Trait: chronic lymphocytic leukemia

Experimental Factor Ontology (EFO) Information
Identifier EFO_0000095
Description B-cell chronic lymphocytic leukemia (B-CLL) is a type of B-cell non-Hodgkin lymphoma, and the most common form of leukemia in Western countries, affecting elderly adults (mean age of 67 and 72 years) with a slight male predominance (1.7:1), and characterized by a highly variable clinical presentation that can include asymptomatic disease or non-specific B-symptoms such as unintentional weight loss, severe fatigue, fever (without evidence of infection), and night sweats as well as cervical lymphadenopathy, splenomegaly and frequent infections. Some patients can also develop autoimmune complications such as autoimmune hemolytic anemia or immune thrombocytopenia. The clinical course is extremely heterogeneous with survival ranging from a few months to several decades. [Orphanet: 67038]
Trait category
Cancer
Immune system disorder
Synonyms 122 synonyms
  • B Cell Chronic Lymphocytic Leukemia
  • B Cell Leukemia, Chronic
  • B Lymphocytic Leukemia, Chronic
  • B cell CLL
  • B cell chronic lymphocytic leukemia
  • B cell lymphocytic leukemia
  • B-CLL
  • B-Cell Chronic Lymphocytic Leukemia
  • B-Cell Leukemia, Chronic
  • B-Cell Leukemias, Chronic
  • B-Lymphocytic Leukemia, Chronic
  • B-Lymphocytic Leukemias, Chronic
  • B-cell CLL
  • B-cell chronic lymphocytic leukaemia/small lymphocytic lymphoma
  • B-cell chronic lymphocytic leukemia
  • B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma
  • B-cell chronic lymphocytic leukemia/small lymphocytic lymphoma (morphologic abnormality)
  • B-cell chronic lymphogenous leukemia
  • B-cell chronic lymphoid leukemia
  • B-cell lymphocytic leukemia
  • BCLL
  • CH LYM LEUK WO ACHV RMSN
  • CHR LYM LEUK W/O RMSION
  • CLL
  • CLL - Chronic lymphocytic leukaemia
  • CLL - Chronic lymphocytic leukemia
  • CLL Lymphoplasmacytoid Lymphoma
  • CLL Lymphoplasmacytoid Lymphomas
  • Chronic B-Cell Leukemia
  • Chronic B-Cell Leukemias
  • Chronic B-Lymphocytic Leukemia
  • Chronic B-Lymphocytic Leukemias
  • Chronic Lymphoblastic Leukemia
  • Chronic Lymphoblastic Leukemias
  • Chronic Lymphocytic Leukemias
  • Chronic lymphatic leukaemia
  • Chronic lymphatic leukemia
  • Chronic lymphocytic leukaemia
  • Chronic lymphocytic leukaemia, B-cell type
  • Chronic lymphocytic leukemia, B-cell type
  • Chronic lymphocytic leukemia, morphology (morphologic abnormality)
  • Chronic lymphoid leukaemia
  • Chronic lymphoid leukaemia, disease
  • Chronic lymphoid leukemia
  • Chronic lymphoid leukemia without mention of having achieved remission
  • Chronic lymphoid leukemia without mention of remission
  • Chronic lymphoid leukemia, disease
  • Chronic lymphoid leukemia, disease (disorder)
  • DIFFUSE WELL DIFFER LYMPHOCYTIC LYMPHOMA
  • Diffuse Well Differentiated Lymphocytic Lymphoma
  • Diffuse Well-Differentiated Lymphocytic Lymphoma
