| Experimental Factor Ontology (EFO) Information | |
| Identifier | EFO_0005952 |
| Description | Distinct from Hodgkin lymphoma both morphologically and biologically, non-Hodgkin lymphoma (NHL) is characterized by the absence of Reed-Sternberg cells, can occur at any age, and usually presents as a localized or generalized lymphadenopathy associated with fever and weight loss. The clinical course varies according to the morphologic type. NHL is clinically classified as indolent, aggressive, or having a variable clinical course. NHL can be of B-or T-/NK-cell lineage. [NCIT: C3211] | Trait category |
Cancer
|
| Synonyms |
5 synonyms
|
| Mapped terms |
11 mapped terms
|
| Child trait(s) | 6 child traits |
| 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) |
|---|---|---|---|---|---|---|
| PGS000080 (CC_NHL) |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Non-Hodgkin's lymphoma | non-Hodgkins lymphoma | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000080/ScoringFiles/PGS000080.txt.gz |
| PGS000641 (PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_P_5e-08_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Non-Hodgkin's lymphoma | non-Hodgkins lymphoma | 12 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000641/ScoringFiles/PGS000641.txt.gz | |
| PGS000642 (PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_PT_UKB_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Non-Hodgkin's lymphoma | non-Hodgkins lymphoma | 10 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000642/ScoringFiles/PGS000642.txt.gz | |
| PGS000643 (PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_PRS-CS_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Nodular lymphoma | follicular lymphoma | 1,048,780 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000643/ScoringFiles/PGS000643.txt.gz | |
| PGS000644 (PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_LASSOSUM_MGI_20200608) |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Nodular lymphoma | follicular lymphoma | 2,209,179 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000644/ScoringFiles/PGS000644.txt.gz | |
| 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) |
Chronic lymphocytic leukemia | 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) |
Chronic lymphocytic leukemia | 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) |
Chronic lymphocytic leukemia | 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) |
Chronic lymphocytic leukemia | 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) |
Chronic lymphocytic leukemia | 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) |
Chronic lymphocytic leukemia | chronic lymphocytic leukemia | 76 | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000651/ScoringFiles/PGS000651.txt.gz | |
| PGS000791 (CC_NHL_IV) |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Non-Hodgkin's lymphoma | non-Hodgkins lymphoma | 19 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000791/ScoringFiles/PGS000791.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 |
| PGS002303 (PRS9_DLBCL) |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Diffuse large B-cell lymphoma | diffuse large B-cell lymphoma | 9 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002303/ScoringFiles/PGS002303.txt.gz |
| PGS002304 (PRS6_FL) |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Follicular lymphoma | follicular lymphoma | 6 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002304/ScoringFiles/PGS002304.txt.gz |
| PGS003448 (PRS15_ALL) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Acute lymphoblastic leukemia | acute lymphoblastic leukemia | 15 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003448/ScoringFiles/PGS003448.txt.gz |
| PGS003451 (PRS2_MZL) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Marginal zone lymphoma | marginal zone B-cell lymphoma | 2 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003451/ScoringFiles/PGS003451.txt.gz |
| PGS003452 (PRS2_WM) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Waldenström macroglobulinemia | Waldenstrom macroglobulinemia | 2 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003452/ScoringFiles/PGS003452.txt.gz |
| PGS003453 (PRS43_CLL) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Chronic lymphocytic leukemia | chronic lymphocytic leukemia | 43 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003453/ScoringFiles/PGS003453.txt.gz |
