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
  • MeSH:D018655
  • NCIt:C51949
  • SNOMEDCT:74765001
Child trait(s) lymphocyte percentage of leukocytes

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows all PGS for "lymphocyte count" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution PGS Scoring File (FTP Link)
PGS000097
(lymph)
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Lymphocyte count lymphocyte count 639
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000097/ScoringFiles/PGS000097.txt.gz
PGS000098
(lymph_p)
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Lymphocyte percentage of white cells lymphocyte percentage of leukocytes 489
http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000098/ScoringFiles/PGS000098.txt.gz
PGS000172
(lymph)
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Lymphocyte count lymphocyte count 621
-
 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000172/ScoringFiles/PGS000172.txt.gz
PGS000173
(lymph_p)
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Lymphocyte percentage of white cells lymphocyte percentage of leukocytes 472
-
 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000173/ScoringFiles/PGS000173.txt.gz

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) 		Evaluated Score 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
PPM000226 PGS000097
(lymph)
 PSS000162|
European Ancestry|
81,455 individuals
 PGP000051 |
Xu Y et al. bioRxiv (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|
European Ancestry|
39,191 individuals
 PGP000051 |
Xu Y et al. bioRxiv (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) —
PPM000228 PGS000098
(lymph_p)
 PSS000163|
European Ancestry|
81,464 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Lymphocyte percentage of white cells — — Pearson correlation coefficent (r): 0.3046 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)
PPM000229 PGS000098
(lymph_p)
 PSS000137|
European Ancestry|
39,178 individuals
 PGP000051 |
Xu Y et al. bioRxiv (2020)
|Pre		 Reported Trait: Lymphocyte percentage of white cells — — Pearson correlation coefficent (r): 0.2817 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|
European Ancestry|
2,314 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Lymphocyte count — — R²: 0.03217 sex, age, 10 genetic PCs —
PPM000528 PGS000172
(lymph)
 PSS000291|
European Ancestry|
39,260 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Lymphocyte count — — R²: 0.10555 sex, age, 10 genetic PCs —
PPM000529 PGS000173
(lymph_p)
 PSS000291|
European Ancestry|
39,260 individuals
 PGP000078 |
Vuckovic D et al. Cell (2020)
 Reported Trait: Lymphocyte percentage of white cells — — R²: 0.06965 sex, age, 10 genetic 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
PSS000136 — — 39,191 individuals,
50.0 % Male samples
 Mean = 43.82 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS000137 — — 39,178 individuals,
50.0 % Male samples
 Mean = 43.82 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS000290 — — 2,314 individuals — European
(French Canadian)		 — CARTaGENE —
PSS000291 — — 39,260 individuals — European — INTERVAL —
PSS000162 — — 81,455 individuals,
45.0 % Male samples
 Mean = 57.23 years
Range = [40.05, 71.07] years		 European — UKB —
PSS000163 — — 81,464 individuals,
46.0 % Male samples
 Mean = 57.22 years
Range = [40.17, 71.1] years		 European — UKB —