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 categories
Cancer
Immune system disorder
Synonyms 19 synonyms
  • B cell CLL
  • B cell chronic lymphocytic leukemia
  • B cell lymphocytic leukemia
  • B-CLL
  • B-cell CLL
  • B-cell chronic lymphocytic leukemia
  • B-cell chronic lymphogenous leukemia
  • B-cell chronic lymphoid leukemia
  • B-cell lymphocytic leukemia
  • BCLL
  • CLL
  • 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 terms 19 mapped terms
  • DOID:1040
  • EFO:0000095
  • GARD:0006104
  • ICD10:C91.1
  • ICD10:C91.10
  • ICD9:204.1
  • MESH:D015451
  • MONDO:0004948
  • MedDRA:10008958
  • NCIT:C3163
  • OMIM:109543
  • OMIM:151400
  • OMIM:609630
  • OMIM:612557
  • OMIM:612558
  • OMIM:612559
  • Orphanet:67038
  • UMLS:C0023434
  • UMLS:C0855095

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 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
https://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
https://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
https://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
https://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
https://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
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000651/ScoringFiles/PGS000651.txt.gz
PGS000874
(PRS41_CLL)
PGP000220 |
Kleinstern G et al. Blood (2018)
Chronic lymphocytic leukemia chronic lymphocytic leukemia 41
-
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000874/ScoringFiles/PGS000874.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
PPM001331 PGS000646
(PRSWEB_PHECODE204.12_GWAS-Catalog-r2019-05-03-X204.12_P_5e-08_MGI_20200608)
PSS000561|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
2,758 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
2,758 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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|
European Ancestry|
756 individuals
PGP000118 |
Fritsche LG et al. Am J Hum Genet (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
PPM002493 PGS000874
(PRS41_CLL)
PSS001123|
Multi-ancestry (including European)|
3,958 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Chronic lymphocytic leukemia OR: 2.49 [2.28, 2.8] C-index: 0.79 [0.78, 0.8] Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.64 [2.94 - 4.51]
PPM002494 PGS000874
(PRS41_CLL)
PSS001123|
Multi-ancestry (including European)|
3,958 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Chronic lymphocytic leukemia in individuals with no family history of hematological cancers OR: 2.46 [2.19, 2.76] C-index: 0.791 [0.77, 0.81] Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.29 [2.49 - 4.35]
PPM002495 PGS000874
(PRS41_CLL)
PSS001123|
Multi-ancestry (including European)|
3,958 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Chronic lymphocytic leukemia in individuals with a family history of hematological cancers OR: 3.79 [2.44, 5.87] C-index: 0.861 [0.82, 0.9] Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 7.58 [2.74 - 21.0]
PPM002496 PGS000874
(PRS41_CLL)
PSS001121|
Ancestry Not Reported|
218 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Chronic lymphocytic leukemia OR: 2.44 [1.65, 3.62] C-index: 0.798 [0.74, 0.85] Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 3.51 [1.39 - 8.86]
PPM002497 PGS000874
(PRS41_CLL)
PSS001122|
Ancestry Not Reported|
153 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Monoclonal B-cell lymphocytosis OR: 2.3 [1.44, 3.67] C-index: 0.773 [0.7, 0.85] Age, sex, study, socioeconomic status (when available) Odds Ratio (OR, top 20% vs middle 20%) = 4.36 [1.45 - 13.1]
PPM002498 PGS000874
(PRS41_CLL)
PSS001119|
Ancestry Not Reported|
1,468 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Chronic lymphocytic leukemia OR: 3.02 [2.49, 3.65] C-index: 0.779 [0.74, 0.81] Age, sex Odds Ratio (OR, top 20% vs middle 20%) = 4.47 [2.76 - 7.24]
PPM002499 PGS000874
(PRS41_CLL)
PSS001120|
Ancestry Not Reported|
1,362 individuals
PGP000220 |
Kleinstern G et al. Blood (2018)
Reported Trait: Monoclonal B-cell lymphocytosis OR: 2.81 [2.18, 3.61] C-index: 0.774 [0.73, 0.82] Age, sex Odds Ratio (OR, top 20% vs middle 20%) = 4.34 [2.21 - 8.50]
PPM002654 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Monoclonal B-cell lymphocytosis OR: 1.86 [1.67, 2.07] C-index: 0.72 [0.69, 0.73] Odds Ratio (OR, top 20% vs middle 20%): 2.38 [1.81, 3.13] Age, sex
PPM002655 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Monoclonal B-cell lymphocytosis OR: 1.15 [1.13, 1.18] C-index: 0.72 [0.7, 0.74] Age, sex An unweighted version of PRS41_CLL was used.
PPM002656 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Low-count monoclonal B-cell lymphocytosis OR: 1.75 [1.55, 1.98] C-index: 0.72 [0.7, 0.75] Odds Ratio (OR, top 20% vs middle 20%): 2.1 [1.53, 2.88] Age, sex
PPM002657 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Low-count monoclonal B-cell lymphocytosis OR: 1.14 [1.11, 1.17] C-index: 0.72 [0.7, 0.75] Age, sex An unweighted version of PRS41_CLL was used.
