non-Hodgkin lymphoma

disease
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Also known as NHLnon-Hodgkin's lymphomanon-Hodgkin's lymphoma (NHL)non-Hodgkins lymphoma

Summary

non-Hodgkin lymphoma (MONDO:0018908) is a cancer (an umbrella term covering 10 Mondo subtypes) with 8 cohort genes (92 GWAS associations across 31 studies; 5 CIViC-evidence somatic drivers; 13 ClinVar predisposition records) and 1,051 clinical trials. Molecularly, EZH2 Y646F confers sensitivity to Tazemetostat in Non-Hodgkin Lymphoma (CIViC Level D). Top therapeutic interventions include rituximab, bendamustine, and plerixafor.

At a glance

  • Classification: Cancer
  • Prevalence: 1-5 / 10 000 (Europe) [Orphanet-validated]
  • Umbrella term: 10 Mondo subtypes
  • Cohort genes: 8
  • GWAS associations: 92
  • ClinVar variants: 13
  • Clinical trials: 1,051
  • Precision-medicine evidence (CIViC): 1 subtype–drug association

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Annual incidence1-5 / 10 00011.6EuropeValidated
Point prevalence1-5 / 10 000EuropeNot yet validated

Identifiers

Disease identifiers

FieldValue
Canonical namenon-Hodgkin lymphoma
Mondo IDMONDO:0018908
EFOEFO:0005952
MeSHD008228
Orphanet547
DOIDDOID:0060060
NCITC3211
UMLSC0024305
MedGen6160
MedDRA10029547
Is cancer (heuristic)yes

Also known as: NHL · non-Hodgkin lymphoma · non-Hodgkin’s lymphoma · non-Hodgkin’s lymphoma (NHL) · non-Hodgkins lymphoma

Data availability: 13 ClinVar variants · 92 GWAS associations (31 studies) · 14 cell lines · 55 intOGen driver records.

Disease family

An umbrella term covering 10 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumorneoplastic disease or syndromeneoplasmhematopoietic and lymphoid system neoplasmhematopoietic and lymphoid cell neoplasmlymphoid neoplasmlymphomanon-Hodgkin lymphoma

Related subtypes (26): prostate lymphoma, nasal cavity lymphoma, bladder lymphoma, tracheal lymphoma, retroperitoneal lymphoma, ureteral lymphoma, ovarian lymphoma, B-cell lymphoma, unclassifiable, with features intermediate between diffuse large b-cell lymphoma and classical Hodgkin lymphoma, pediatric lymphoma, adult lymphoma, breast lymphoma, heart lymphoma, chest wall lymphoma, lung lymphoma, mediastinal malignant lymphoma, eye lymphoma, B-cell neoplasm, gastrointestinal lymphoma, Hodgkins lymphoma, peripheral T-cell lymphoma, not otherwise specified, composite lymphoma, AIDS-related primary central nervous system lymphoma, primary organ-specific lymphoma, extranodal nasal NK/T cell lymphoma, methotrexate-associated lymphoproliferative disorders, progressive transformation of germinal centers

Subtypes (10): lymphoblastic lymphoma, lymphosarcoma, acute lymphoblastic leukemia, lymphoma, non-Hodgkin, familial, B-cell non-Hodgkin lymphoma, T-cell non-Hodgkin lymphoma, lung non-Hodgkin lymphoma, ocular adnexal lymphoma, large-cell immunoblastic lymphoma, gastric non-hodgkin lymphoma

Genetics & variants

GWAS landscape

92 GWAS associations across 31 studies. Top hits map to 33 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs126823749e-29PCAT1, CASC8, POU5F1B?0.93
rs12196511e-25FGFR2?1.09
rs29815841e-21FGFR2?0.94
rs109082783e-21HNF1B?1.06
rs20974421e-19HLA-DRA - HLA-DRB9?1.36
rs45387462e-17HLA-DQB1T1.22
rs1121495732e-17TOX3?1.08
rs785405261e-15LINC01488 - PNCRNA-D?1.13
rs354097102e-15HLA-DQB1?1.09
rs74637082e-15PCAT1, PRNCR1, CASC19?1.08
rs28583146e-15HLA-DQB1 - MTCO3P1G0.16
rs341021541e-14HLA-DRB1 - HLA-DQA1G1.43
rs116517551e-14HNF1B?1.06
rs14859958e-14LINC01488?0.95
rs92737362e-13HLA-DQB1?1.12
rs29763843e-13PSCA, JRK?1.07
rs38066245e-13EOMES - LINC01980G1.14
rs359236438e-13GRAMD1BG1.19
rs176769492e-12PHLPP1 - BCL2A0.78
rs25851813e-12PSCA - LY6K?1.05
rs24719601e-11UQCRHP1 - AIF1A1.23
rs37890681e-11MIR4435-2HG, BCL2L11G1.13
rs132552921e-11PVT1C0.13
rs123656992e-11Y_RNA - CXCR5G0.16
rs27659742e-11CELF2C0.13
rs1494826082e-11SNHG10A1.67
rs1504805672e-11MTCO3P1 - HLA-DQB3?0.17
rs1831615003e-11LINC01523A3.03
rs79192085e-11LINC00841 - LINC03089?1.23
rs40076426e-11CDKN2B-AS1?0.96

