cbio-kb

A living knowledge base of cBioPortal publications

cbio-kb is a structured, cross-linked reading of the primary literature behind cBioPortal studies. It follows the LLM knowledge base pattern described by Andrej Karpathy (idea file gist): raw source documents are incrementally compiled by an LLM into a directory of interlinked Markdown pages, with the LLM maintaining summaries, backlinks, and indexes as the corpus grows.

Every paper in the corpus is distilled into a standardized page — cohort, methods, key findings, clinical implications, open questions — and every gene, cancer type, dataset, drug, and assay mentioned gets its own page that aggregates what the corpus collectively says about it.

The goal is to make it fast to answer questions like:

What has been published about FGFR3 in urothelial carcinoma ?
Which studies profiled the MSK-IMPACT cohort, and what did they find?
Where has erdafitinib resistance been characterized?
What methods have been used to detect clonal hematopoiesis in solid-tumor sequencing?

Every claim on an entity page is traceable back to a specific paper via PMID: citations, and every paper page links out to the entities it touches. Nothing is invented — unverified terms are flagged rather than canonicalized.

News

2026-05-15 — 🎯 50/50 paper-loop complete (10 iterations × 5 papers, every 30 min). Final batch (PMIDs 29489754, 29596782, 29610475, 29617662, 29622463) — Düsseldorf pediatric HBOC germline cohort (n=372, 11 LP/PV genes incl. ATM OR=3.2) (PMID 29489754); TCGA MC3 pan-cancer mutation-calling resource (Ellrott et al., 7-caller consensus, 10,000+ tumors, the canonical TCGA mutation MAF) (PMID 29596782); prad_p1000 prostate cancer meta-cohort (1,013 tumors, long-tail SMG discovery USP28/USP7/SMARCA1) (PMID 29610475); TCGA pan-cancer fusion atlas (Gao et al., 33 tumor types, novel TRABD-DDR2/PPP1R1B-ERBB2/IKZF3-ERBB2/TMEM87B-MERTK fusions) (PMID 29617662); TCGA pan-cancer aneuploidy/chr3p deletion atlas (CRISPR-Cas9 functional validation) (PMID 29622463). 68 new entity pages incl. the full TCGA cohort code family (KICH/KIRC/KIRP/LAML/LGG/LIHC/MESO/PANCAN/PCPG/SARC/TGCT/THCA/UVM) and 28 new methods (mc3-pipeline/gatk-cocleaning/vep/vcf2maf/star-fusion/ericscript/agfusion/netmhc4/hmmcopy/ichorcna/etc.). Across the full 50-paper loop: zero malformed brackets emitted by any agent — the prompt tightening + lint enforcement framework worked end-to-end.
2026-05-15 — Added 5 papers (PMIDs 29301960, 29316426, 29337640, 29420467, 29422544) — iteration #9 of the 30-min loop. DFCI ccRCC PBRM1/SMARCA4-loss as anti-PD-(L)1 response biomarker (BRG1 KO immune-priming functional validation) (PMID 29301960); MSK CRC IMPACT 1134-tumor cohort (KRAS/NRAS/BRAF Level 1 anti-EGFR resistance, NCOA4-RET/CUL1-BRAF/AGAP3-BRAF/ETV6-NTRK3 fusion landscape) (PMID 29316426); MSK NSCLC anti-PD-1 prospective cohort (TMB-by-IMPACT predicts ICI benefit, JAK2 LOH primary resistance, STK11 NDB enrichment) (PMID 29337640); SUMMIT basket trial neratinib for HER2/HER3-mutant solid tumors (n=141, breast 32% ORR, ERBB2 mutation context determines response, GRB7-ERBB2 fusion) (PMID 29420467); first WES landscape of vulvar SCC (Korean n=15, HPV-stratified TP53/CDKN2A vs BRCA2/FBXW7 mutation patterns) (PMID 29422544). 13 new entity pages (5 genes, 1 cancer type VSC, 5 datasets, 2 methods sequenza/nexus-copy-number). normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 28985567, 28988769, 29033130, 29100075, 29122777) — iteration #8 of the 30-min loop. Reddy DLBCL 1001-tumor genomic landscape + CRISPR essential screen (3-tier genomic risk classifier; ABC/GCB cell-of-origin functional dependencies) (PMID 28985567); TCGA expanded bladder cancer (n=412, five mRNA subtypes including novel neuronal subtype, 58 SMGs, 67% APOBEC mutation share) (PMID 28988769); Riaz CA209-038 melanoma anti-PD-1 paired pre/on-therapy genomics (immunoediting evidence, clonal TMB biomarker, T-cell repertoire dynamics) (PMID 29033130); TCGA SARC comprehensive sarcoma genomics (n=206, only 3 pan-sarcoma SMGs, SCNA-driven biology, histology-specific immune signatures) (PMID 29100075); MSK metastatic esophagogastric (n=341, trastuzumab-resistance ERBB2 quantification, MSI-H immunotherapy framework) (PMID 29122777). 53 new entity pages (47 genes incl. T-cell synapse CD247/CD28/CD3D/CD3E/CD3G + immunotherapy targets ICOS/TIGIT/VSIR + DLBCL drivers KLHL6/KLHL14/PIM2/POU2F2/ZBTB7A/ZFAT, 1 cancer type USARC, 5 datasets). normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 28667006, 28726821, 28783718, 28825054, 28927585) — iteration #7 of the 30-min loop. ICGC cholangiocarcinoma multi-omic landmark (n=489, four molecular clusters, FGFR2 3’UTR fusion mechanism, IDH1/IDH2 31.6% in IHCH Cluster 4) (PMID 28667006); DKFZ medulloblastoma WGS landmark (n=491 + 1,256 methylation, KBTBD4 in-frame insertions, SNCAIP/PRDM6 enhancer-hijacking, eight methylation subtypes) (PMID 28726821); MET500 pan-cancer metastatic landscape (n=500, 12.2% germline DDR, GREB1-NR4A3 / CIC-CITED1 / NOTCH2 fusion families) (PMID 28783718); MSK-IMPACT prostate disease-state cohort (n=504, 22% somatic HR alterations, PALB2 / FANCA / RAD50 PARPi candidacy) (PMID 28825054); NOL10/USF1/rs4519489 prostate cancer prognostic axis (eQTL-driven oncogene mechanism, GWAS-CRISPRi convergence) (PMID 28927585). 40 new entity pages (25 genes, 4 datasets, 3 drugs apalutamide/flutamide/dutasteride, 8 methods incl. snps-seq/emsa/crispri/crispr-base-editing/luciferase-reporter-assay). normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 28445469, 28472509, 28481359, 28485815, 28583311) — iteration #6 of the 30-min loop. Includes the seminal MSK-IMPACT 10K-patient prospective cohort landmark (Zehir et al.) (PMID 28481359) — first systematic clinical-grade pan-cancer NGS at scale, defining the actionability/MSI/lineage-restricted-driver framework. TRACERx 100-patient NSCLC ctDNA dynamics (70-day relapse lead-time, multiregion exome phylogenetics) (PMID 28445469); MSK 41-patient anaplastic oligodendroglioma cohort (TERT/IDH1/CIC canonical signature, NGS-defined GBM-like 1p/19q-intact subset) (PMID 28472509); NIH 63-tumor uterine clear cell carcinoma exome (TAF1 nominated as novel CCEC driver) (PMID 28485815); MSK NMIBC bladder cohort (n=105, ARID1A predicts BCG-recurrence HR=3.14, FGFR3-TACC3 in low-grade Ta) (PMID 28583311). 