  • LYMPHOCYTIC LEUKEMIA CHRONIC B
  • LYMPHOCYTIC LYMPHOMA DIFFUSE WELL DIFFER
  • LYMPHOCYTIC LYMPHOMA WELL DIFFER
  • LYMPHOMA LYMPHOCYTIC DIFFUSE WELL DIFFER
  • LYMPHOMA LYMPHOCYTIC WELL DIFFER
  • LYMPHOMA SMALL
  • Leukemia, B Cell, Chronic
  • Leukemia, B-Cell, Chronic
  • Leukemia, Chronic B-Cell
  • Leukemia, Chronic B-Lymphocytic
  • Leukemia, Chronic Lymphoblastic
  • Leukemia, Chronic Lymphocytic
  • Leukemia, Lymphoblastic, Chronic
  • Leukemia, Lymphocytic, Chronic
  • Leukemia, Lymphocytic, Chronic, B Cell
  • Leukemia, Lymphocytic, Chronic, B-Cell
  • Leukemias, Chronic B-Cell
  • Leukemias, Chronic B-Lymphocytic
  • Leukemias, Chronic Lymphoblastic
  • Leukemias, Chronic Lymphocytic
  • Lymphoblastic Leukemia, Chronic
  • Lymphoblastic Leukemias, Chronic
  • Lymphocytic Leukemia, Chronic
  • Lymphocytic Leukemia, Chronic, B Cell
  • Lymphocytic Leukemia, Chronic, B-Cell
  • Lymphocytic Leukemias, Chronic
  • Lymphocytic Lymphoma
  • Lymphocytic Lymphoma, Diffuse, Well Differentiated
  • Lymphocytic Lymphoma, Diffuse, Well-Differentiated
  • Lymphocytic Lymphoma, Small
  • Lymphocytic Lymphoma, Well Differentiated
  • Lymphocytic Lymphoma, Well-Differentiated
  • Lymphocytic Lymphomas
  • Lymphocytic Lymphomas, Small
  • Lymphocytic Lymphomas, Well-Differentiated
  • Lymphoid leukemia, chronic
  • Lymphoma, CLL Lymphoplasmacytoid
  • Lymphoma, Lymphocytic
  • Lymphoma, Lymphocytic, Diffuse, Well Differentiated
  • Lymphoma, Lymphocytic, Diffuse, Well-Differentiated
  • Lymphoma, Lymphocytic, Well Differentiated
  • Lymphoma, Lymphocytic, Well-Differentiated
  • Lymphoma, Lymphoplasmacytoid, CLL
  • Lymphoma, Small Cell
  • Lymphoma, Small Lymphocytic
  • Lymphoma, Small Lymphocytic, Plasmacytoid
  • Lymphoma, Small-Cell
  • Lymphoma, Well-Differentiated Lymphocytic
  • Lymphomas, CLL Lymphoplasmacytoid
  • Lymphomas, Lymphocytic
  • Lymphomas, Small Lymphocytic
  • Lymphomas, Small-Cell
  • Lymphomas, Well-Differentiated Lymphocytic
  • Lymphoplasmacytoid Lymphoma, CLL
  • Lymphoplasmacytoid Lymphomas, CLL
  • SMALL LYMPHOMA
  • Small Cell Lymphoma
  • Small Lymphocytic Lymphoma
  • Small Lymphocytic Lymphomas
  • Small-Cell Lymphoma
  • Small-Cell Lymphomas
  • Well-Differentiated Lymphocytic Lymphoma
  • Well-Differentiated Lymphocytic Lymphomas
  • chronic B-cell lymphocytic leukemia
  • chronic lymphatic leukemia
  • chronic lymphocytic leukemia
  • chronic lymphocytic leukemia (CLL)
  • chronic lymphogenous leukemia
  • hematopoeitic - chronic lymphocytic leukemia (CLL)
  • lymphoplasmacytic leukemia
  • small lymphocytic lymphoma
Mapped term(s) 18 mapped terms
  • DOID:1040
  • GARD:0006104
  • ICD10:C91.1
  • ICD10:C91.10
  • ICD9:204.1
  • MESH:D015451
  • MONDO:0004948
  • MSH:D015451
  • MedDRA:10008958
  • NCIT:C3163
  • NCIt:C27911
  • NCIt:C3163
  • OMIM:109543
  • OMIM:151400
  • Orphanet:67038
  • SNOMEDCT:51092000
  • UMLS:C0023434
  • UMLS:C0855095