| PGS003454 (PRS5_DLBCL) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Diffuse large B-cell lymphoma | diffuse large B-cell lymphoma | 5 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003454/ScoringFiles/PGS003454.txt.gz |
| PGS003455 (PRS7_FL) |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Follicular lymphoma | follicular lymphoma | 7 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003455/ScoringFiles/PGS003455.txt.gz |
| PGS004248 (PRS20_nhl) |
PGP000542 | Kim ES et al. NPJ Precis Oncol (2023) |
Non-Hodgkin's lymphoma | non-Hodgkins lymphoma | 20 | - |
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004248/ScoringFiles/PGS004248.txt.gz |
|
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 |
|---|---|---|---|---|---|---|---|---|---|
| PPM000200 | PGS000080 (CC_NHL) |
PSS000119| European Ancestry| 412,765 individuals |
PGP000050 | Graff RE et al. Nat Commun (2021) |
Reported Trait: Non-Hodgkin's lymphoma | OR: 1.25 [1.2, 1.3] | — | — | Genotyping reagent kit (GERA cohort only), genotyping array (UK Biobank only), age, sex, 10 PCs. | Results from meta-analysis of GERA and UKB |
| PPM002046 | PGS000080 (CC_NHL) |
PSS001019| European Ancestry| 391,968 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |Ext. |
Reported Trait: Incident non-hodgkin's lymphoma | HR: 1.16 [1.09, 1.24] | AUROC: 0.677 C-index: 0.676 (0.01) |
— | Age at assessment, sex, genotyping array, PCs(1-15) | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
| PPM017168 | PGS000080 (CC_NHL) |
PSS010148| European Ancestry| 721 individuals |
PGP000443 | Byrne S et al. Int J Epidemiol (2023) |Ext. |
Reported Trait: Non-Hodgkin's lymphoma | HR: 1.19 [1.11, 1.28] | — | — | age at baseline, sex (where relevant), assessment centre, 40 principal components of ancestries (PCs), Townsend Index, education, birth location, income, lifestyle index, additional cancer-specific covariates | — |
| PPM001326 | PGS000641 (PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_P_5e-08_UKB_20200608) |
PSS000580| European Ancestry| 9,952 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Non-Hodgkins lymphoma | OR: 1.211 [1.133, 1.294] β: 0.191 (0.034) |
AUROC: 0.541 [0.521, 0.561] | Nagelkerke's Pseudo-R²: 0.00682 Brier score: 0.0821 Odds Ratio (OR, top 1% vs. Rest): 2.05 [1.24, 3.4] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_P_5e-08_UKB_20200608 |
| PPM001327 | PGS000642 (PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_PT_UKB_20200608) |
PSS000580| European Ancestry| 9,952 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Non-Hodgkins lymphoma | OR: 1.239 [1.16, 1.324] β: 0.214 (0.0337) |
AUROC: 0.547 [0.527, 0.566] | Nagelkerke's Pseudo-R²: 0.0087 Brier score: 0.082 Odds Ratio (OR, top 1% vs. Rest): 2.05 [1.24, 3.4] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE202.2_GWAS-Catalog-r2019-05-03-X202.2_PT_UKB_20200608 |
| PPM001328 | PGS000643 (PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_PRS-CS_MGI_20200608) |
PSS000560| European Ancestry| 3,256 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Nodular lymphoma | OR: 1.133 [1.005, 1.277] β: 0.125 (0.061) |
AUROC: 0.532 [0.497, 0.568] | Nagelkerke's Pseudo-R²: 0.00282 Brier score: 0.0825 Odds Ratio (OR, top 1% vs. Rest): 2.49 [1.1, 5.65] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_PRS-CS_MGI_20200608 |
| PPM001329 | PGS000644 (PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_LASSOSUM_MGI_20200608) |
PSS000560| European Ancestry| 3,256 individuals |
PGP000118 | Fritsche LG et al. Am J Hum Genet (2020) |
Reported Trait: Nodular lymphoma | OR: 1.149 [1.021, 1.294] β: 0.139 (0.0606) |
AUROC: 0.538 [0.504, 0.573] | Nagelkerke's Pseudo-R²: 0.00349 Brier score: 0.0825 Odds Ratio (OR, top 1% vs. Rest): 1.48 [0.538, 4.05] |
age, sex, batch PCs 1-4 | Cancer PRSweb PheWAS Results: PRSWEB_PHECODE202.21_C-FOLLICULAR-LYMPHOMA_LASSOSUM_MGI_20200608 |
| 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 |
| PPM002062 | PGS000791 (CC_NHL_IV) |
PSS001019| European Ancestry| 391,968 individuals |
PGP000186 | Kachuri L et al. Nat Commun (2020) |
Reported Trait: Incident non-hodgkin's lymphoma | HR: 1.15 [1.08, 1.22] | AUROC: 0.677 C-index: 0.674 (0.01) |
