Trait: lymphocyte count

Experimental Factor Ontology (EFO) Information
Identifier EFO_0004587
Description
  • A quantification of lymphocytes in blood.
Trait category
Hematological measurement
Synonyms lymphocyte counts
Mapped term(s) 3 mapped terms
  • MSH:D018655
  • NCIt:C51949
  • SNOMEDCT:74765001

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Number of Variants PGS Scoring File (FTP Link)
PGS000097 lymph PGP000051
Xu Y et al. bioRxiv (2020)
Pre
Lymphocyte count 639 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000097/ScoringFiles/PGS000097.txt.gz
PGS000172 lymph PGP000078
Vuckovic D et al. medRxiv (2020)
Pre
Lymphocyte count 621 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000172/ScoringFiles/PGS000172.txt.gz

PGS 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)
Evaluated Score PGS Sample Set ID
(PSS ID)
Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000226 PGS000097 (lymph) PSS000162 PGP000051
Xu Y et al. (2020)
Pre
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)
PPM000227 PGS000097 (lymph) PSS000136 PGP000051
Xu Y et al. (2020)
Pre
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)
PPM000550 PGS000172 (lymph) PSS000290 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Lymphocyte count : 0.03216861060721 sex, age, 10 genetic PCs
PPM000528 PGS000172 (lymph) PSS000291 PGP000078
Vuckovic D et al. (2020)
Pre
Reported Trait: Lymphocyte count : 0.105545616995283 sex, age, 10 genetic PCs

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
PSS000290 2,314 individuals European
(French Canadian)
CARTaGENE
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
PSS000291 39,260 individuals European INTERVAL