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 divided by the total number of white blood cells in the sample, and the result presented as a ratio, fraction, quotient or percentage.
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
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 cells lymphocyte percentage of leukocytes 22,363
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 cells lymphocyte percentage of leukocytes 472
-
 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 leukocytes 15,143
-
 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 percentage lymphocyte percentage of leukocytes 66,778
-
 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 percentage lymphocyte percentage of leukocytes 775,312
-
 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 percentage lymphocyte percentage of leukocytes 979,739
-
 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 percentage lymphocyte percentage of leukocytes 20,804
-
 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 percentage lymphocyte percentage of leukocytes 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004359/ScoringFiles/PGS004359.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
PPM000228 PGS000098
(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): 0.33396 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. Cell Genom (2022)
 Reported Trait: Lymphocyte percentage of white cells — — Pearson correlation coefficent (r): 0.3313 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) —
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 —
PPM007054 PGS001414
(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 —
PPM007050 PGS001414
(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 —
PPM007051 PGS001414
(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 —
PPM007052 PGS001414
(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 —
PPM007053 PGS001414
(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 —
PPM010763 PGS001986
(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 —
PPM010764 PGS001986
(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 —
PPM010765 PGS001986
(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 —
PPM010766 PGS001986
(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 —
PPM010767 PGS001986
(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 —
PPM010768 PGS001986
(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 —
PPM010769 PGS001986
(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 —
PPM010770 PGS001986
(portability-PLR_lymphocyte_perc)
 PSS009021|
African Ancestry|
3,695 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.1726 [0.1411, 0.2038] sex, age, birth date, deprivation index, 16 PCs —
PPM012471 PGS002203
(portability-ldpred2_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): 0.3116 [0.2989, 0.3243] sex, age, birth date, deprivation index, 16 PCs —
PPM012472 PGS002203
(portability-ldpred2_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): 0.2932 [0.2645, 0.3213] sex, age, birth date, deprivation index, 16 PCs —
PPM012473 PGS002203
(portability-ldpred2_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): 0.2976 [0.2751, 0.3198] sex, age, birth date, deprivation index, 16 PCs —
PPM012474 PGS002203
(portability-ldpred2_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): 0.2842 [0.2297, 0.3369] sex, age, birth date, deprivation index, 16 PCs —
PPM012475 PGS002203
(portability-ldpred2_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): 0.2664 [0.2428, 0.2897] sex, age, birth date, deprivation index, 16 PCs —
PPM012476 PGS002203
(portability-ldpred2_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): 0.2567 [0.2122, 0.3] sex, age, birth date, deprivation index, 16 PCs —
PPM012477 PGS002203
(portability-ldpred2_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): 0.1725 [0.1327, 0.2117] sex, age, birth date, deprivation index, 16 PCs —
PPM012478 PGS002203
(portability-ldpred2_lymphocyte_perc)
 PSS009021|
African Ancestry|
3,695 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Lymphocyte percentage — — Partial Correlation (partial-r): 0.164 [0.1324, 0.1953] sex, age, birth date, deprivation index, 16 PCs —
PPM017905 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010503|
South Asian Ancestry|
6,004 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM017485 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010923|
European Ancestry|
19,370 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017569 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010839|
European Ancestry|
3,981 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017737 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010587|
Greater Middle Eastern Ancestry|
1,120 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017821 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010251|
European Ancestry|
2,258 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM017989 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010419|
East Asian Ancestry|
1,749 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.07 sex, age, deprivation index, PC1-16 —
