Polygenic Score (PGS) ID: PGS001969

Predicted Trait
Reported Trait Neutrophil count
Mapped Trait(s) neutrophil count (EFO_0004833)
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_neutrophil
Development Method
Name Penalized regression (bigstatsr)
Parameters HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 71,566
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
PPM010629 PSS008786|
European Ancestry|
6,419 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.3157 [0.2934, 0.3376] sex, age, birth date, deprivation index, 16 PCs
PPM010627 PSS009458|
European Ancestry|
19,382 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.3305 [0.3179, 0.343] sex, age, birth date, deprivation index, 16 PCs
PPM010628 PSS009232|
European Ancestry|
3,992 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.3137 [0.2853, 0.3414] sex, age, birth date, deprivation index, 16 PCs
PPM010631 PSS008338|
South Asian Ancestry|
6,060 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.2983 [0.2751, 0.3211] sex, age, birth date, deprivation index, 16 PCs
PPM010632 PSS008115|
East Asian Ancestry|
1,761 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.2374 [0.1926, 0.2813] sex, age, birth date, deprivation index, 16 PCs
PPM010633 PSS007902|
African Ancestry|
2,336 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.1856 [0.146, 0.2246] sex, age, birth date, deprivation index, 16 PCs
PPM010634 PSS009006|
African Ancestry|
3,697 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.1384 [0.1066, 0.17] sex, age, birth date, deprivation index, 16 PCs
PPM010630 PSS008560|
Greater Middle Eastern Ancestry|
1,149 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Neutrophil count Partial Correlation (partial-r): 0.267 [0.212, 0.3204] 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
PSS009006 3,697 individuals African unspecified Nigeria (West Africa) UKB
PSS009232 3,992 individuals European Poland (NE Europe) UKB
PSS008560 1,149 individuals Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB
PSS009458 19,382 individuals European UK (+ Ireland) UKB
PSS008338 6,060 individuals South Asian India (South Asia) UKB
PSS008786 6,419 individuals European Italy (South Europe) UKB
PSS008115 1,761 individuals East Asian China (East Asia) UKB
PSS007902 2,336 individuals African American or Afro-Caribbean Carribean UKB