16 new entity pages plus expansions for ODG3/FLC/UCCC and 10K-paper drivers (CDK5RAP2-BRAF, DNAJB1-PRKACA fusions). normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 28196596, 28199314, 28336552, 28373299, 28445112) — iteration #5 of the 30-min loop. Gardner SCLC PDX EZH2-driven SLFN11 silencing as chemoresistance mechanism (tazemetostat resensitization rationale) (PMID 28196596); EWSR1::BEND2 fusion bladder sarcoma case reclassification + new MN1 / EWSR1-non-ETS sarcoma family (PMID 28199314); MSK-IMPACT 860-patient prospective LUAD actionability cohort (level 1/2 OncoKB matched-therapy uptake) (PMID 28336552); TSAM acral melanoma multi-omic landscape (TERT 41% aberrations, PAK1 amplifications, low UV signature, SV-dominant) (PMID 28373299); HMGA1/HMGA2 endometrial polyp WGS (translocation-driven enhancer hijacking, novel UBE2A driver) (PMID 28445112). 51 new entity pages (28 genes, 3 cancer types ASTB/ACRM/ULM, 3 datasets, 4 drugs, 13 methods incl. variant scorers alphamissense/cadd/revel/splice-ai). normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 28007021, 28027327, 28052061, 28068672, 28162975) — iteration #4 of the 30-min loop. Columbia PIPseq pediatric pan-cancer precision oncology cohort (n=101, 36 cancer types, 38% actionable alterations, 14% germline predisposition) (PMID 28007021); IGR metastatic breast cancer WES (n=216, 4 prospective trials, ESR1 endocrine-resistance enrichment, APOBEC subclonal mutagenesis) (PMID 28027327); TCGA esophageal-stomach integrated landmark (n=559, ESCC three-subtype framework, EAC = CIN-gastric equivalence) (PMID 28052061); TRMT10A-USP10-BRCA1 axis in mCRPC PARPi resistance (spautin-1+olaparib synergy) (PMID 28068672); TCGA pheochromocytoma/paraganglioma (n=173, CSDE1 novel driver, MAML3 fusions defining Wnt-altered metastasis subtype) (PMID 28162975). 70+ new entity pages spanning the pediatric oncology ontology branch (JMML/AMKL/CML/HL/ATRT/EPM/etc.), endocrine PCC/PGL (PHC, PGNG), and PARPi/SBRT/PCC drug & method classes. normalize-brackets no-op again.
2026-05-15 — Added 5 papers (PMIDs 27713405, 27749842, 27776115, 27826200, 27959731) — iteration #3 of the 30-min loop. MSKCC unclassified RCC (n=62, four molecular subsets: NF2-loss, mTORC1-hyperactive, FH-deficient, ALK-translocation, novel TPM3-ALK fusion) (PMID 27713405); Weill Cornell urothelial carcinoma pre/post-cisplatin clonal evolution (n=72, ATM/RB1/FANCC-loss signature depleted, APOBEC3A/L1CAM resistance signatures) (PMID 27749842); St. Jude DUX4/ERG B-ALL subtype landmark (n=1,913, IGH-DUX4 universal, favorable outcome despite IKZF1 loss) (PMID 27776115); Duke pancreatic SBRT review (33 Gy/5-fraction reference regimen, SMAD4/TGF-β biomarker) (PMID 27826200); WashU prospective decitabine AML/MDS trial (n=116, TP53-mutant 100% blast clearance, sub-clonal resistance through epigenetic regulators) (PMID 27959731). 40 new entity pages (14 genes, 3 cancer types URCC/RCC/NCCRCC, 4 datasets, 6 drugs incl. decitabine/azacitidine, 13 methods incl. SBRT family + AML panels). normalize-brackets no-op again.
2026-05-15 — Added 4 papers (PMIDs 27276561, 27346245, 27442865, 27646943) — iteration #2 of the 30-min loop. Papaemmanuil pan-AML genomic classification (n=1,540, 11 subgroups, chromatin–spliceosome boundary with MDS) (PMID 27276561); Tansir young-onset NSCLC genomics review (germline P/LP enrichment, RET/ROS1 fusion skew) (PMID 27346245); MSK head-and-neck IMPACT410 advanced-disease cohort (n=151, ETV6-NTRK3 reclassification, novel EWSR1-ATF1 in clear-cell odontogenic carcinoma, 18 cancer subtypes) (PMID 27442865); MSK germ cell tumor cisplatin-resistance landscape (n=180, TP53 exclusive to resistance, novel RAC1 hotspots) (PMID 27646943). 31 new entity pages (6 genes, 14 cancer types, 3 datasets, 8 drugs). normalize-brackets no-op again.
2026-05-15 — Added 4 papers (PMIDs 26997480, 27149842, 27158780, 27161491) — first iteration of the 30-min /loop toward 50-paper target. UCLA anti-PD-1 melanoma WES + RNA-seq with the IPRES innate-resistance transcriptomic signature (PMID 26997480); DFCI CRC WES n=619 (90 SMGs, 73 novel CRC drivers, MHC-I/APM mutation–TIL link) (PMID 27149842); Campbell pan-NSCLC integrated TCGA n=1,144 with novel SMGs (CMTR2, PPP3CA, RIT1) and 47–53% neoepitope coverage (PMID 27158780); Pereira METABRIC v2 expanded breast cancer drivers (n=2,433, 40 driver genes incl. AGTR2, AHNAK2, USP9X) (PMID 27161491). 56 new entity pages (44 genes, 3 datasets, 6 methods incl. polysolver/netmhcpan/ascat/math-score). Agents emitted zero bracket warnings — normalize-brackets no-op.
2026-05-15 — Added 5 papers (PMIDs 26878173, 26901067, 26928463, 26950094, 26977886) — first batch under the new deterministic bracket-normalizer + lint enforcement, and the agents emitted zero malformed Obsidian-style links (vs. ~1,200 in the previous batch). MSKCC advanced thyroid (PDTC + ATC, 117 tumors, MSK-IMPACT) — BRAF/RAS dichotomy with stepwise TERT-promoter enrichment (PMID 26878173); MSKCC plasmacytoid bladder cancer — CDH1 truncating mutations as pathognomonic marker (PMID 26901067); FHCRC mCRPC rapid-autopsy multi-tumor cohort — Fanconi-anemia / ATM-deficient subset as carboplatin-response biomarker (PMID 26928463); UNIGE NB-UVB phototherapy NanoSeq — first quantitative duplex-sequencing measurement of in-vivo therapy-induced somatic mutation burden (PMID 26950094); BCGSC extra-cranial malignant rhabdoid tumor multi-omic landscape — quiet somatic genome with HOX-cluster super-enhancers as epigenetic dependencies (PMID 26977886). 39 new entity pages (25 genes incl. full FA core complex; 5 cancer types THPD/SRCBC/BCC/MRT/MRTL; 5 datasets; 2 drugs; 2 methods nanoseq/polygenic-risk-score). Also: shipped cbio-kb wiki normalize-brackets CLI + lint enforcement so dangerous bracket shapes now fail CI before the publish workflow runs.