R²: 0.227 | Age at assessment, sex, genotyping array, PCs(1-15) | C-index calculated as a weighted average between 1 and 5 years and AUC at 5 years. |
| 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. |
| PPM013032 | PGS002303 (PRS9_DLBCL) |
PSS009657| European Ancestry| 308 individuals |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Reported Trait: Diffuse large B-cell lymphoma | — | AUROC: 0.56 [0.53, 0.6] | — | — | — |
| PPM013040 | PGS002303 (PRS9_DLBCL) |
PSS009657| European Ancestry| 308 individuals |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Reported Trait: Diffuse large B-cell lymphoma | — | — | Hazard ratio (HR top 5% vs average): 1.6 [1.01, 2.54] | Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) | — |
| PPM013033 | PGS002304 (PRS6_FL) |
PSS009658| European Ancestry| 197 individuals |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Reported Trait: Follicular lymphoma | — | AUROC: 0.61 [0.59, 0.63] | — | — | — |
| PPM013041 | PGS002304 (PRS6_FL) |
PSS009658| European Ancestry| 197 individuals |
PGP000328 | Choi J et al. Int J Cancer (2020) |
Reported Trait: Follicular lymphoma | — | — | Hazard ratio (HR top 5% vs average): 2.33 [1.38, 3.93] | Age, birth cohort, genotyping array, top 10 PCs for ancestry and sex (for nonsex specific cancer only) | — |
| PPM017230 | PGS003448 (PRS15_ALL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 0.95 [0.9, 1.0] | — | — | — | — |
| PPM017238 | PGS003448 (PRS15_ALL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 0.99 [0.94, 1.04] | — | — | — | — |
| PPM017246 | PGS003448 (PRS15_ALL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 1.01 [0.95, 1.06] | — | — | — | — |
| PPM017254 | PGS003448 (PRS15_ALL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 1.02 [0.93, 1.12] | — | — | — | — |
| PPM017227 | PGS003451 (PRS2_MZL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 1.26 [1.09, 1.46] | — | — | — | — |
| PPM017235 | PGS003451 (PRS2_MZL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 1.53 [1.34, 1.75] | — | — | — | — |
| PPM017243 | PGS003451 (PRS2_MZL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 1.39 [1.21, 1.61] | — | — | — | — |
| PPM017251 | PGS003451 (PRS2_MZL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 2.43 [1.93, 3.06] | — | — | — | — |
| PPM017228 | PGS003452 (PRS2_WM) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 1.07 [1.01, 1.14] | — | — | — | — |
| PPM017236 | PGS003452 (PRS2_WM) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 1.24 [1.18, 1.31] | — | — | — | — |
| PPM017244 | PGS003452 (PRS2_WM) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 1.12 [1.05, 1.19] | — | — | — | — |
| PPM017252 | PGS003452 (PRS2_WM) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 1.18 [1.07, 1.3] | — | — | — | — |
| PPM017224 | PGS003453 (PRS43_CLL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 2.17 [2.07, 2.28] | — | — | — | — |
| PPM017232 | PGS003453 (PRS43_CLL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 1.17 [1.12, 1.22] | — | — | — | — |
| PPM017240 | PGS003453 (PRS43_CLL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 1.12 [1.07, 1.17] | — | — | — | — |
| PPM017248 | PGS003453 (PRS43_CLL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 1.15 [1.07, 1.24] | — | — | — | — |
| PPM017225 | PGS003454 (PRS5_DLBCL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 1.33 [1.14, 1.54] | — | — | — | — |
| PPM017233 | PGS003454 (PRS5_DLBCL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 2.69 [2.35, 3.08] | — | — | — | — |
| PPM017249 | PGS003454 (PRS5_DLBCL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 2.1 [1.63, 2.72] | — | — | — | — |
| PPM017241 | PGS003454 (PRS5_DLBCL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 1.66 [1.42, 1.94] | — | — | — | — |
| PPM017226 | PGS003455 (PRS7_FL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Chronic lymphocytic leukemia | OR: 1.07 [0.98, 1.17] | — | — | — | — |
| PPM017234 | PGS003455 (PRS7_FL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Diffuse large B-cell lymphoma | OR: 1.28 [1.19, 1.39] | — | — | — | — |
| PPM017242 | PGS003455 (PRS7_FL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Follicular lymphoma | OR: 2.77 [2.52, 3.04] | — | — | — | — |
| PPM017250 | PGS003455 (PRS7_FL) |
PSS010176| European Ancestry| 20,134 individuals |
PGP000448 | Berndt SI et al. Leukemia (2022) |
