Polygenic Score (PGS) ID: PGS001959

Predicted Trait
Reported Trait High light scatter reticulocyte count
Mapped Trait(s) reticulocyte measurement (EFO_0010700)
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_HLR_reticulocyte
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 78,803
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
PPM010548 PSS009207|
European Ancestry|
3,919 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.4054 [0.3788, 0.4313] sex, age, birth date, deprivation index, 16 PCs
PPM010549 PSS008761|
European Ancestry|
6,289 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.3962 [0.3751, 0.4169] sex, age, birth date, deprivation index, 16 PCs
PPM010550 PSS008535|
Greater Middle Eastern Ancestry|
1,124 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.3255 [0.2717, 0.3772] sex, age, birth date, deprivation index, 16 PCs
PPM010551 PSS008313|
South Asian Ancestry|
5,923 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.3191 [0.296, 0.3418] sex, age, birth date, deprivation index, 16 PCs
PPM010552 PSS008090|
East Asian Ancestry|
1,715 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.2778 [0.2333, 0.3212] sex, age, birth date, deprivation index, 16 PCs
PPM010553 PSS007877|
African Ancestry|
2,293 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.2182 [0.1787, 0.257] sex, age, birth date, deprivation index, 16 PCs
PPM010554 PSS008981|
African Ancestry|
3,600 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.2136 [0.1822, 0.2447] sex, age, birth date, deprivation index, 16 PCs
PPM010547 PSS009433|
European Ancestry|
19,088 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: High light scatter reticulocyte count Partial Correlation (partial-r): 0.4069 [0.395, 0.4186] 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
PSS007877 2,293 individuals African American or Afro-Caribbean Carribean UKB
PSS008981 3,600 individuals African unspecified Nigeria (West Africa) UKB
PSS009207 3,919 individuals European Poland (NE Europe) UKB
PSS008535 1,124 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS008761 6,289 individuals European Italy (South Europe) UKB
PSS008090 1,715 individuals East Asian China (East Asia) UKB
PSS008313 5,923 individuals South Asian India (South Asia) UKB
PSS009433 19,088 individuals European UK (+ Ireland) UKB