Polygenic Score (PGS) ID: PGS000097

Predicted Trait
Reported Trait Lymphocyte count
Mapped Trait(s) lymphocyte count (EFO_0004587)
Additional Trait Information LYMPH#
Released in PGS: Feb. 19, 2020

Score Details

Score Construction
PGS Name lymph
Variants
Original Genome Build GRCh37
Number of Variants 639
Development Method
Name Regularized Regression (Elastic Net)
Parameters Variants included in the regression were selected according to their GWAS significance (p < 8.31e-9) and a subsequent conditional analysis (r2 threshold = 0.9); effect sizes of variants are estimated by regularized regression
PGS Source
PGS Catalog Publication (PGP) ID PGP000051
Citation (link to publication) Xu Y et al. bioRxiv (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
407,277 individuals,
46.0 % Male samples
European
Score Development/Training
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
325,822 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [38.87, 72.91] years
European 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 ID)
PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000227 PSS000136 PGP000051
Xu Y et al. (2020)
Reported Trait: Lymphocyte count Pearson correlation coefficent (r): 0.3511 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)
PPM000226 PSS000162 PGP000051
Xu Y et al. (2020)
Reported Trait: Lymphocyte count Pearson correlation coefficent (r): 0.369 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)

Evaluated Samples

PGS Sample Set ID
(PSS ID)
Detailed Phenotype Description Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000136 39,191 individuals,
50.0 % Male samples
Mean = 43.82 years
Range = [18.0, 76.4] years
European INTERVAL
PSS000162 81,455 individuals,
45.0 % Male samples
Mean = 57.23 years
Range = [40.05, 71.07] years
European UKB