2026-05-14 — Added 5 papers (PMIDs 26804919, 26824661, 26829750, 26855148, 26862087) covering rare-cancer landscapes and a TCGA pan-glioma landmark. BCM periampullary/biliary WES with ELF3 tumor suppressor and WNT-pathway taxonomy (PMID 26804919); TCGA pan-glioma integrated multi-platform analysis (1,122 cases, six LGm methylation subtypes superseding prior LGG/GBM analyses) (PMID 26824661); two adenoid cystic carcinoma genomic studies revealing MYB enhancer hijacking with JQ1 sensitivity (PMID 26829750) and NFIB rearrangements pushing translocation prevalence to 60% (PMID 26862087); WCM neuroendocrine prostate cancer multi-omic characterization with 70-gene NEPC classifier (PMID 26855148). 42 new entity pages (29 genes, 2 cancer types AMPCA/DA, 5 datasets, 6 methods incl. radia/mutcomfocal/tumor-map/estimate/ingenuity-pathway-analysis/variantdx). Also tightened paper-compiler and crosslinker agent prompts to forbid Obsidian wiki-link syntax ([[...]]) after the recent multi-hour pandoc hang.
2026-05-14 — Added 30 papers (PMIDs 25409260–26760213) in a six-wave /loop covering 2014–2016 cancer genomics. Landmark immuno-oncology: Snyder CTLA-4 melanoma neoantigen tetrapeptide signature (PMID 25409260) and Van Allen ipilimumab melanoma neoantigen+cytolytic axis (PMID 26359337); Rizvi/MSKCC TMB→pembrolizumab response in NSCLC (PMID 25765070). TCGA multi-platform landmarks: papillary thyroid (PMID 25417114), HNSCC (PMID 25631445), cutaneous melanoma BRAF/RAS/NF1/Triple-WT subtypes (PMID 26091043), lobular breast cancer (ILC) (PMID 26451490), prostate 7-subtype integrated analysis (PMID 26544944). Other landmark cohorts: BC Cancer breast PDX single-cell clonal dynamics (PMID 25470049); Schulze/INSERM HCC WES with AFB1 signatures (PMID 25822088); UTSW microdissected PDAC WES (PMID 25855536); SU2C-PCF mCRPC prospective WES (PMID 26000489); UCologne SCLC universal TP53/RB1 loss (PMID 26168399); Landau/Broad CLL 538-tumor WES discovering RPS15 (PMID 26466571); SickKids medulloblastoma primary/recurrence pairs (PMID 26760213). Rare-cancer / novel-driver discovery: UTUC vs UCB (PMID 26278805), desmoplastic melanoma NFKBIE promoter hotspot (PMID 26343386), MD Anderson ACC MYBL1-NFIB fusions (PMID 26631609), QIMR uveal melanoma PLCB4 p.D630Y (PMID 26683228), Mayo PCNSL TOX/PRKCD biallelic loss (PMID 25991819), Tianjin gastric NRG1-ERBB4 axis (PMID 25583476). Translational reviews: cholangiocarcinoma precision medicine (FGFR2, IDH1) (PMID 25526346), gut-liver microbiome/bile-acid in CCA (PMID 25608663). Methods firsts: Bu rat somatic-editing ER+ breast cancer model via intraductal AAV/CRISPR (PMID 26437033); CLL del(13q)/SF3B1 H3B-8800 splicing-modulator PoC (PMID 26200345). Race-specific genomics: Case Western AA colorectal SMGs (PMID 25583493); DFCI metastatic cSCC OncoPanel (PMID 25589618); MSKCC breast ACC (PMID 26095796); Columbia CTCL Sézary/MF WES (PMID 26551667); Peifer/UCologne neuroblastoma TERT rearrangements (PMID 26466568). ~675 unique gene-page touches, 25 new datasets, 14 new cancer types, ~28 new drugs (incl. gut-microbiome/bile-acid tools, splicing modulator H3B-8800, MDM2 nutlin/AMG-232), ~25 new methods (incl. aav-crispr-somatic-editing, pyclone, titan-cna, paradigm, isopure, oncosign, expands, sleeping-beauty-transposon-screen, shatterseek, dna-methylation-array, whole-genome-bisulfite-seq). Wave commits: e960567, 04ca78a, f82deca, d38f6e4, 5bcc14b, 5361db5.
2026-05-12 — Added 25 papers (PMIDs 24487277–25401301) in a five-wave batch covering 2014 cancer genomics. Landmarks: TCGA STAD (PMID 25079317), TCGA LUAD (PMID 25079552), TCGA KICH (PMID 25155756). Reviews: Llovet HCC genomics+therapy (PMID 24735922, PMID 24798001), NPC immunotherapy (PMID 24952746), HDGC/STAD susceptibility (PMID 24816255). Rare-cancer discovery: Ewing WGS (PMID 25223734) and EWS-FLI1 heMSC origin (PMID 25186949), uterine carcinosarcoma (PMID 25233892), MPNST PRC2 loss (PMID 25240281), cSCC (PMID 25303977), non-clear-cell RCC (PMID 25401301), thymic epithelial tumors / GTF2I L404H (PMID 24974848), SMARCA4-deficient SCCO (PMID 24658004), gallbladder SEMA7A/YAP-TEAD (PMID 24997986), RHOA yeast-complementation functional dissection (PMID 24816253). Translational: BLCA ERCC2-cisplatin biomarker (PMID 25096233), CRC primary-met concordance for anti-EGFR (PMID 25164765), MSKCC PRAD organoid drug screen (PMID 25201530), MSKCC BLCA MSK-IMPACT (PMID 25092538), MSKCC PRAD SHQ1 (PMID 25024180), ccRCC TRACERx multi-region (PMID 24487277), ESCC genomics (PMID 24686850), ESCC microbiome (PMID 24670651). ~400 gene-page touches, ~20 new datasets, ~80 new drugs (mostly Chinese-trial NPC investigational IO agents and HCC TKIs), ~30 new methods. HN1→JPT1 HUGO normalization applied.
2026-05-10 — Added 5 more papers spanning brain, head & neck, hematologic, sarcoma, and bladder genomics: UCSF low-grade-glioma paired initial/recurrent WES showing temozolomide-driven hypermutation in 6/10 treated patients progressing to GBM (PMID 24336570); sinonasal adenoid cystic carcinoma molecular profiling with canonical and noncanonical MYB/MYBL1::NFIB plus novel ESRRG/DNM3 fusions (PMID 24418857); Broad multiple myeloma WES/WGS revealing pervasive subclonal architecture and paradoxical BRAF-WT activation by BRAF inhibitors (PMID 24434212); NCI/COG pediatric rhabdomyosarcoma comprehensive genomics defining PAX-fusion genotype as superior to histology with RTK/RAS/PIK3CA altered in 93% (PMID 24436047); TCGA muscle-invasive bladder cancer with 32 SMGs, APOBEC-dominant mutagenesis, and 69% therapeutically targetable (PMID 24476821). 137 unique genes touched, 4 new datasets, 4 new methods (droplet-digital-pcr, trusight-oncology-500). Brontictuzumab and PLX4720 added as corpus-grown drugs.
2026-05-09 — Added 5 more rare-cancer and discovery papers (2013–2014): JHU biliary tract WES (IHCH/GBC, BAP1/ARID1A/PBRM1 chromatin axis) (PMID 24185509); Broad melanoma BRAF-inhibitor resistance WES (MAP2K2/MITF as novel resistance) (PMID 24265153); JHU pancreatic acinar cell carcinoma + pancreatoblastoma first WES (KRAS-absent, Fanconi/DDR-targetable in >43%) (PMID 24293293); Cambridge CIMR landmark CALR discovery in JAK2/MPL-negative MPN (PMID 24325359); BC Cancer POG metastatic NEN WGTA (manifest mismatch flagged — actual paper Wee 2025) (PMID 24326773). 83 unique genes touched, 5 new datasets, 16 new cancer-type pages spanning MPN-spectrum and neuroendocrine OncoTree codes, 11 new methods (mutational-signatures, viper, strelka, bwa, star, rsem, edger, msi-pcr-pentaplex, qmsp, tsne, consensus-hierarchical-clustering).