Reported Trait: Marginal zone lymphoma | OR: 0.94 [0.81, 1.09] | — | — | — | — |
| PPM020305 | PGS004248 (PRS20_nhl) |
PSS011328| European Ancestry| 133,830 individuals |
PGP000542 | Kim ES et al. NPJ Precis Oncol (2023) |
Reported Trait: Non-Hodgkin's lymphoma | HR: 1.16 [1.03, 1.3] | — | — | first 10 genetic principal components | — |
| PPM020313 | PGS004248 (PRS20_nhl) |
PSS011329| European Ancestry| 115,207 individuals |
PGP000542 | Kim ES et al. NPJ Precis Oncol (2023) |
Reported Trait: Non-Hodgkin's lymphoma | HR: 1.22 [1.1, 1.36] | — | — | first 10 genetic principal components | — |
|
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 |
|---|---|---|---|---|---|---|---|---|
| PSS000560 | PheCode:202.21; ICD9CM:202.00, 202.01, 202.02, 202.03, 202.04, 202.05, 202.06, 202.07, 202.08; ICD10CM:C82, C82.0, C82.00, C82.01, C82.02, C82.03, C82.04, C82.05, C82.06, C82.07, C82.08, C82.09, C82.1, C82.10, C82.11, C82.12, C82.13, C82.14, C82.15, C82.16, C82.17, C82.18, C82.19, C82.2, C82.20, C82.21, C82.22, C82.23, C82.24, C82.25, C82.26, C82.27, C82.28, C82.29, C82.3, C82.30, C82.31, C82.32, C82.33, C82.34, C82.35, C82.36, C82.37, C82.38, C82.39, C82.4, C82.40, C82.41, C82.42, C82.43, C82.44, C82.45, C82.46, C82.47, C82.48, C82.49, C82.5, C82.50, C82.51, C82.52, C82.53, C82.54, C82.55, C82.56, C82.57, C82.58, C82.59, C82.6, C82.60, C82.61, C82.62, C82.63, C82.64, C82.65, C82.66, C82.67, C82.68, C82.69, C82.8, C82.80, C82.81, C82.82, C82.83, C82.84, C82.85, C82.86, C82.87, C82.88, C82.89, C82.9, C82.90, C82.91, C82.92, C82.93, C82.94, C82.95, C82.96, C82.97, C82.98, C82.99 | — | [
|
— | European | — | MGI | — |
| PSS000561 | PheCode:204.12; ICD9CM:204.10, 204.11, 204.12; ICD10CM:C91.1, C91.10, C91.11, C91.12 | — | [
|
— | European | — | MGI | — |
| PSS010176 | — | — | [
|
— | European | — | NR | Inter- Lymph Consortium |
| PSS011328 | — | — | 133,830 individuals, 0.0 % Male samples |
— | European (British) |
— | UKB | — |
| PSS011329 | — | — | 115,207 individuals, 100.0 % Male samples |
— | European (British) |
— | UKB | — |
| PSS000580 | PheCode:202.2; ICD9:200, 200.2, 200.8, 202.1, 202.2, 202.8, 202.9; ICD10:B21.1, C82.0, C82.1, C82.2, C82.7, C82.9, C83.0, C83.1, C83.2, C83.3, C83.4, C83.5, C83.6, C83.7, C83.8, C83.9, C84.0, C84.1, C84.2, C84.3, C84.4, C84.5, C85.0, C85.1, C85.7, C85.9, C96.7, C96.9, L41.2 | — | [
|
— | European | — | UKB | — |
| PSS000581 | PheCode:204.12; ICD9:204.1; ICD10:C91.1 | — | [
|
— | European | — | UKB | — |
| PSS010148 | — | — | [
|
— | European | — | UKB | — |
| 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. | — | [ ,
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. | — | [ ,
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. | — | [ ,
42.28 % Male samples |
— | European | — | MAYO | Possibly significant sample overlap between this dataset and the dataset used to source PRS41_CLL. |
| PSS009657 | diffuse large B-cell lymphoma (ICD-10 = C83.3) | — | 308 individuals | — | European | — | UKB | — |
| PSS009658 | follicular lymphoma (ICD- 10 = C82 or ICD-O: 9690) | — | 197 individuals | — | European | — | UKB | — |
| PSS001119 | Cases were individuals with chronic lymphocytic leukemia. | — | [
|
— | Not reported | — | MAYO | Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium |
| PSS001120 | Cases were individuals with monoclonal B-cell lymphocytosis. | — | [
|
— | Not reported | — | MAYO | Cases were obtained from the Genetic Epidemiology of CLL (GEC) Consortium |
| PSS001121 | Cases were individuals with chronic lymphocytic leukemia. | — | [
|
— | 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. | — | [
|
— | 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. | — | [ ,
60.81 % Male samples |
— | European, NR | — | 8 cohorts
|
Possible significant sample overlap between this dataset and the dataset used to source PRS41_CLL. |
| PSS001019 | Individuals with at least one recorded incident diagnosis of a borderline, in situ, or malignant primary cancer were defined as cases. | — | [
|
— | European | — | UKB | — |
| PSS000119 | Cancer diagnoses were obtained from reigstry data in GERA, and ICD-9/10 codes mapped to ICD-O-3 codes in UK Biobank. Cancers for this phenotype were classified using the following SEER site recode(s): 33041, and 33042 | — | [ ,
46.0 % Male samples |
Mean = 58.0 years | European | — | GERA, UKB | — |