Associated Polygenic Score(s)

Polygenic Score (PGS) ID PGS Name PGS Publication (PGP) ID Reported Trait Mapped Trait(s) (Ontology) Number of Variants PGS Scoring File (FTP Link)
PGS000646 PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 32 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000646/ScoringFiles/PGS000646.txt.gz
PGS000647 PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 32 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000647/ScoringFiles/PGS000647.txt.gz
PGS000648 PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 44 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000648/ScoringFiles/PGS000648.txt.gz
PGS000649 PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 27 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000649/ScoringFiles/PGS000649.txt.gz
PGS000650 PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 6 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000650/ScoringFiles/PGS000650.txt.gz
PGS000651 PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608 PGP000118 Fritsche LG et al. Am J Hum Genet (2020) Lymphoid leukemia, chronic chronic lymphocytic leukemia 76 http://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000651/ScoringFiles/PGS000651.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
PPM001331 PGS000646 (PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608) PSS000561 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 2.104 [1.628, 2.718]
β: 0.744 (0.131)
AUROC: 0.696 [0.628, 0.765] Nagelkerke's Pseudo-R²: 0.0973
Brier score: 0.0779
Odds Ratio (OR, top 1% vs. Rest): 11.3 [3.76, 33.9]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608
PPM001332 PGS000647 (PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608) PSS000581 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.874 [1.639, 2.144]
β: 0.628 (0.0685)
AUROC: 0.675 [0.64, 0.707] Nagelkerke's Pseudo-R²: 0.0689
Brier score: 0.0795
Odds Ratio (OR, top 1% vs. Rest): 4.11 [1.97, 8.6]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_UKB_20200608
PPM001333 PGS000648 (PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608) PSS000561 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 2.124 [1.648, 2.738]
β: 0.753 (0.13)
AUROC: 0.696 [0.621, 0.764] Nagelkerke's Pseudo-R²: 0.102
Brier score: 0.0776
Odds Ratio (OR, top 1% vs. Rest): 12.9 [4.45, 37.6]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_MGI_20200608
PPM001334 PGS000649 (PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608) PSS000581 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.85 [1.619, 2.114]
β: 0.615 (0.0681)
AUROC: 0.672 [0.637, 0.703] Nagelkerke's Pseudo-R²: 0.0665
Brier score: 0.0796
Odds Ratio (OR, top 1% vs. Rest): 2.52 [1.04, 6.08]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_PT_UKB_20200608
PPM001335 PGS000650 (PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608) PSS000561 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.368 [1.097, 1.705]
β: 0.313 (0.113)
AUROC: 0.577 [0.511, 0.645] Nagelkerke's Pseudo-R²: 0.0205
Brier score: 0.0822
Odds Ratio (OR, top 1% vs. Rest): 2.0 [0.308, 13.0]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_PT_MGI_20200608
PPM001336 PGS000651 (PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608) PSS000561 PGP000118
Fritsche LG et al. (2020)
Reported Trait: Lymphoid leukemia, chronic OR: 1.32 [1.041, 1.675]
β: 0.278 (0.121)
AUROC: 0.573 [0.503, 0.644] Nagelkerke's Pseudo-R²: 0.0145
Brier score: 0.0823
Odds Ratio (OR, top 1% vs. Rest): 4.84 [1.23, 19.0]
age, sex, batch PCs 1-4 Cancer PRSweb PheWAS Results: PRSWEB_PHECODE204.12_UKBB-SAIGE-HRC-X204.12_LASSOSUM_MGI_20200608

Evaluated Samples

PGS Sample Set ID
(PSS ID)
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
PSS000581 PheCode:204.12; ICD9:204.1; ICD10:C91.1
[
  • 249 cases
  • , 2,509 controls
]
European UKB
PSS000561 PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12
[
  • 69 cases
  • , 687 controls
]
European MGI