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
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Synonyms |
122 synonyms
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Mapped term(s) |
18 mapped terms
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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 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 |
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 |
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PSS000581 | PheCode:204.12; ICD9:204.1; ICD10:C91.1 | — | [
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— | European | — | UKB | — |
PSS000561 | PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12 | — | [
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— | European | — | MGI | — |