PPM018073 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010335|
African Ancestry|
2,324 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018157 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010755|
African Ancestry|
3,666 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.02 sex, age, deprivation index, PC1-16 —
PPM017653 PGS003557
(cont-decay-lymphocyte_perc)
 PSS010671|
European Ancestry|
6,258 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Lymphocyte percentage — — partial-R2: 0.09 sex, age, deprivation index, PC1-16 —
PPM019024 PGS003941
(INI30180)
 PSS011139|
European Ancestry|
65,814 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Lymphocyte percentage — — R²: 0.12323 [0.1186, 0.12787]
PGS R2 (no covariates): 0.09003 [0.08592, 0.09414]
Incremental R2 (full-covars): 0.09003		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019025 PGS003941
(INI30180)
 PSS011110|
European Ancestry|
2,810 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Lymphocyte percentage — — R²: 0.11201 [0.09038, 0.13364]
PGS R2 (no covariates): 0.08186 [0.06274, 0.10098]
Incremental R2 (full-covars): 0.08335		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019026 PGS003941
(INI30180)
 PSS011112|
South Asian Ancestry|
1,428 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Lymphocyte percentage — — R²: 0.07411 [0.04855, 0.09967]
PGS R2 (no covariates): 0.05351 [0.03131, 0.07571]
Incremental R2 (full-covars): 0.05293		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019027 PGS003941
(INI30180)
 PSS011154|
African Ancestry|
1,154 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Lymphocyte percentage — — R²: 0.06881 [0.0414, 0.09623]
PGS R2 (no covariates): 0.0468 [0.02366, 0.06995]
Incremental R2 (full-covars): 0.04285		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM019028 PGS003941
(INI30180)
 PSS011168|
Multi-ancestry (excluding European)|
7,732 individuals
 PGP000502 |
Tanigawa Y et al. AJHG (2023)
 Reported Trait: Lymphocyte percentage — — R²: 0.15346 [0.13894, 0.16798]
PGS R2 (no covariates): 0.11132 [0.09834, 0.12431]
Incremental R2 (full-covars): 0.07958		 age, sex, age^2, age*sex, Townsend deprivation index, genotype PCs (PC1-PC18) —
PPM020474 PGS004359
(X30180.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Lymphocyte percentage — — PGS R2 (no covariates): 0.22005 — —

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
PSS010923 — — 19,370 individuals,
46.0 % Male samples
 Mean = 56.9 years
Sd = 7.9 years		 European white British UKB —
PSS011154 — — 1,154 individuals — African unspecified — UKB —
PSS010671 — — 6,258 individuals,
45.0 % Male samples
 Mean = 54.5 years
Sd = 8.4 years		 European Italian UKB —
PSS006991 — — 6,120 individuals — African unspecified — UKB —
PSS006992 — — 1,654 individuals — East Asian — UKB —
PSS006993 — — 24,130 individuals — European non-white British ancestry UKB —
PSS006994 — — 7,491 individuals — South Asian — UKB —
PSS006995 — — 65,520 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS010419 — — 1,749 individuals,
33.0 % Male samples
 Mean = 52.5 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS011168 — — 7,732 individuals — East Asian, Other admixed ancestry East Asian, Other admixed ancestry UKB —
PSS008801 — — 6,417 individuals — European Italy (South Europe) UKB —
PSS000291 — — 39,260 individuals — European — INTERVAL —
PSS007917 — — 2,337 individuals — African American or Afro-Caribbean Carribean UKB —
PSS010839 — — 3,981 individuals,
38.0 % Male samples
 Mean = 54.3 years
Sd = 7.5 years		 European Polish UKB —
PSS008575 — — 1,150 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009473 — — 19,383 individuals — European UK (+ Ireland) UKB —
PSS010587 — — 1,120 individuals,
59.0 % Male samples
 Mean = 52.0 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010335 — — 2,324 individuals,
36.0 % Male samples
 Mean = 52.4 years
Sd = 8.0 years		 African American or Afro-Caribbean Caribbean UKB —
PSS000137 — — 39,178 individuals,
50.0 % Male samples
 Mean = 43.82 years
Range = [18.0, 76.4] years		 European — INTERVAL —
PSS009247 — — 3,992 individuals — European Poland (NE Europe) UKB —
PSS011364 — — 56,192 individuals — European — UKB —
PSS008353 — — 6,056 individuals — South Asian India (South Asia) UKB —
PSS000163 — — 81,464 individuals,
46.0 % Male samples
 Mean = 57.22 years
Range = [40.17, 71.1] years		 European — UKB —
PSS011110 — — 2,810 individuals — European
(non-white British ancestry)		 — UKB —
PSS011112 — — 1,428 individuals — South Asian — UKB —
PSS010755 — — 3,666 individuals,
47.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010503 — — 6,004 individuals,
55.0 % Male samples
 Mean = 53.3 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS010251 — — 2,258 individuals,
45.0 % Male samples
 Mean = 58.0 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS009021 — — 3,695 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008130 — — 1,761 individuals — East Asian China (East Asia) UKB —
PSS011139 — — 65,814 individuals — European
(white British ancestry)		 — UKB —