Trait: lymphocyte percentage of leukocytes

Experimental Factor Ontology (EFO) Information
Identifier EFO_0007993
Description A calculated measurement in which the number of lymphocytes in a specified sample of blood is divide... d by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage. Show more
Trait category
Hematological measurement
Synonyms 5 synonyms
  • blood lymphocyte count to total leukocyte count ratio
  • lymphocyte count as percentage of total white blood cells
  • lymphocyte count to total WBC count ratio
  • lymphocyte percentage
  • lymphocyte percentage of white cells
Mapped term CMO:0000371

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
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Polygenic Score ID & Name
PGS Publication ID (PGP)
Reported Trait
Mapped Trait(s) (Ontology)
Number of Variants
Ancestry distribution
GWAS
Dev
Eval
Scoring File (FTP Link)
PGS000098
(lymph_p)
PGP000051 |
Xu Y et al. Cell Genom (2022)
Lymphocyte percentage of white cellslymphocyte percentage of leukocytes22,363
G
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000098/ScoringFiles/PGS000098.txt.gz
PGS000173
(lymph_p)
PGP000078 |
Vuckovic D et al. Cell (2020)
Lymphocyte percentage of white cellslymphocyte percentage of leukocytes472
G
-
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000173/ScoringFiles/PGS000173.txt.gz
PGS001414
(GBE_INI30180)
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Lymphocyte %lymphocyte percentage of leukocytes15,143
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001414/ScoringFiles/PGS001414.txt.gz
PGS001986
(portability-PLR_lymphocyte_perc)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Lymphocyte percentagelymphocyte percentage of leukocytes66,778
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001986/ScoringFiles/PGS001986.txt.gz
PGS002203
(portability-ldpred2_lymphocyte_perc)
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Lymphocyte percentagelymphocyte percentage of leukocytes775,312
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002203/ScoringFiles/PGS002203.txt.gz
PGS003557
(cont-decay-lymphocyte_perc)
PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		Lymphocyte percentagelymphocyte percentage of leukocytes979,739
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003557/ScoringFiles/PGS003557.txt.gz
PGS003941
(INI30180)
PGP000502 |
Tanigawa Y et al. AJHG (2023)
Lymphocyte percentagelymphocyte percentage of leukocytes20,804
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003941/ScoringFiles/PGS003941.txt.gz
PGS004359
(X30180.score)
PGP000561 |
Jung H et al. Commun Biol (2024)
Lymphocyte percentagelymphocyte percentage of leukocytes1,059,939
-
D
E
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004359/ScoringFiles/PGS004359.txt.gz
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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.