2026-05-09 — Added 5 more 2013–2014 papers spanning bladder, brain, and lymphoma genomics: MSKCC bladder integrated genomics with MK-2206 sensitivity profiling (PMID 23897969); a co-clinical trials review covering KRAS-mutant LUAD selumetinib+docetaxel and PDAC saridegib failures (PMID 23999436); TCGA glioblastoma 2013 543-patient multi-platform analysis with TERT/ATRX dichotomy and MGMT subtype-specific methylation (PMID 24120142); BGI bladder WGS/WES identifying STAG2 as a novel driver and 32% SCCS-pathway alteration rate (PMID 24121792); IDIBAPS mantle cell lymphoma WGS+WES with NOTCH2 as independent prognostic factor (PMID 24145436). 102 unique genes touched, 4 new datasets, 9 new methods (RPPA, HM27/HM450 methylation arrays, BreakDancer, BamBam, PRADA, MEMo, INVEX, array-cgh-agilent-1m).
2026-05-09 — Added 5 more 2013 papers covering rare-cancer and pediatric genomics: adenoid cystic carcinoma MSKCC WES/WGS (PMID 23685749) and Sanger 24-sample cohort with SPEN/FGFR2 mutations (PMID 23778141); TCGA clear-cell renal cell carcinoma 446-sample multi-platform characterization (PMID 23792563); VHL-loss HIF-isoform-specific scRNA-seq mouse model (PMID 23797736, manifest mismatch flagged); ICGC PedBrain pilocytic astrocytoma WGS demonstrating 100% MAPK alteration with novel NTRK2 fusions (PMID 23817572). 109 unique genes touched (~50 new), 11 new methods (CREST, dRanger-class SV callers, ANNOVAR, Oncotator, Pindel, etc.). Belzutifan added as corpus-grown drug.
2026-05-09 — Added 5 landmark 2013 genomics papers spanning five cancer types: esophageal adenocarcinoma WES/WGS revealing the RAC1-GEF (ELMO1/DOCK2) axis (PMID 23525077), oral squamous cell carcinoma multi-platform profiling with NOTCH1 as tumor suppressor and 80% targetable rate (PMID 23619168), prostate cancer chromoplexy WGS introducing ChainFinder/CLONET (PMID 23622249), the TCGA AML 200-case study with mutation-sparse genomes and NPM1+DNMT3A+FLT3 triple-mutant subtype (PMID 23634996), and TCGA endometrial carcinoma defining four molecular subgroups (POLE ultramutated, MSI, copy-number low, serous-like) (PMID 23636398). 151 unique genes touched (68 new), 5 new datasets, 7 new methods (ABSOLUTE, ChainFinder, CLONET, dRanger, BreakPointer, Indelocator, MuTect).
2026-05-06 — Added 5 landmark genomics papers: cBioPortal platform (PMID 19176454), MSKCC prostate integrative profiling (PMID 20579941), pancreatic neuroendocrine exome sequencing (PMID 21252315), TCGA ovarian carcinoma (PMID 21720365), and NHL histone-modifier mutations (PMID 21796119). 17 new gene pages, 4 cancer types, 4 datasets created.
2026-05-06 — Added 12 papers spanning sarcoma genomics (PMID 20601955), lung adenocarcinoma somatic mutations (PMID 18948947), GIST germline variants (PMID 36593350), AURORA metastatic breast cancer multiomics (PMID 36585450), myoepithelial carcinoma WGS (PMID 36577525), bladder cancer primary-metastasis concordance (PMID 36543146), HGSOC TME atlas (PMID 36517593), KRASG12C-EGFR resistance in CRC (PMID 36355783), FBXO7-CHEK1 synthetic lethality (PMID 36334560), metastatic urothelial carcinoma molecular landscape (PMID 36333289), gallbladder cancer genomics (PMID 36228155), and NSCLC multimodal ICI prediction (PMID 36038778). Also shipped wiki append-citation CLI for 29% token-efficiency improvement.
2026-05-01 — Added 11 papers: the landmark 2008 TCGA glioblastoma interim analysis (PMID 18772890) plus 10 from 2024–2025 covering MSK-CHORD multimodal NLP, MiMSI MSI classifier, PDAC MAPK-subtype atlas, HGSOC fallopian-tube precursor spatial atlas, normal-skin melanocyte cell-of-origin atlas, CALGB 90601 mUC cfDNA, and others.

Browse

Section	Count	What you’ll find
Papers	252	Per-publication summaries: cohort, methods, findings, citations
Genes	1334	Alterations, co-occurrence, therapeutic relevance across the corpus
Cancer types	225	OncoTree-anchored disease pages linking studies and alterations
Datasets	241	cBioPortal studies with cohort details and linked publications
Drugs	248	Targeted therapies, resistance patterns, evidence in the corpus
Methods	281	Sequencing assays, gene panels, and analytical pipelines
Themes	2	Cross-cutting syntheses (in progress)

Papers

18772890 — Comprehensive genomic characterization defines human glioblastoma genes and core pathways
18948947 — Somatic mutations affect key pathways in lung adenocarcinoma
19176454 — Phase 3 Randomized Trial on Larynx Preservation Comparing Sequential vs Alternating Chemotherapy and Radiotherapy
20579941 — Integrative genomic profiling of human prostate cancer
20601955 — Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy
21252315 — DAXX/ATRX, MEN1 and mTOR Pathway Genes are Frequently Altered in Pancreatic Neuroendocrine Tumors
21720365 — Integrated Genomic Analyses of Ovarian Carcinoma
21796119 — Frequent mutation of histone modifying genes in non-Hodgkin lymphoma
21798893 — The Mutational Landscape of Head and Neck Squamous Cell Carcinoma
21798897 — Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1
21909114 — Somatic mutations in STAG2 are associated with separated megakaryocyte nuclear lobes in myelodysplastic syndromes
22037554 — ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors
22138691 — AI-driven multimodal algorithm predicts immunotherapy and targeted therapy outcomes in clear cell renal cell carcinoma
22158541 — Distinct and convergent effects of SF3B1 mutations in human breast cancer
22158988 — Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways
22343534 — Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
22367537 — Novel Strategy for Acquiring Metabolically-Tagged Nascent Extracellular Vesicles: Implications for Identifying Surface Protein Markers of Extracellular Vesicles From Neuroblastoma Cells Cultured With Native Serum
22460905 — The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity
22495314 — The clonal and mutational evolution spectrum of primary triple negative breast cancers
22522925 — The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
22610119 — Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
22622578 — Melanoma genome sequencing reveals frequent PREX2 mutations
22634756 — Hepatitis B virus integration and hepatocarcinogenesis
22722201 — The landscape of cancer genes and mutational processes in breast cancer
22722202 — Sequence analysis of mutations and translocations across breast cancer subtypes
22722829 — Novel mutations target distinct subgroups of medulloblastoma
22722839 — The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer
22802077 — CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set
22810696 — Comprehensive molecular characterization of human colon and rectal cancer
