Polygenic Score (PGS) ID: PGS000105

Predicted Trait
Reported Trait Neutrophil count
Mapped Trait(s) neutrophil count (EFO_0004833)
Additional Trait Information NEUT#
Released in PGS Catalog: Feb. 19, 2020
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Score Details

Score Construction
PGS Name neut
Development Method
Name Regularized Regression (Elastic Net)
Parameters Bi-allelic variants (MAF > 0.01, INFO > 0.4, missingness rate < 0.1) with LD thinning (r2 threshold = 0.5)
Variants
Original Genome Build GRCh37
Number of Variants 23,864
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000051
Citation (link to publication) Xu Y et al. Cell Genom (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
406,788 individuals (100%)
Score Development/Training
European: 100%
325,430 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
406,788 individuals,
46.0 % Male samples
European UKB
Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
325,430 individuals,
46.0 % Male samples
European UKB Mean = 57.23 years
Range = [38.87, 72.91] years

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
PPM000242 PSS000170|
European Ancestry|
81,358 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Neutrophil count Pearson correlation coefficent (r): 0.36386 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment) UKB Testing Set - these samples were held out from Score Development (regression training) but overlap with the samples used for variant selection (GWAS)
PPM000243 PSS000144|
European Ancestry|
39,138 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Neutrophil count Pearson correlation coefficent (r): 0.35194 age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical covariates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)

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
PSS000144 39,138 individuals,
50.0 % Male samples
Mean = 43.84 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000170 81,358 individuals,
45.0 % Male samples
Mean = 57.19 years
Range = [40.19, 72.44] years
European UKB