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90651054Sato G202343,098334,343Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis.
GCST90308764Sato G202329,753150,462Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis.
GCST90651069Sato G202329,753150,462Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis.
GCST90267403Berndt SI202213,76318,862Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes.
GCST90477247Verma A20245,910443,358Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90011819Rashkin SR20202,400410,350Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts.
GCST90651049Sato G20231,997334,343Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis.
GCST90435644Zhou W20181,793404,466Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90079638Backman JD20211,579386,126Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083624Backman JD20211,579386,126Exome sequencing and analysis of 454,787 UK Biobank participants.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory5
Tier 4: intronic/intergenic45

MAF distribution

BucketVariants
common (>=0.05)45
low_freq (0.01-0.05)0
rare (<0.01)2
unknown3

Functional consequences

ConsequenceCount
intron_variant28
intergenic_variant14
regulatory_region_variant5
non_coding_transcript_exon_variant3

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs126823748127398703C>A,G,T0.05intron_variantPCAT1, CASC8, POU5F1B9e-29Tier 4: intronic/intergenic
rs121965110121584987G>A,C,T0.05intron_variantFGFR21e-25Tier 4: intronic/intergenic
rs298158410121590702A>C,G,T0.05intron_variantFGFR21e-21Tier 4: intronic/intergenic
rs109082781737739961A>C,G,T0.05intron_variantHNF1B3e-21Tier 4: intronic/intergenic
rs2097442632454414G>A,T0.05intron_variantHLA-DRA - HLA-DRB91e-19Tier 4: intronic/intergenic
rs4538746632664336C>A,G,T0.05intron_variantHLA-DQB12e-17Tier 4: intronic/intergenic
rs1121495731652547333G>C,T0.05intron_variantTOX32e-17Tier 4: intronic/intergenic
rs785405261169516650C>T0.05regulatory_region_variantLINC01488 - PNCRNA-D1e-15Tier 3: regulatory
rs35409710632661126G>A0.05intron_variantHLA-DQB12e-15Tier 4: intronic/intergenic
rs74637088127091810G>A,C,T0.05non_coding_transcript_exon_variantPCAT1, PRNCR1, CASC192e-15Tier 4: intronic/intergenic
rs2858314632695671G>A,C0.233intergenic_variantHLA-DQB1 - MTCO3P16e-15Tier 4: intronic/intergenic
rs34102154632604329G>A0.05regulatory_region_variantHLA-DRB1 - HLA-DQA11e-14Tier 3: regulatory
rs116517551737739849T>C0.05intron_variantHNF1B1e-14Tier 4: intronic/intergenic
rs14859951169492939G>A,C0.05non_coding_transcript_exon_variantLINC014888e-14Tier 4: intronic/intergenic
rs9273736632661595G>A,C0.05intron_variantHLA-DQB12e-13Tier 4: intronic/intergenic
rs29763848142671576T>A,C0.05intergenic_variantPSCA, JRK3e-13Tier 4: intronic/intergenic
rs3806624327723132A>C,G,T0.05regulatory_region_variantEOMES - LINC019805e-13Tier 3: regulatory
rs3592364311123484683A>G0.05intron_variantGRAMD1B8e-13Tier 4: intronic/intergenic
rs176769491863118405G>A,C0.05intergenic_variantPHLPP1 - BCL22e-12Tier 4: intronic/intergenic
rs25851818142690296C>A0.05intergenic_variantPSCA - LY6K3e-12Tier 4: intronic/intergenic
rs2471960631612762G>A,T0.05intron_variantUQCRHP1 - AIF11e-11Tier 4: intronic/intergenic
rs37890682111151670A>G0.05intron_variantMIR4435-2HG, BCL2L111e-11Tier 4: intronic/intergenic
rs132552928128064327C>T0.267intron_variantPVT11e-11Tier 4: intronic/intergenic
rs1236569911118872577G>A0.137regulatory_region_variantY_RNA - CXCR52e-11Tier 3: regulatory
rs27659741011246455C>A,G,T0.389intron_variantCELF22e-11Tier 4: intronic/intergenic
rs1494826081495525224A>G0.001intron_variantSNHG102e-11Tier 4: intronic/intergenic
rs150480567632712473intergenic_variantMTCO3P1 - HLA-DQB32e-11Tier 4: intronic/intergenic
rs1831615002048008648A>C,G0intron_variantLINC015233e-11Tier 4: intronic/intergenic
rs79192081044178109G>A,T0.05intergenic_variantLINC00841 - LINC030895e-11Tier 4: intronic/intergenic
rs4007642922093300A>C,T0.05intron_variantCDKN2B-AS16e-11Tier 4: intronic/intergenic

ClinVar germline variants

13 retrieved; paginated sample, class counts are floors:

6 pathogenic, 3 conflicting classifications of pathogenicity, 1 pathogenic/likely pathogenic, 1 benign, 1 likely benign, 1 uncertain significance