22817889 — A Landscape of Driver Mutations in Melanoma
22820256 — Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations
22832583 — Dissecting the genomic complexity underlying medulloblastoma
22842228 — Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma
22895193 — Recurrent R-spondin fusions in colon cancer
22941188 — Integrative genome analyses identify key somatic driver mutations of small cell lung cancer
22941189 — Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer
22960745 — Comprehensive genomic characterization of squamous cell lung cancers
22980975 — Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing
23000897 — Comprehensive molecular portraits of human breast tumors
23103869 — Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
23334666 — The genetic landscape of high-risk neuroblastoma
23334668 — The genomic landscape of hypodiploid acute lymphoblastic leukemia
23415222 — Evolution and impact of subclonal mutations in chronic lymphocytic leukemia
23525077 — Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity
23619168 — Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers
23622249 — Punctuated Evolution of Prostate Cancer Genomes
23634996 — Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
23636398 — Integrated genomic characterization of endometrial carcinoma
23685749 — The mutational landscape of adenoid cystic carcinoma
23778141 — Whole exome sequencing of adenoid cystic carcinoma
23792563 — Comprehensive molecular characterization of clear cell renal cell carcinoma
23797736 — HIFα isoform specific activities drive cell-type specificity of VHL-associated oncogenesis
23817572 — Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma
23897969 — Prevalence and Co-Occurrence of Actionable Genomic Alterations in High-Grade Bladder Cancer
23999436 — New cast for a new era: preclinical cancer drug development revisited
24120142 — The Somatic Genomic Landscape of Glioblastoma
24121792 — Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation
24145436 — Landscape of somatic mutations and clonal evolution in mantle cell lymphoma
24185509 — Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas
24265153 — The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma
24293293 — Whole exome sequencing of pancreatic neoplasms with acinar differentiation
24325359 — Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2
24326773 — Genomic and transcriptomic landscapes of metastatic neuroendocrine neoplasms from distinct primary sites and their clinical implications
24336570 — Mutational Analysis Reveals the Origin and Therapy-driven Evolution of Recurrent Glioma
24418857 — Molecular Profiling of Sinonasal Adenoid Cystic Carcinoma: Canonical and Noncanonical Gene Fusions and Mutation
24434212 — Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy
24436047 — Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors
24476821 — Comprehensive molecular characterization of urothelial bladder carcinoma
24487277 — Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing
24658004 — Recurrent SMARCA4 mutations in small cell carcinoma of the ovary
24670651 — Exploring the Diagnostic and Predictive Value of Oral Microbiome in Esophageal Cancer: A Systematic Review and Meta-Analysis
24686850 — Genomic and molecular characterization of esophageal squamous cell carcinoma
24735922 — Molecular Profiling of Liver Tumors: Classification and Clinical Translation for Decision Making
24798001 — Molecular therapies and precision medicine for hepatocellular carcinoma
24816253 — Divergent Morphologies and Common Signaling Features of Active and Inactive Oncogenic RHOA Mutants in Yeast
24816255 — Familial Non-Hereditary Gastric Cancer: Diagnosis, Management, Molecular Characteristics and Future Perspective
24892406 — Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach
24952746 — Novel Therapeutic Development for Nasopharyngeal Carcinoma
24974848 — A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors
24997986 — Matrix stiffness induced gallbladder fibroblasts activation and paracrine SEMA7A promotes gallbladder cancer cell epithelial-mesenchymal transition and cancer stem cell-like properties by modulating AKT/p300 signalling
25024180 — Copy number alteration burden predicts prostate cancer relapse
25079317 — Comprehensive molecular characterization of gastric adenocarcinoma
25079552 — Comprehensive molecular profiling of lung adenocarcinoma
25092538 — Genomic Predictors of Survival in Patients with High-Grade Urothelial Carcinoma of the Bladder
25096233 — Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma
25155756 — The somatic genomic landscape of chromophobe renal cell carcinoma
25164765 — Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions
25186949 — EWS::FLI1 expression in human embryonic mesenchymal stem cells leads to transcriptional reprograming, defective DNA damage repair and Ewing sarcoma
25201530 — Organoid cultures derived from patients with advanced prostate cancer
25223734 — Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations
25233892 — Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes
25240281 — PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors
25303977 — Mutational landscape of aggressive cutaneous squamous cell carcinoma
25401301 — Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes
25409260 — Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma
25417114 — Integrated Genomic Characterization of Papillary Thyroid Carcinoma
25470049 — Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution
25526346 — Chronic Liver Disease Associated Cholangiocarcinoma: Genomic Insights and Precision Therapeutic Strategies
25583476 — Mutational landscape of gastric adenocarcinoma in Chinese: Implications for prognosis and therapy
25583493 — Novel recurrently mutated genes in African American colon cancers
25589618 — Genomic analysis of metastatic cutaneous squamous cell carcinoma
25608663 — Targeting the gut-liver axis in cholangiocarcinoma: mechanisms, therapeutic advances, and future directions
25631445 — Comprehensive genomic characterization of head and neck squamous cell carcinomas
25730765 — The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias
25765070 — Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer
25822088 — Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets
25855536 — Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets
25991819 — Genome-wide analysis uncovers novel recurrent alterations in primary central nervous system lymphomas
26000489 — Integrative clinical genomics of advanced prostate cancer
26091043 — Genomic Classification of Cutaneous Melanoma
26095796 — Genomic landscape of adenoid cystic carcinoma of the breast