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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
PPM000228PGS000098
(lymph_p)
PSS000163|
European Ancestry|
81,464 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Lymphocyte percentage of white cells——Pearson correlation coefficent (r): 0.33396age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical cova... riates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)Show moreUKB Testing Set - these samples were held out from Score Development (regression training) but overl... ap with the samples used for variant selection (GWAS)Show more
PPM000229PGS000098
(lymph_p)
PSS000137|
European Ancestry|
39,178 individuals
PGP000051 |
Xu Y et al. Cell Genom (2022)
Reported Trait: Lymphocyte percentage of white cells——Pearson correlation coefficent (r): 0.3313age, sex, 10 PCs of ancestry, lifestyle factors (diet, smoking, alcohol consumption), technical cova... riates (the time between venepuncture and full blood cell analysis, seasonal effects, centre of sample collection, time dependent drift of equipment, systematic differences in equipment)Show more—
PPM000529PGS000173
(lymph_p)
PSS000291|
European Ancestry|
39,260 individuals
PGP000078 |
Vuckovic D et al. Cell (2020)
Reported Trait: Lymphocyte percentage of white cells——R²: 0.06965sex, age, 10 genetic PCs—
PPM007050PGS001414
(GBE_INI30180)
PSS006991|
African Ancestry|
6,120 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Lymphocyte %——R²: 0.03982 [0.03051, 0.04913]
Incremental R2 (full-covars): 0.01769
PGS R2 (no covariates): 0.02018 [0.01341, 0.02694]		age, sex, UKB array type, Genotype PCs—
PPM007051PGS001414
(GBE_INI30180)
PSS006992|
East Asian Ancestry|
1,654 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Lymphocyte %——R²: 0.08102 [0.05624, 0.10581]
Incremental R2 (full-covars): 0.04011
PGS R2 (no covariates): 0.03886 [0.02091, 0.05682]		age, sex, UKB array type, Genotype PCs—
PPM007052PGS001414
(GBE_INI30180)
PSS006993|
European Ancestry|
24,130 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Lymphocyte %——R²: 0.09934 [0.09229, 0.10639]
Incremental R2 (full-covars): 0.08221
PGS R2 (no covariates): 0.084 [0.0774, 0.09059]		age, sex, UKB array type, Genotype PCs—
PPM007053PGS001414
(GBE_INI30180)
PSS006994|
South Asian Ancestry|
7,491 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Lymphocyte %——R²: 0.05905 [0.04893, 0.06918]
Incremental R2 (full-covars): 0.05259
PGS R2 (no covariates): 0.05171 [0.04216, 0.06126]		age, sex, UKB array type, Genotype PCs—
PPM007054PGS001414
(GBE_INI30180)
PSS006995|
European Ancestry|
65,520 individuals
PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
Reported Trait: Lymphocyte %——R²: 0.10838 [0.10395, 0.11281]
Incremental R2 (full-covars): 0.08842
PGS R2 (no covariates): 0.08835 [0.08426, 0.09245]		age, sex, UKB array type, Genotype PCs—
PPM010763PGS001986
(portability-PLR_lymphocyte_perc)
PSS009473|
European Ancestry|
19,383 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.314 [0.3012, 0.3266]sex, age, birth date, deprivation index, 16 PCs—
PPM010764PGS001986
(portability-PLR_lymphocyte_perc)
PSS009247|
European Ancestry|
3,992 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.2972 [0.2686, 0.3253]sex, age, birth date, deprivation index, 16 PCs—
PPM010765PGS001986
(portability-PLR_lymphocyte_perc)
PSS008801|
European Ancestry|
6,417 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.3022 [0.2798, 0.3243]sex, age, birth date, deprivation index, 16 PCs—
PPM010766PGS001986
(portability-PLR_lymphocyte_perc)
PSS008575|
Greater Middle Eastern Ancestry|
1,150 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.2825 [0.228, 0.3353]sex, age, birth date, deprivation index, 16 PCs—
PPM010767PGS001986
(portability-PLR_lymphocyte_perc)
PSS008353|
South Asian Ancestry|
6,056 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.2722 [0.2487, 0.2954]sex, age, birth date, deprivation index, 16 PCs—
PPM010768PGS001986
(portability-PLR_lymphocyte_perc)
PSS008130|
East Asian Ancestry|
1,761 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.2475 [0.2028, 0.291]sex, age, birth date, deprivation index, 16 PCs—
PPM010769PGS001986
(portability-PLR_lymphocyte_perc)
PSS007917|
African Ancestry|
2,337 individuals
PGP000263 |
Privé F et al. Am J Hum Genet (2022)
Reported Trait: Lymphocyte percentage——Partial Correlation (partial-r): 0.1708 [0.131, 0.21]sex, age, birth date, deprivation index, 16 PCs—
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Evaluated Samples

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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
PSS000137——39,178 individuals,
50.0 % Male samples
Mean = 43.82 years
Range = [18.0, 76.4] years		European—INTERVAL—
PSS000163——81,464 individuals,
46.0 % Male samples
Mean = 57.22 years
Range = [40.17, 71.1] years		European—UKB—
PSS000291——39,260 individuals—European—INTERVAL—
PSS006991——6,120 individuals—African unspecified—UKB—
PSS006992——1,654 individuals—East Asian—UKB—
PSS006993——24,130 individuals—Europeannon-white British ancestryUKB—
PSS006994——7,491 individuals—South Asian—UKB—
PSS006995——65,520 individuals—Europeanwhite British ancestryUKBTesting cohort (heldout set)
PSS007917——2,337 individuals—African American or Afro-CaribbeanCarribeanUKB—
PSS008130——1,761 individuals—East AsianChina (East Asia)UKB—
PSS008353——6,056 individuals—South AsianIndia (South Asia)UKB—
PSS008575——1,150 individuals—Greater Middle Eastern (Middle Eastern, North African or Persian)Iran (Middle East)UKB—
PSS008801——6,417 individuals—EuropeanItaly (South Europe)UKB—
PSS009021——3,695 individuals—African unspecifiedNigeria (West Africa)UKB—
PSS009247——3,992 individuals—EuropeanPoland (NE Europe)UKB—
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