ClinVarVariant (HGVS)GeneClassificationReview
31907NM_004048.4(B2M):c.286G>A (p.Asp96Asn)B2MPathogeniccriteria provided, single submitter
13970NM_004333.6(BRAF):c.1405G>C (p.Gly469Arg)BRAFPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
13971NM_004333.6(BRAF):c.1406G>C (p.Gly469Ala)BRAFPathogeniccriteria provided, single submitter
7765NM_032977.4(CASP10):c.1241C>T (p.Ala414Val)CASP10Pathogenicno assertion criteria provided
7766NM_032977.4(CASP10):c.769C>T (p.Gln257Ter)CASP10Pathogenicno assertion criteria provided
7767NM_032977.4(CASP10):c.1042_1043insA (p.Gly348fs)CASP10Pathogenicno assertion criteria provided
6192NM_003579.4(RAD54L):c.1331T>A (p.Val444Glu)RAD54LPathogenicno assertion criteria provided
13972NM_004333.6(BRAF):c.1781A>G (p.Asp594Gly)BRAFConflicting classifications of pathogenicitycriteria provided, conflicting classifications
801487NM_003579.4(RAD54L):c.796G>C (p.Val266Leu)RAD54LConflicting classifications of pathogenicitycriteria provided, conflicting classifications
12367NM_000546.6(TP53):c.974G>T (p.Gly325Val)TP53Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
801489NM_003579.4(RAD54L):c.1870-1G>ALRRC41Uncertain significancecriteria provided, single submitter
5638NM_012415.3(RAD54B):c.1778A>G (p.Asn593Ser)RAD54BBenigncriteria provided, single submitter
801488NM_003579.4(RAD54L):c.888C>T (p.Asp296=)RAD54LLikely benigncriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 36 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
EZH2ActALL,AML,DLBCLNOS,ES,MLYM,NHLCIViC #63
BRAFActBLCA,BRCA,CHOL,CLLSLL,COAD,COADREAD,CSCC,DLBCLNOS,GBM,GIST,HGGNOS,LGGNOS,LUAD,MEL,MLYM,NSCLC,OVT,PAST,PCM,PRAD,PRCC,PROSTATE,READ,SACA,SKCM,STAD,UCEC,WDTCCIViC #5
TP53LoFACC,ALL,AML,ANGS,ANSC,BCC,BL,BLADDER,BLCA,BRCA,CCRCC,CEAD,CESC,CHOL,CHRCC,CLLSLL,COAD,COADREAD,CSCC,DLBCLNOS,EGC,ES,ESCA,ESCC,GB,GBC,GBM,GIST,HCC,HGGNOS,HNSC,LGGNOS,LIPO,LMS,LNM,LUAD,LUSC,MBL,MEL,MLYM,MT,NBL,NETNOS,NHL,NPC,NSCLC,OS,OVT,PAAD,PANCREAS,PAST,PCM,PLMESO,PRAD,PRCC,PROSTATE,RCC,READ,SACA,SARCNOS,SCLC,SIC,SKCM,SKIN,SOFT_TISSUE,STAD,STOMACH,THYM,UCEC,UCS,UTUC,VULVA,WDTC,WTCIViC #45
B2MLoFCESC,DLBCLNOS,HNSC,MEL,MLYM,NHL,NSCLCCIViC #537
RAD54LCIViC #6676

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
EZH2Orphanet:3447Weaver syndrome
BRAFOrphanet:1340Cardiofaciocutaneous syndrome
BRAFOrphanet:146Differentiated thyroid carcinoma
BRAFOrphanet:251615Pilomyxoid astrocytoma
BRAFOrphanet:389Langerhans cell histiocytosis
BRAFOrphanet:500Noonan syndrome with multiple lentigines
BRAFOrphanet:54595Craniopharyngioma
BRAFOrphanet:58017Classic hairy cell leukemia
BRAFOrphanet:626Large/giant congenital melanocytic nevus
BRAFOrphanet:648Noonan syndrome
BRAFOrphanet:840Syringocystadenoma papilliferum
BRAFOrphanet:96253Cushing disease
TP53Orphanet:1333Familial pancreatic carcinoma
TP53Orphanet:145Hereditary breast and/or ovarian cancer syndrome
TP53Orphanet:1501Adrenocortical carcinoma
TP53Orphanet:210159Adult hepatocellular carcinoma
TP53Orphanet:251576Gliosarcoma
TP53Orphanet:251579Giant cell glioblastoma
TP53Orphanet:251899Choroid plexus carcinoma
TP53Orphanet:2807Papilloma of choroid plexus
TP53Orphanet:293199Pleomorphic rhabdomyosarcoma
TP53Orphanet:3318Essential thrombocythemia
TP53Orphanet:524Li-Fraumeni syndrome
TP53Orphanet:52688Myelodysplastic syndrome
TP53Orphanet:585909B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2)
TP53Orphanet:667662Breast implant-associated anaplastic large cell lymphoma
TP53Orphanet:668Osteosarcoma
TP53Orphanet:67038B-cell chronic lymphocytic leukemia
TP53Orphanet:70573Small cell lung cancer
TP53Orphanet:96253Cushing disease
TP53Orphanet:99756Alveolar rhabdomyosarcoma
TP53Orphanet:99757Embryonal rhabdomyosarcoma
CASP10Orphanet:3261Autoimmune lymphoproliferative syndrome
B2MOrphanet:314652Variant ABeta2M amyloidosis
B2MOrphanet:34592Immunodeficiency by defective expression of MHC class I
RAD54LOrphanet:227535Hereditary breast cancer

Cohort genes → proteins

8 cohort genes, 8 distinct canonical proteins.