PPM002658 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: High-count monoclonal B-cell lymphocytosis OR: 2.14 [1.8, 2.56] C-index: 0.73 [0.69, 0.77] Odds Ratio (OR, top 20% vs middle 20%): 3.13 [1.97, 4.98] Age, sex
PPM002659 PGS000874
(PRS41_CLL)
PSS001173|
European Ancestry|
3,191 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: High-count monoclonal B-cell lymphocytosis OR: 1.19 [1.14, 1.23] C-index: 0.725 [0.69, 0.77] Age, sex An unweighted version of PRS41_CLL was used.
PPM002660 PGS000874
(PRS41_CLL)
PSS001172|
European Ancestry|
3,327 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Chronic lymphocytic leukemia OR: 2.53 [2.27, 2.81] C-index: 0.77 [0.75, 0.79] Odds Ratio (OR, top 20% vs middle 20%): 3.49 [2.70, 4.51] Age, sex
PPM002661 PGS000874
(PRS41_CLL)
PSS001172|
European Ancestry|
3,327 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Chronic lymphocytic leukemia OR: 1.23 [1.2, 1.26] C-index: 0.775 [0.76, 0.79] Age, sex An unweighted version of PRS41_CLL was used.
PPM002662 PGS000874
(PRS41_CLL)
PSS001171|
African Ancestry|
408 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Chronic lymphocytic leukemia OR: 1.76 [1.34, 2.31] C-index: 0.62 [0.57, 0.68] Age, sex
PPM002663 PGS000874
(PRS41_CLL)
PSS001171|
African Ancestry|
408 individuals
PGP000234 |
Kleinstern G et al. Leukemia (2021)
|Ext.
Reported Trait: Chronic lymphocytic leukemia OR: 1.07 [1.01, 1.13] C-index: 0.57 [0.53, 0.64] Age, sex An unweighted version of PRS41_CLL was used.

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
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
PSS001119 Cases were individuals with chronic lymphocytic leukemia.
[
  • 201 cases
  • , 1,267 controls
]
Not reported MAYO Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001120 Cases were individuals with monoclonal B-cell lymphocytosis.
[
  • 95 cases
  • , 1,267 controls
]
Not reported MAYO Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001121 Cases were individuals with chronic lymphocytic leukemia.
[
  • 135 cases
  • , 83 controls
]
Not reported NR Cases and controls were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001122 Cases were individuals with monoclonal B-cell lymphocytosis.
[
  • 95 cases
  • , 58 controls
]
Not reported NR Cases and controls were obtained from the Genetic Epidemiology of CLL (GEC) Consortium
PSS001123 Cases were individuals with chronic lymphocytic leukemia (CLL). Of the 3,958 individuals, 242 had a family history (FH) of hematological cancers, whereas 2,409 had no FH of hematological cancers. Of the 242 individuals with a FH, 112 had CLL. Of the 2,409 without a FH, 783 had CLL. FH was defined as a person self-reporting any hematological maligcancy among first-degree relatives. Hematological malignancies were defined as any non-Hodgkin lymphoma, Hodgkin lymphoma, multiple myeloma, or leukemia.
[
  • 1,499 cases
  • , 2,459 controls
]
,
60.81 % Male samples
European, NR 8 cohorts
  • BC
  • ,ENGELA
  • ,EpiLymph
  • ,MAYO
  • ,NCI-SEER
  • ,NSW
  • ,SCALE
  • ,UCSF2
Possible significant sample overlap between this dataset and the dataset used to source PRS41_CLL.
PSS001171 Cases were individuals with chronic lymphocytic leukemia (CLL). CLL diagnoses were made based on the 1996 NCI working group criteria and updated to the 2008 International Workshop CLL criteria wherever possible.
[
  • 173 cases
  • , 235 controls
]
,
66.91 % Male samples
African American or Afro-Caribbean MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL. Additional cases were obtained from Duke University and Cornell
PSS001172 Cases were individuals with chronic lymphocytic leukemia (CLL). CLL diagnoses were made based on the 1996 NCI working group criteria and updated to the 2008 International Workshop CLL criteria wherever possible.
[
  • 696 cases
  • , 2,631 controls
]
,
45.36 % Male samples
European MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL. Additional cases were obtained from Duke University and Cornell
PSS001173 Cases were individuals with monoclonal B-cell lymphocytosis (MBL) from two Mayo Clincs.Within the Mayo Clinic Biobank, MBL was screened for using a highly sensitive, 8-color (CD38, CD45, Kappa, Lambda, CD19, CD23, CD5 and CD20) flow-cytometry assay with the capacity to detect clonal B-cell counts to the 0.005% level (1/20,000 events), and for each individual, 500,000 PBMC events were typically captured. Of the 560 MBL cases, 396 had low-count MBL (LC-MBL) and 164 had high-count MBL (HC-MBL). Wiithin the Mayo Clinic Biobank only a subset of participants had a complete blood count. therefore the percent of clonal B-cells out of total B-cells was used to categorize participants as LC- and HC-MBL. Based on prior evidence, those MBL individuals with a percent clonal B-cell <85% were defined as LC-MBL and those with percent clonal B-cells ≥85% as HC-MBL. Within the Mayo Clinic Chronic lymphocytic leukemia (CLL) Resource, MBL was classified by LC-MBL or HC-MBL according to the B-cell clone size of below or above 0.5 × 109/L threshold, respectively.
[
  • 560 cases
  • , 2,631 controls
]
,
42.28 % Male samples
European MAYO Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL.
PSS000581 PheCode:204.12; ICD9:204.1; ICD10:C91.1
[
  • 249 cases
  • , 2,509 controls
]
European UKB