Polygenic Score (PGS) ID: PGS001909

Predicted Trait
Reported Trait Red blood cell (erythrocyte) count
Mapped Trait(s) erythrocyte count (EFO_0004305)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-PLR_erythrocyte
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 81,887
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
PPM010155 PSS009399|
European Ancestry|
19,422 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.3987 [0.3868, 0.4105] sex, age, birth date, deprivation index, 16 PCs
PPM010156 PSS009173|
European Ancestry|
4,001 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.404 [0.3776, 0.4296] sex, age, birth date, deprivation index, 16 PCs
PPM010157 PSS008727|
European Ancestry|
6,437 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.3387 [0.3169, 0.3602] sex, age, birth date, deprivation index, 16 PCs
PPM010158 PSS008501|
Greater Middle Eastern Ancestry|
1,153 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.3306 [0.2777, 0.3815] sex, age, birth date, deprivation index, 16 PCs
PPM010159 PSS008279|
South Asian Ancestry|
6,078 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.2916 [0.2684, 0.3145] sex, age, birth date, deprivation index, 16 PCs
PPM010160 PSS008056|
East Asian Ancestry|
1,762 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.2689 [0.2247, 0.3119] sex, age, birth date, deprivation index, 16 PCs
PPM010161 PSS007843|
African Ancestry|
2,342 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.1886 [0.149, 0.2275] sex, age, birth date, deprivation index, 16 PCs
PPM010162 PSS008947|
African Ancestry|
3,711 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Red blood cell (erythrocyte) count Partial Correlation (partial-r): 0.1298 [0.098, 0.1614] 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
PSS008947 3,711 individuals African unspecified Nigeria (West Africa) UKB
PSS008501 1,153 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009173 4,001 individuals European Poland (NE Europe) UKB
PSS008727 6,437 individuals European Italy (South Europe) UKB
PSS009399 19,422 individuals European UK (+ Ireland) UKB
PSS008279 6,078 individuals South Asian India (South Asia) UKB
PSS008056 1,762 individuals East Asian China (East Asia) UKB
PSS007843 2,342 individuals African American or Afro-Caribbean Carribean UKB