Evidence partition

SubsetGenes
civic_only1
multi_evidence7

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
EZH2HGNC:3527ENSG00000106462Q15910Histone-lysine N-methyltransferase EZH2civic_evidence
BRAFHGNC:1097ENSG00000157764P15056Serine/threonine-protein kinase B-rafclinvar
TP53HGNC:11998ENSG00000141510P04637Cellular tumor antigen p53clinvar
CASP10HGNC:1500ENSG00000003400Q92851Caspase-10clinvar
LRRC41HGNC:16917ENSG00000132128Q15345Leucine-rich repeat-containing protein 41clinvar
RAD54BHGNC:17228ENSG00000197275Q9Y620DNA repair and recombination protein RAD54Bclinvar
B2MHGNC:914ENSG00000166710P61769Beta-2-microglobulinclinvar
RAD54LHGNC:9826ENSG00000085999Q92698DNA repair and recombination protein RAD54-likeclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
EZH2Histone-lysine N-methyltransferase EZH2Catalytic subunit of the PRC2/EED-EZH2 complex, a Polycomb group (PcG) complex that methylates ‘Lys-9’ (H3K9me) and ‘Lys-27’ (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene.
BRAFSerine/threonine-protein kinase B-rafProtein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus.
TP53Cellular tumor antigen p53Multifunctional transcription factor that induces cell cycle arrest, DNA repair or apoptosis upon binding to its target DNA sequence.
CASP10Caspase-10Involved in the activation cascade of caspases responsible for apoptosis execution.
LRRC41Leucine-rich repeat-containing protein 41Probable substrate recognition component of an ECS (Elongin BC-CUL2/5-SOCS-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins.
RAD54BDNA repair and recombination protein RAD54BMultifunctional ATPase that could play with RAD54, a redundant role in homologous recombination (HR), a major pathway for repairing DNA double-strand breaks (DSBs), single-stranded DNA (ssDNA) gaps, and stalled or collapsed replication for…
B2MBeta-2-microglobulinComponent of the class I major histocompatibility complex (MHC).
RAD54LDNA repair and recombination protein RAD54-likeMultifunctional ATPase that plays a role in homologous recombination (HR) which is a major pathway for repairing DNA double-strand breaks (DSBs), single-stranded DNA (ssDNA) gaps, and stalled or collapsed replication forks.

Protein-family classification

Druggable: 6 · Difficult: 1 · Unknown: 1 · Druggable fraction: 0.75

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Enzyme (other)46.0×0.013
Antibody/Immunoglobulin13.6×0.424
Kinase13.5×0.424
Transcription factor11.0×0.805
Other/Unknown10.2×0.999

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
EZH2Enzyme (other)yes2.1.1.356SANT/Myb, SET_dom, EZH1/EZH2_N
BRAFKinaseyes2.7.10.2Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, PKC_DAG/PE
TP53Transcription factornop53_tumour_suppressor, p53-like_TF_DNA-bd_sf, p53_tetrameristn
CASP10Enzyme (other)yes3.4.22.63Pept_C14_p20, DED_dom, Pept_C14_p10
LRRC41Other/UnknownnoLeu_rpt_41, LRR_dom_sf
RAD54BEnzyme (other)yes3.6.4.B9SNF2_N, Helicase_C-like, Helicase_ATP-bd
B2MAntibody/ImmunoglobulinyesIg/MHC_CS, Ig_C1-set, Ig-like_dom
RAD54LEnzyme (other)yes3.6.4.B9SNF2_N, Helicase_C-like, Helicase_ATP-bd

Expression context

Cohort genes with no expression data: 0.

6 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)8
unknown0

Top tissues across cohort

TissueCohort genes
ventricular zone3
ganglionic eminence2
colonic epithelium2
granulocyte2
monocyte2
right uterine tube2
embryo1
buccal mucosa cell1
calcaneal tendon1
tendon of biceps brachii1
adenohypophysis1
left uterine tube1
male germ line stem cell (sensu Vertebrata) in testis1
primordial germ cell in gonad1
leukocyte1
left testis1
right testis1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
EZH2216ubiquitousmarkerganglionic eminence, ventricular zone, embryo
BRAF265ubiquitousmarkerbuccal mucosa cell, colonic epithelium, calcaneal tendon
TP53223ubiquitousmarkerventricular zone, ganglionic eminence, tendon of biceps brachii
CASP10206ubiquitousmarkercolonic epithelium, granulocyte, monocyte
LRRC41281ubiquitousmarkerright uterine tube, left uterine tube, adenohypophysis
RAD54B201ubiquitousyesright uterine tube, primordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis
B2M134ubiquitousmarkergranulocyte, monocyte, leukocyte
RAD54L173ubiquitousyesleft testis, right testis, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 2.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TP5322,736
EZH29,646
BRAF7,394
RAD54L2,927
RAD54B2,743
CASP101,242
LRRC41683
B2M415

Intra-cohort edges

ABSources
BRAFTP53string_interaction
CASP10TP53string_interaction

Structural data

PDB: 6 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
B2MP617691,226
TP53P04637313
BRAFP15056131
EZH2Q1591038
RAD54BQ9Y6204
RAD54LQ926981

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
LRRC41Q1534571.96
CASP10Q9285169.54