26168399 — Comprehensive genomic profiles of small cell lung cancer
26200345 — SF3B1 mutation accelerates the development of CLL via activation of the mTOR pathway
26278805 — Genomic Characterization of Upper Tract Urothelial Carcinoma
26343386 — Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway
26359337 — Genomic correlates of response to CTLA-4 blockade in metastatic melanoma
26437033 — Rat somatic genome editing enables ER+ breast cancer modeling
26451490 — Comprehensive molecular portraits of invasive lobular breast cancer
26466568 — Telomerase activation by genomic rearrangements in high-risk neuroblastoma
26466571 — Mutations driving CLL and their evolution in progression and relapse
26544944 — The Molecular Taxonomy of Primary Prostate Cancer
26551667 — The mutational landscape of cutaneous T-cell lymphoma and Sézary syndrome
26631609 — Novel MYBL1 gene rearrangements with recurrent MYBL1-NFIB fusions in salivary adenoid cystic carcinomas lacking t(6;9) translocations
26683228 — Deep sequencing of uveal melanoma identifies a recurrent mutation in PLCB4
26760213 — Divergent clonal selection dominates medulloblastoma at recurrence
26804919 — Ampullary cancers harbor ELF3 tumor suppressor gene mutations and exhibit frequent WNT dysregulation
26824661 — Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma
26829750 — An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma
26855148 — Divergent clonal evolution of castration resistant neuroendocrine prostate cancer
26862087 — Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma
26878173 — Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers
26901067 — Frequent somatic CDH1 loss-of-function mutations in plasmacytoid-variant bladder cancer
26928463 — Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer
26950094 — Mutation burden of narrowband ultraviolet B phototherapy (NB-UVB) in human skin: relevance to NB-UVB lifetime exposures and skin cancer surveillance
26977886 — Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways
26997480 — Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma
27149842 — Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma
27158780 — Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
27161491 — The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes
27276561 — Genomic Classification and Prognosis in Acute Myeloid Leukemia
27346245 — A profile of lung cancer in the young population with a highlight on the Indian perspective
27442865 — The Molecular Landscape of Recurrent and Metastatic Head and Neck Cancers: Insights From a Precision Oncology Sequencing Platform
27634761 — A platform-independent AI tumor lineage and site (ATLAS) classifier
27646943 — Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors
27698471 — Anti-tubulin drugs conjugated to anti-ErbB antibodies selectively radiosensitize
27713405 — Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets
27749842 — Clonal Evolution of Chemotherapy-resistant Urothelial Carcinoma
27776115 — Deregulation of DUX4 and ERG in acute lymphoblastic leukemia
27806376 — Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
27826200 — A current perspective on stereotactic body radiation therapy for pancreatic cancer
27959731 — TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes
28007021 — Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations
28027327 — Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis
28045614 — Altering the Natural History of Oligometastatic Prostate Cancer With Local Therapies: Reality Versus Illusion
28052061 — Integrated genomic characterization of oesophageal carcinoma
28068672 — Targeting the ATM-TRMT10A-BRCA1 axis confers synthetic lethality to PARP inhibition in metastatic castration-resistant prostate cancer
28162975 — Comprehensive molecular characterization of pheochromocytoma and paraganglioma
28196596 — Chemosensitive Relapse in Small Cell Lung Cancer Proceeds through an EZH2-SLFN11 Axis
28199314 — EWSR1::BEND2 fusion sarcoma of the urinary bladder – a case report and review of literature
28336552 — Prospective comprehensive molecular characterization of lung adenocarcinomas for efficient patient matching to approved and emerging therapies
28373299 — Integrated genomic analyses reveal frequent aberrations in acral melanoma
28445112 — Genomic landscape of endometrial polyps
28445469 — Phylogenetic ctDNA analysis depicts early stage lung cancer evolution
28472509 — Multicenter phase II study of temozolomide and myeloablative chemotherapy with autologous stem cell transplant for newly diagnosed anaplastic oligodendroglioma
28481359 — Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients
28485815 — Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing
28583311 — Next-generation Sequencing of Nonmuscle Invasive Bladder Cancer Reveals Potential Biomarkers and Rational Therapeutic Targets
28667006 — Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma
28726821 — The whole-genome landscape of medulloblastoma subtypes
28783718 — Integrative Clinical Genomics of Metastatic Cancer
28825054 — Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making
28872634 — Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features
28927585 — Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus
28985567 — Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma
28988769 — Comprehensive molecular characterization of muscle invasive bladder cancer
29033130 — Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab
29100075 — Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas
29122777 — Genetic predictors of response to systemic therapy in esophagogastric cancer
29301960 — Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma
29316426 — Clinical sequencing defines the genomic landscape of metastatic colorectal cancer
29337640 — Molecular Determinants of Response to Anti–Programmed Cell Death (PD)-1 and Anti–Programmed Death-Ligand 1 (PD-L1) Blockade in Patients With Non–Small-Cell Lung Cancer Profiled With Targeted Next-Generation Sequencing
29420467 — HER kinase inhibition in patients with HER2- and HER3-mutant cancers
29422544 — Mutational signatures and chromosome alteration profiles of squamous cell carcinomas of the vulva
29489754 — Germline variants observed in pediatric cancer patients related to hereditary breast and ovarian cancer in adults
29596782 — Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines
29610475 — The long tail of oncogenic drivers in prostate cancer
29617662 — Driver Fusions and Their Implications in the Development and Treatment of Human Cancers
29622463 — Genomic and Functional Approaches to Understanding Cancer Aneuploidy
30179230 — Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy
