB
PSS008122 1,722 individuals East Asian China (East Asia) UKB
PSS008793 6,297 individuals European Italy (South Europe) UKB
PSS008345 5,935 individuals South Asian India (South Asia) UKB