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 139. Enrichment computed across 8 evidence-associated genes (6 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
TP53 Regulates Transcription of Caspase Activators and Caspases2317.2×0.002TP53, CASP10
Loss of function of TP53 in cancer due to loss of tetramerization ability11903.3×0.024TP53
Regulation of PTEN gene transcription259.5×0.024TP53, EZH2
Regulation of TP53 Expression1951.7×0.029TP53
Transcriptional activation of cell cycle inhibitor p211475.8×0.029TP53
Signaling by MRAS-complex mutants1475.8×0.029BRAF
Signalling to p38 via RIT and RIN1380.7×0.029BRAF
FasL/ CD95L signaling1380.7×0.029CASP10
Activation of NOXA and translocation to mitochondria1317.2×0.029TP53
Negative feedback regulation of MAPK pathway1317.2×0.029BRAF
ARMS-mediated activation1271.9×0.029BRAF
RUNX3 regulates CDKN1A transcription1271.9×0.029TP53
Modulation by Mtb of host immune system1271.9×0.029B2M
Prolonged ERK activation events1237.9×0.029BRAF
TRAIL signaling1237.9×0.029CASP10
SHOC2 M1731 mutant abolishes MRAS complex function1237.9×0.029BRAF
Gain-of-function MRAS complexes activate RAF signaling1237.9×0.029BRAF
PI5P Regulates TP53 Acetylation1211.5×0.029TP53
Activation of PUMA and translocation to mitochondria1190.3×0.029TP53
Nef mediated downregulation of MHC class I complex cell surface expression1190.3×0.029B2M
Signaling by FGFR31190.3×0.029BRAF
Infection with Mycobacterium tuberculosis1190.3×0.029B2M
RHOBTB3 ATPase cycle1190.3×0.029LRRC41
Oxidative Stress Induced Senescence230.2×0.029TP53, EZH2
Class I MHC mediated antigen processing & presentation223.4×0.029LRRC41, B2M
Endosomal/Vacuolar pathway1173.0×0.030B2M
Signaling by FGFR41173.0×0.030BRAF
Frs2-mediated activation1158.6×0.030BRAF
TP53 Regulates Transcription of Death Receptors and Ligands1158.6×0.030TP53
Urea cycle1146.4×0.030TP53

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
determination of adult lifespan3162.0×9e-05TP53, RAD54B, RAD54L
T cell differentiation in thymus3154.1×9e-05BRAF, TP53, B2M
positive regulation of cellular senescence2324.1×0.001TP53, B2M
positive regulation of execution phase of apoptosis2210.7×0.002TP53, CASP10
chromosome organization2145.3×0.003TP53, RAD54L
reciprocal meiotic recombination2140.4×0.003RAD54B, RAD54L
response to ionizing radiation2102.8×0.006RAD54B, RAD54L
negative regulation of iron ion transport12106.5×0.008B2M
negative regulation of helicase activity12106.5×0.008TP53
cellular response to actinomycin D12106.5×0.008TP53
regulation of intrinsic apoptotic signaling pathway by p53 class mediator12106.5×0.008TP53
negative regulation of G1 to G0 transition12106.5×0.008TP53
positive regulation of neuron apoptotic process268.0×0.008TP53, CASP10
cellular response to xenobiotic stimulus260.2×0.008BRAF, TP53
antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent11053.2×0.010B2M
regulation of iron ion transport11053.2×0.010B2M
positive regulation of mitochondrial membrane permeability11053.2×0.010TP53
hepatocyte homeostasis11053.2×0.010EZH2
cellular response to iron(III) ion11053.2×0.010B2M
oligodendrocyte apoptotic process11053.2×0.010TP53
negative regulation of glucose catabolic process to lactate via pyruvate11053.2×0.010TP53
negative regulation of pentose-phosphate shunt11053.2×0.010TP53
negative regulation of forebrain neuron differentiation11053.2×0.010B2M
regulation of gliogenesis1702.2×0.011EZH2
obsolete homolactic fermentation1702.2×0.011TP53
cellular response to trichostatin A1702.2×0.011EZH2
CD4-positive or CD8-positive, alpha-beta T cell lineage commitment1702.2×0.011BRAF
signal transduction by p53 class mediator1702.2×0.011TP53
negative regulation of miRNA processing1702.2×0.011TP53
intrinsic apoptotic signaling pathway in response to hypoxia1702.2×0.011TP53