30325352 — A radiogenomic dataset of non-small cell lung cancer
34433969 — A Clinically Applicable Integrative Molecular Classification of Meningiomas
34493726 — Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors
35764743 — Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer
35927489 — Molecular map of chronic lymphocytic leukemia and its impact on outcome
36038778 — Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer
36228155 — Comprehensive Molecular Characterization of Gallbladder Carcinoma and Potential Targets for Intervention
36333289 — Collaborative study from the Bladder Cancer Advocacy Network for the genomic analysis of metastatic urothelial cancer
36334560 — CHEK1 is a synthetic lethal interactor of FBXO7 in colonic epithelial cells
36355783 — Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer
36357680 — Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer
36493333 — Molecular Classification of Appendiceal Adenocarcinoma
36517593 — Ovarian cancer mutational processes drive site-specific immune evasion
36543146 — Genomic heterogeneity as a barrier to precision oncology in urothelial cancer
36577525 — Whole-genome characterization of myoepithelial carcinomas of the soft tissue
36585450 — Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis
36593350 — Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations
36723991 — Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells
36862133 — Overcoming barriers to tumor genomic profiling through direct-to-patient outreach
37078708 — TP53 mutations identify high-risk events for peripheral T-cell lymphoma treated with CHOP-based chemotherapy
37084736 — Genomic Mapping of Metastatic Organotropism in Lung Adenocarcinoma
37202560 — An integrated tumor, immune and microbiome atlas of colon cancer
37315267 — Extremity Rhabdomyosarcoma: An Integrated Clinicopathologic and Genomic Study to Improve Risk Stratification
37350195 — Distinct genomic landscapes in radiation-associated angiosarcoma compared with other radiation-associated sarcoma histologies
37397861 — Multi-institutional Prognostic Modeling in Head and Neck Cancer: Evaluating Impact and Generalizability of Deep Learning Approaches
37406106 — Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer
37477937 — Novel Genomic Risk Stratification Model for Primary Gastrointestinal Stromal Tumors (GIST) in the Adjuvant Therapy Era
37591896 — Genomic analysis and clinical correlations of non-small cell lung cancer brain metastasis
37643132 — Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets
37651310 — Molecular characterization of endometrial carcinomas in Black and White patients reveals disparate drivers with therapeutic implications
37682528 — Clinical and Genomic Landscape of FGFR3-Altered Urothelial Carcinoma and Treatment Outcomes with Erdafitinib: A Real-World Experience
37699004 — Clinical and molecular characteristics of early-onset vs average-onset esophagogastric cancer
37730754 — Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression and relapse
37769223 — Targeted Molecular Profiling of Circulating Cell-Free DNA in Patients With Advanced Hepatocellular Carcinoma
37910594 — Tumor Volume Growth Rates and Doubling Times during Active Surveillance of IDH-mutant Low-Grade Glioma
38117484 — The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen
38147626 — High-risk and silent clonal hematopoietic genotypes in patients with nonhematologic cancer
38362943 — RADCURE: An open-source head and neck cancer CT dataset for clinical radiation therapy insights
38412093 — The genomic and evolutionary landscapes of anaplastic thyroid carcinoma
38488807 — Developing Novel Genomic Risk Stratification Models in Soft Tissue and Uterine Leiomyosarcoma
38488813 — Integrative Molecular Analyses of the MD Anderson Prostate Cancer Patient-derived Xenograft (MDA PCa PDX) Series
38497151 — Validation of LymphGen classification on a 400-gene clinical next-generation sequencing panel in diffuse large B-cell lymphoma: real-world experience from a cancer center
38630790 — Diffuse pleural mesotheliomas with genomic near-haploidization: a newly recognized subset with distinct clinical, histologic, and molecular features
38653864 — Nivolumab for mismatch-repair-deficient or hypermutated gynecologic cancers: a phase 2 trial with biomarker analyses
38758238 — Genome-wide loss of heterozygosity predicts aggressive, treatment-refractory behavior in pituitary neuroendocrine tumors
38780927 — Intensity-Modulated Reirradiation Therapy With Nivolumab in Recurrent or Second Primary Head and Neck Squamous Cell Carcinoma: A Nonrandomized Controlled Trial
38864854 — A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: the Hidden-Genome Classifier
38895302 — Molecular effects of indoor tanning
38922339 — Tumor-agnostic genomic and clinical analysis of BRAF fusions identify actionable targets
38949888 — Microsatellite Instability, Tumor Mutational Burden, and Response to Immune Checkpoint Blockade in Patients with Prostate Cancer
38995739 — A Phase II study assessing Long-Term Response to Ibrutinib Monotherapy in recurrent or refractory CNS Lymphoma
39091884 — Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma
39147831 — DNA liquid biopsy-based prediction of cancer-associated venous thromboembolism
39214094 — Distinct clinical outcomes and biological features of specific KRAS mutants in human pancreatic cancer
39289779 — Real-world experience with circulating tumor DNA in cerebrospinal fluid from patients with central nervous system tumors
39305899 — The landscape of drug sensitivity and resistance in sarcoma
39386723 — Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma
39506116 — Automated real-world data integration improves cancer outcome prediction
39746944 — A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing
39753968 — Clinicogenomic landscape of pancreatic adenocarcinoma identifies KRAS mutant dosage as prognostic of overall survival
39975212 — Somatic mutations distinguish melanocyte subpopulations in human skin
40256659 — Circulating Tumor DNA and Response to Cisplatin-based Chemotherapy in Patients with Metastatic Urothelial Carcinoma Enrolled in CALGB 90601 (Alliance)
41941260 — Radiation Oncology-Biology Integration Network (ROBIN): Bridging the gap between biological research and clinical practice

Genes