Therapeutics

Drugs indicated for this disease

6 approved, 51 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
Brentuximab VedotinApproved (phase 4)
CarmustineApproved (phase 4)
IdelalisibApproved (phase 4)
MethotrexateApproved (phase 4)
PlerixaforApproved (phase 4)
RituximabApproved (phase 4)
AllopurinolPhase 3 (in late-stage trials)
AmoxicillinPhase 3 (in late-stage trials)
AsparaginasePhase 3 (in late-stage trials)
BendamustinePhase 3 (in late-stage trials)
BortezomibPhase 3 (in late-stage trials)
Calcium CarbonatePhase 3 (in late-stage trials)
CarboplatinPhase 3 (in late-stage trials)
CisplatinPhase 3 (in late-stage trials)
ClarithromycinPhase 3 (in late-stage trials)
CopanlisibPhase 3 (in late-stage trials)
CyclosporinePhase 3 (in late-stage trials)
CytarabinePhase 3 (in late-stage trials)
DaunorubicinPhase 3 (in late-stage trials)
DexamethasonePhase 3 (in late-stage trials)
DoxorubicinPhase 3 (in late-stage trials)
EnzastaurinPhase 3 (in late-stage trials)
ErgocalciferolPhase 3 (in late-stage trials)
EtoposidePhase 3 (in late-stage trials)
FilgrastimPhase 3 (in late-stage trials)
FludarabinePhase 3 (in late-stage trials)
GemcitabinePhase 3 (in late-stage trials)
HistaminePhase 3 (in late-stage trials)
Ibritumomab TiuxetanPhase 3 (in late-stage trials)
IbrutinibPhase 3 (in late-stage trials)
IdarubicinPhase 3 (in late-stage trials)
IfosfamidePhase 3 (in late-stage trials)
Inotuzumab OzogamicinPhase 3 (in late-stage trials)
LenalidomidePhase 3 (in late-stage trials)
Lisocabtagene MaraleucelPhase 3 (in late-stage trials)
MetronidazolePhase 3 (in late-stage trials)
MosunetuzumabPhase 3 (in late-stage trials)
Mycophenolate MofetilPhase 3 (in late-stage trials)
ObinutuzumabPhase 3 (in late-stage trials)
OfatumumabPhase 3 (in late-stage trials)
OxaliplatinPhase 3 (in late-stage trials)
PaclitaxelPhase 3 (in late-stage trials)
PixantronePhase 3 (in late-stage trials)
Polatuzumab VedotinPhase 3 (in late-stage trials)
PrednisolonePhase 3 (in late-stage trials)
PrednisonePhase 3 (in late-stage trials)
SargramostimPhase 3 (in late-stage trials)
SirolimusPhase 3 (in late-stage trials)
TOSITUMOMAB 131IPhase 3 (in late-stage trials)
Tacrolimus AnhydrousPhase 3 (in late-stage trials)
TisagenlecleucelPhase 3 (in late-stage trials)
TocilizumabPhase 3 (in late-stage trials)
TositumomabPhase 3 (in late-stage trials)
VincristinePhase 3 (in late-stage trials)
VinorelbinePhase 3 (in late-stage trials)
YTTRIUM Y 90 IBRITUMOMAB TIUXETANPhase 3 (in late-stage trials)
ZanubrutinibPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): 1018 ISS, ANTINEOPLASTON A10, Acalabrutinib, Acetaminophen, Aldesleukin, Amifostine, Ascorbic Acid, Atezolizumab, Atorvastatin, Belinostat, Bevacizumab, Blinatumomab, Busulfan, CPI 613, Clofarabine, Crisantaspase, Denileukin Diftitox, Diphenhydramine, Durvalumab, Duvelisib, Entospletinib, Epcoritamab, Epirubicin, Epratuzumab, Etoposide Phosphate, Fludarabine Phosphate, Gallium Nitrate, Golcadomide, Irinotecan, Lamivudine, Lomustine, Loncastuximab Tesirine, Melphalan, Methylprednisolone, Mitoxantrone, Motexafin Gadolinium, Motixafortide, Nivolumab, Odronextamab, Ondansetron, Panobinostat, Pegargiminase, Pegfilgrastim, Pembrolizumab, Potassium Iodide, Romiplostim, Tafasitamab, Temozolomide, Temsirolimus, Tetracycline, Thalidomide, Tislelizumab, Topotecan, Treosulfan, Tucidinostat, Umbralisib, Venetoclax, Vorinostat.

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 4 · Undrugged: 4

Druggability breadth: 6 of 8 evidence-associated genes (75%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
EZH2TAZEMETOSTAT
BRAFVEMURAFENIB
TP53NITROFURANTOIN

Top cohort targets by molecule count

SymbolMoleculesMax phase
TP531964
BRAF484
EZH264
RAD54L12
CASP1000
LRRC4100
RAD54B00
B2M00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
TAZEMETOSTAT4EZH2
VEMURAFENIB4BRAF
PONATINIB4BRAF
FEDRATINIB4BRAF
SORAFENIB4BRAF
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF
INFIGRATINIB4BRAF
REGORAFENIB4BRAF
DABRAFENIB4BRAF
COBIMETINIB4BRAF
NILOTINIB4BRAF
ABEMACICLIB4BRAF
ENCORAFENIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF
DASATINIB4BRAF
ERLOTINIB4BRAF
GEFITINIB4BRAF
IMATINIB4BRAF
NITROFURANTOIN4TP53
DIOSMIN4TP53
VERTEPORFIN4TP53
CANDESARTAN CILEXETIL4TP53
DIENESTROL4TP53
CLOTRIMAZOLE4TP53
COLCHICINE4TP53
NABUMETONE4TP53
SALMETEROL XINAFOATE4TP53

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 5.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
BRAF1,442Binding:1400, Functional:37, ADMET:5
TP53869Binding:775, ADMET:83, Functional:10, Toxicity:1
EZH2839Binding:833, Functional:6
CASP1022Binding:21, Functional:1
B2M5Binding:5
RAD54L3Functional:2, Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
EZH22.1.1.356[histone H3]-lysine27 N-trimethyltransferase
BRAF2.7.10.2, 2.7.11.1non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
CASP103.4.22.63caspase-10
RAD54B3.6.4.B9
RAD54L3.6.4.B9

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
EZH2839
BRAF1,442
TP53869

Pharmacogenomics

Cohort genes with a PharmGKB record: 8; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Drug repurposing candidates

30 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

CompoundMax phaseCohort target (bioactivity)
TAZEMETOSTAT4EZH2
VEMURAFENIB4BRAF
PONATINIB4BRAF
FEDRATINIB4BRAF
SORAFENIB4BRAF
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF
INFIGRATINIB4BRAF
REGORAFENIB4BRAF
DABRAFENIB4BRAF
COBIMETINIB4BRAF
NILOTINIB4BRAF
ABEMACICLIB4BRAF
ENCORAFENIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF
DASATINIB4BRAF
ERLOTINIB4BRAF
GEFITINIB4BRAF
IMATINIB4BRAF
NITROFURANTOIN4TP53
DIOSMIN4TP53
VERTEPORFIN4TP53
CANDESARTAN CILEXETIL4TP53
DIENESTROL4TP53
CLOTRIMAZOLE4TP53
COLCHICINE4TP53
NABUMETONE4TP53
SALMETEROL XINAFOATE4TP53

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3EZH2, BRAF, TP53
BPhased (≥1) drug, not yet approved1RAD54L
CDruggable family + PDB, no drug2RAD54B, B2M
DDruggable family + AlphaFold only, no drug1CASP10
EDifficult family or no structure, no drug1LRRC41

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
CASP1022
LRRC410
RAD54B0
B2M5

Clinical trials & evidence

Clinical trials

Clinical trials: 1,051.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE2304
PHASE1304
Not specified179
PHASE1/PHASE2162
PHASE353
EARLY_PHASE126
PHASE418
PHASE2/PHASE35

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06665737PHASE4NOT_YET_RECRUITINGOutcomes of Early and Late Administration G-CSF for Primary Prophylaxis in Non-Hodgkin’s Lymphoma Patients
NCT06876649PHASE4RECRUITINGA Master Protocol to Evaluate the Long-Term Safety of (LY3527727) Pirtobrutinib
NCT06876662PHASE4RECRUITINGA Study of (LY3527727) Pirtobrutinib in Participants With Previously Treated Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma or Non-Hodgkin Lymphoma
NCT07016165PHASE4RECRUITINGCiprofloxacin vs Ceftazidime for Empirical Treatment of High-Risk Neutropenic Fever in Children With Hematologic Malignancies
NCT00090038PHASE4COMPLETEDEffect of Rituximab on Immunological Recall Response to Specific Antigens in the Treatment of Non-Hodgkin’s Lymphoma
NCT00162955PHASE4COMPLETEDPrevention of CHOP-induced Chronic Cardiotoxicity
NCT00277160PHASE4COMPLETEDA Study of Primary Prophylaxis With Neulasta (Pegfilgrastim) Versus Secondary Prophylaxis After Chemotherapy in Elderly Subjects (>/= 65 Years Old) With Cancer
NCT00352703PHASE4COMPLETEDPROMPT - Palifermin in Reduction of Oral Mucositis in PBSC Transplantation
NCT00430352PHASE4COMPLETEDMAXIMA Study: A Study of Maintenance Therapy With MabThera (Rituximab) in Patients With Non-Hodgkin’s Lymphoma.
NCT00797810PHASE4UNKNOWNIntensification Therapy of Mature B-ALL, Burkitt and Burkitt Like and Other High Grade Non-Hodgkin’s Lymphoma in Adults
NCT00808171PHASE4COMPLETEDEvaluation of the Analgesy With Emla and/or Nitrous Oxide in Pediatric Patients for Lumbar Puncture
NCT00926757PHASE4COMPLETEDProphylactic Use of Entecavir for Non-Hodgkin’s Lymphoma Patients With Resolved Hepatitis B
NCT00969462PHASE4COMPLETEDDoxorubicin Pharmacokinetics and Response in Non Hodgkin’s Lymphoma
NCT01124526PHASE4COMPLETEDEfficacy Response Duration and Toxicity of Rituximab, Fludarabine, and Cyclophosphamide (RFC) as 1st Line Treatment and Rituximab (R) in Maintenance Treatment in Follicular Non Hodgkin (FNH) Lymphoma
NCT01164475PHASE4COMPLETEDEvaluation of Approved Weight-Based Dose Compared to Fixed Dose of Plerixafor in Patients With Non-Hodgkin’s Lymphoma (NHL) Weighing Less Than 70 Kilograms
NCT01180049PHASE4COMPLETEDComparison Of 2 Doses Of Temsirolimus (Torisel) In Patients With Mantle Cell Lymphoma
NCT02782845PHASE4COMPLETEDAn Expanded Access Program of Pegfilgrastim (Neulastim) in Participants With Non-Hodgkin’s Lymphoma (NHL)
NCT05191225PHASE4UNKNOWNUltrafast Truxima Infusion in Non-Hodgkin’s Lymphoma: Txagorapid Study
NCT00877214PHASE3ACTIVE_NOT_RECRUITINGSignificance of Duration of Maintenance Therapy With Rituximab in Non-Hodgkin Lymphomas
NCT03844048PHASE3ACTIVE_NOT_RECRUITINGAn Extension Study of Venetoclax for Subjects Who Have Completed a Prior Venetoclax Clinical Trial
NCT04459416PHASE3ACTIVE_NOT_RECRUITINGManaging Pain and Symptom Burden Caused by Chemotherapy in People With Myeloma or Lymphoma
NCT05171647PHASE3ACTIVE_NOT_RECRUITINGA Study Evaluating Efficacy and Safety of Mosunetuzumab in Combination With Polatuzumab Vedotin Compared to Rituximab in Combination With Gemcitabine Plus Oxaliplatin in Participants With Relapsed or Refractory Aggressive B-Cell Non-Hodgkin’s Lymphoma
NCT05645107PHASE3RECRUITINGA Study to Evaluate Efficacy, Safety, and PK of XEMBIFY®+Standard Medical Treatment (SMT) Compared to Placebo+SMT to Prevent Infections in Participants With HGG and Recurrent or Severe Infections Associated With B-cell Chronic Lymphocytic Leukemia, Multiple Myeloma, and Non-Hodgkin Lymphoma
NCT06520163PHASE3RECRUITINGComparison Study of EAP and Disease-Specific Chemotherapy Regimens in Hematopoietic Stem Cell Mobilization for Lymphoma
NCT07188558PHASE3RECRUITINGA Study to Investigate Ronde-cel Versus Investigator’s Choice CD19 CAR T-Cell Therapy
NCT07202052PHASE2/PHASE3RECRUITINGRole of Antibiotic Therapy or Immunoglobulin On iNfections in hAematoLogy Platform Trial (RATIONAL-PT)
NCT07582432PHASE3RECRUITINGA Clinical Trial to Evaluate Efficacy, Safety, and Pharmacokinetics of Gamunex in Participants With Chronic Lymphocytic Leukemia, Multiple Myeloma, or Non-Hodgkin Lymphoma
NCT00039910PHASE3COMPLETEDSafety and Efficacy of (PN-152,243)/PN-196,444 in the Prevention of Thrombocytopenia
NCT00057343PHASE3TERMINATEDSafety and Efficacy of Zevalin in the Treatment of Non-Hodgkin’s Lymphoma
NCT00078598PHASE3UNKNOWNA Study of Rituximab Versus Iodine I 131 Tositumomab Therapy for Patients With Non-Hodgkin’s Lymphoma
NCT00091676PHASE3UNKNOWNStudy of the BiovaxId Tumor Derived Idiotype Vaccine in Patients With Follicular Lymphoma
NCT00129090PHASE3COMPLETEDMega-CHOEP: Conventional Chemo Vs HD Chemo Followed by Auto SCT in Younger Pts With Aggressive Non-Hodgkin’s Lymphoma
NCT00133302PHASE3TERMINATEDStudy of Standard CHOP Versus Biweekly CHOP in Aggressive Non-Hodgkin’s Lymphoma (JCOG9809)
NCT00139841PHASE3COMPLETEDSafety and Efficacy of Treanda™ (Bendamustine HCl) in Patients With Indolent Non-Hodgkin’s Lymphoma (NHL) Who Are Refractory to Rituximab
NCT00145652PHASE3COMPLETEDAdjuvant I.V. Iron Therapy During Erythropoetin Treatment of Anemic Patients With Lymphoproliferative Disorders.
NCT00152139PHASE3COMPLETEDStem Cell Transplantation for Patients With Hematologic Malignancies
NCT00269113PHASE3COMPLETEDA Study of MabThera (Rituximab) in Patients With Advanced Non-Hodgkin’s Lymphoma
NCT00312845PHASE3COMPLETEDStudy of VELCADE and Rituximab in Patients With Relapsed or Refractory B-cell Non-Hodgkin’s Lymphoma
NCT00332202PHASE3COMPLETEDPRELUDE:Study to Investigate the Prevention of Relapse in Lymphoma Using Daily Enzastaurin
NCT00352846PHASE3COMPLETEDEffect of Zoledronic Acid on Chemotherapy Induced Bone Loss

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
RITUXIMAB4129
BENDAMUSTINE426
PLERIXAFOR424
2-MERCAPTOETHANESULFONIC ACID412
OBINUTUZUMAB48
CLOFARABINE47
DOXORUBICIN47
MITOXANTRONE47
PEGFILGRASTIM47
POLATUZUMAB VEDOTIN47
UBLITUXIMAB46
VINCRISTINE46
AXICABTAGENE CILOLEUCEL45
BRENTUXIMAB VEDOTIN45
OFATUMUMAB45
BELINOSTAT44
BORTEZOMIB D-MANNITOL44
FLUDARABINE PHOSPHATE44
PALIFERMIN44
PIRTOBRUTINIB44
ROMIDEPSIN44
TEMSIROLIMUS44
MOSUNETUZUMAB43
VENETOCLAX43
ALEMTUZUMAB42
DIPHENHYDRAMINE42
ETOPOSIDE PHOSPHATE42
IBRUTINIB42
MOXETUMOMAB PASUDOTOX42
PANOBINOSTAT42

Precision-medicine subtype map (CIViC)

Drug × molecular subtype: 1 predictive associations from 2 curated evidence items.

Molecular subtypeTherapyEffectLevelCIViC
EZH2 Y646FTazemetostatSensitivity/ResponseCIViC DEID11000 +1