ABCB1 · ABCB11 · ABCC2 · ABL1 · ACADL · ACTA2 · ACTB · ACTG1 · ACTN4 · ACVR1B · ACVR1C · ACVR2A · ADAM2 · ADAMTS13 · ADAMTS5 · ADCY2 · ADORA2A · AFDN · AGAP3 · AGK · AGTR2 · AHNAK2 · AHR · AIG1 · AJAP1 · AJUBA · AKAP6 · AKAP9 · AKT1 · AKT2 · AKT3 · ALB · ALDH1A1 · ALDH1L2 · ALDOC · ALK · ALKBH5 · ALMS1 · AMER1 · ANKRD36 · ANKRD62 · APC · APEX1 · APOB · APOBEC3A · APOBEC3B · APOE · AR · ARAF · ARHGAP26 · ARHGAP35 · ARHGAP6 · ARHGEF18 · ARHGEF3 · ARHGEF5 · ARID1A · ARID1B · ARID2 · ARID4A · ARID5B · ASCC2 · ASCL1 · ASCL4 · ASH2L · ASNS · ASPM · ASPSCR1 · ASXL1 · ASXL2 · ASXL3 · ATF1 · ATM · ATP8B2 · ATR · ATRX · ATXN1 · AURKA · AURKB · AURKC · AXIN1 · AXIN2 · AXL · B2M · BANF1 · BAP1 · BARD1 · BAZ1A · BAZ2B · BBC3 · BCL10 · BCL11A · BCL11B · BCL2 · BCL2L1 · BCL2L11 · BCL6 · BCL7A · BCL9 · BCL9L · BCLAF1 · BCOR · BCR · BEND2 · BICC1 · BIRC2 · BIRC3 · BIRC7 · BLK · BLM · BMP4 · BMPR1A · BOC · BRAF · BRCA1 · BRCA2 · BRCC3 · BRD2 · BRD3 · BRD4 · BRD7 · BRD9 · BRIP1 · BRPF1 · BST2 · BTG1 · BTG2 · BTK · BTLA · BUB1 · BUB1B · C19ORF38 · C1QA · C2CD4C · CACNA1A · CACNA1D · CACNG6 · CADM2 · CALR · CANX · CAPZA2 · CARD11 · CASP1 · CASP8 · CBFA2T3 · CBFB · CBL · CCDC149 · CCDC6 · CCDC74A · CCL13 · CCL2 · CCL5 · CCL7 · CCL8 · CCN2 · CCNB1 · CCND1 · CCND2 · CCND3 · CCNE1 · CCNE2 · CD24 · CD247 · CD274 · CD276 · CD28 · CD3D · CD3E · CD3G · CD4 · CD44 · CD5 · CD58 · CD70 · CD74 · CD79B · CD80 · CD86 · CD8A · CD8B · CD99 · CDH1 · CDH13 · CDH2 · CDK12 · CDK2 · CDK4 · CDK5RAP2 · CDK6 · CDK7 · CDK8 · CDKAL1 · CDKN1A · CDKN1B · CDKN2A · CDKN2B · CDKN2C · CEACAM1 · CEBPA · CENPF · CFH · CGAS · CHD1 · CHD2 · CHD3 · CHD5 · CHD6 · CHD7 · CHD8 · CHEK1 · CHEK2 · CHFR · CHGA · CHGB · CHRNA7 · CIC · CITED1 · CLCN6 · CLDN11 · CLDN18 · CLPTM1L · CLTC · CMTR2 · CNR1 · COBL · COL14A1 · COL1A1 · COL1A2 · COL22A1 · COL4A1 · COL4A2 · COL6A3 · COL8A1 · CP · CPM · CPQ · CPT1C · CRACDL · CREB1 · CREBBP · CRKL · CRLF2 · CRTC1 · CSDE1 · CSF1R · CSMD1 · CSMD3 · CSNK2B · CTCF · CTDNEP1 · CTLA4 · CTNNA1 · CTNNB1 · CTNND1 · CTTN · CUL1 · CUL3 · CUL4A · CXCL1 · CXCL10 · CXCL16 · CXCL9 · CYLD · CYP11B1 · CYP1A1 · CYP21A2 · CYP7A1 · DAAM2 · DAXX · DBH · DCC · DCLK1 · DDIT3 · DDR2 · DDX1 · DDX3X · DDX41 · DEK · DEPDC5 · DHFR · DICER1 · DIS3 · DKK1 · DKK2 · DLC1 · DLEU1 · DLEU2 · DLK1 · DLL3 · DLST · DMD · DNAJB1 · DNAJB6 · DNM2 · DNM3 · DNMT3A · DNMT3B · DOCK2 · DOCK7 · DOT1L · DSCAM · DUX4 · DVL3 · DYRK1A · E2F1 · E2F3 · EBF1 · ECT2 · EDC4 · EED · EGF · EGFR · EGLN1 · EGR1 · EGR2 · EIF1AX · EIF2D · ELF3 · ELF4 · ELK4 · ELMO1 · ELOC · EML4 · EML6 · EMSY · EN1 · ENOSF1 · EOMES · EP300 · EP400 · EPAS1 · EPC1 · EPCAM · EPHA2 · EPHA3 · EPHA4 · EPHA6 · EPHA7 · EPHB1 · EPHB6 · ERBB2 · ERBB3 · ERBB4 · ERC1 · ERCC2 · ERCC4 · ERG · ERRFI1 · ESPL1 · ESR1 · ESRRG · ETS2 · ETV1 · ETV3 · ETV4 · ETV5 · ETV6 · EWSR1 · EXO1 · EXT2 · EZH1 · EZH2 · FAAH2 · FADD · FAM131B · FAM3C · FANCA · FANCB · FANCC · FANCD2 · FANCE · FANCF · FANCG · FANCI · FANCL · FANCM · FAP · FASN · FAT1 · FAT2 · FAT3 · FAT4 · FBN1 · FBXO24 · FBXO7 · FBXW7 · FER · FEV · FGA · FGF16 · FGF19 · FGF2 · FGF3 · FGF4 · FGF9 · FGFR1 · FGFR2 · FGFR3 · FGFR4 · FGR · FH · FHIT · FLCN · FLG · FLI1 · FLT1 · FLT3 · FLT3LG · FLT4 · FMN2 · FN1 · FOS · FOXA1 · FOXA2 · FOXD3 · FOXM1 · FOXN4 · FOXO1 · FOXO3 · FOXP1 · FOXP2 · FOXP3 · FOXQ1 · FPR1 · FRAS1 · FRS2 · FSIP1 · FSIP2 · FUBP1 · FUS · FZD8 · G6PD · GAB2 · GABRA6 · GALNT7 · GATA2 · GATA3 · GATA4 · GATA6 · GCC2 · GEN1 · GFAP · GFI1 · GFI1B · GGNBP2 · GH1 · GJC1 · GLI1 · GLI2 · GLI3 · GLIS2 · GLUL · GNA11 · GNA13 · GNAI1 · GNAQ · GNAS · GNLY · GPBAR1 · GPC3 · GPR149 · GPS2 · GRB10 · GRB7 · GREB1 · GRIN2A · GRP · GSE1 · GSK3B · GSTM1 · GTF2I · GZMA · GZMB · GZMH · H1-4 · H1-5 · H3-3A · HACD1 · HAVCR2 · HCK · HDAC2 · HECTD4 · HECW1 · HERC1 · HERC2 · HES1 · HGF · HIF1A · HLA-A · HLA-B · HLA-C · HLA-DPA1 · HLA-E · HMCN1 · HMGA1 · HMGA2 · HMOX1 · HNF1A · HNF1B · HNF4A · HOTAIR · HOXA7 · HOXB13 · HOXD13 · HOXD8 · HRAS · HSPA1A · HSPA5 · HSPG2 · HTR1F · ICOS · IDH1 · IDH2 · IDO1 · IFITM1 · IFNE · IFNG · IGF1 · IGF1R · IGF2 · IGF2R · IGFBP2 · IGFN1 · IGH · IKBKB · IKZF1 · IKZF2 · IKZF3 · IL10 · IL12B · IL17RC · IL17RD · IL17RE · IL1B · IL23R · IL36A · IL4R · IL6R · IL6ST · IL7R · INHBA · INO80 · INO80D · INPP4A · INPP4B · INPPL1 · INSR · IRF1 · IRF2 · IRF4 · IRF6 · IRF7 · IRF9 · IRS2 · ISG15 · ISL1 · ITGAE · ITGB1 · ITK · ITM2A · ITPKB · JAG1 · JAG2 · JAK1 · JAK2 · JAK3 · JAM3 · JARID2 · JAZF1 · JPT1 · JUN · JUP · KANSL1 · KAT6A · KAT6B · KBTBD4 · KCNJ3 · KDM4B · KDM4C · KDM4D · KDM5A · KDM5B · KDM5C · KDM5D · KDM6A · KDR · KEAP1 · KEL · KIAA1549 · KIF1B · KIF5B · KIT · KLF15 · KLF4 · KLF5 · KLF6 · KLHL14 · KLHL6 · KLK3 · KLRK1 · KMT2A · KMT2B · KMT2C · KMT2D · KMT2E · KNSTRN · KRAS · KRT14 · KRT17 · KRT19 · KRT20 · KRT5 · KRT6A · L1CAM · LAG3 · LAMA5 · LANCL2 · LCK · LDB1 · LGR5 · LIF · LIPA · LLGL1 · LMCD1 · LOX · LOXL2 · LRMDA · LRP1 · LRP1B · LRP2 · LSAMP · LSS · LTK · LTO1 · LUM · LXN · LYN · LZTR1 · MACF1 · MACROD2 · MAGEA6 · MAGEB10 · MAGI2 · MAGI3 · MALAT1 · MAML1 · MAML2 · MAML3 · MAP10 · MAP2K1 · MAP2K2 · MAP2K4 · MAP2K7 · MAP3K1 · MAP3K13 · MAP3K15 · MAP3K5 · MAP3K7 · MAP3K8 · MAPK1 · MAPK3 · MATR3 · MAX · MB21D2 · MC1R · MCL1 · MCM2 · MDM2 · MDM4 · MECOM · MED1 · MED12 · MED13 · MEF2B · MEGF8 · MEIS1 · MEN1 · MEOX2 · MERTK · MET · METTL3 · MFAP5 · MGA · MGAT4C · MGMT · MICA · MIDN · MIR15A · MIR17HG · MIR205 · MIR21 · MITF · MKI67 · MKRN1 · MLANA · MLH1 · MLH3 · MLLT10 · MLLT11 · MLLT3 · MN1 · MPL · MRE11 · MRPS31 · MSH2 · MSH3 · MSH6 · MSL3 · MSMB · MSRA · MT1E · MT1H · MT2A · MTAP · MTOR · MUC1 · MUC12 · MUC16 · MUC3A · MUC4 · MUTYH · MX1 · MYB · MYBL1 · MYC · MYCBP2 · MYCL · MYCN · MYD88 · MYH11 · MYL9 · MYLK · MYO3A · MYO6 · MYOCD · MYOD1 · NACC2 · NALCN · NAPRT · NAV2 · NAV3 · NBN · NCAM1 · NCOA1 · NCOA2 · NCOA3 · NCOA4 · NCOR1 · NCOR2 · NDRG1 · NDUFS1 · NEAT1 · NECTIN4 · NEGR1 · NEK5 · NEUROD1 · NF1 · NF2 · NFATC1 · NFATC2 · NFE2 · NFE2L2 · NFIB · NFKB1 · NFKBIA · NFKBIE · NGFR · NHERF1 · NIN · NIPBL · NKAIN2 · NKD1 · NKX2-1 · NKX3-1 · NOL10 · NOTCH1 · NOTCH2 · NOTCH3 · NOTCH4 · NPAS3 · NPM1 · NQO1 · NR0B1 · NR1H4 · NR3C1 · NR4A3 · NRAS · NRF1 · NRG1 · NRXN3 · NSD1 · NSD2 · NSD3 · NT5C2 · NT5E · NTHL1 · NTNG1 · NTRK1 · NTRK2 · NTRK3 · NUAK1 · NUMB · NUP214 · NUP98 · NUTM1 · NXF1 · OLIG1 · OLIG2 · OMG · OR5L1 · OSBPL3 · OTX2 · P2RY8 · PABPC1 · PADI2 · PAG1 · PAIP1 · PAK1 · PAK2 · PAK3 · PALB2 · PALLD · PAPPA2 · PARD3 · PARP1 · PARP2 · PARP6 · PARS2 · PASK · PATZ1 · PAX2 · PAX3 · PAX5 · PAX7 · PAX8 · PBRM1 · PCDH18 · PCNA · PDCD1 · PDCD1LG2 · PDCD6 · PDE4DIP · PDGFA · PDGFRA · PDGFRB · PDHB · PDIA3 · PDSS2 · PDXDC1 · PDZD2 · PEG10 · PGD · PGR · PHF3 · PHF6 · PHOX2A · PHOX2B · PICALM · PIEZO2 · PIK3C2A · PIK3C2G · PIK3C3 · PIK3CA · PIK3CB · PIK3CD · PIK3CG · PIK3R1 · PIK3R2 · PIM1 · PIM2 · PINK1 · PINX1 · PLAG1 · PLCB3 · PLCB4 · PLCE1 · PLCG1 · PLK1 · PLXNA1 · PLXNB1 · PLXNC1 · PMEL · PML · PMS2 · PNKD · PNMT · POC5 · POLD1 · POLD2 · POLE · POLR2A · POT1 · POU2AF3 · POU2F2 · POU6F2 · PPARG · PPARGC1A · PPM1D · PPP1R1B · PPP2R1A · PPP2R2A · PPP2R5A · PPP3CA · PPP6C · PRDM1 · PRDM6 · PRDM9 · PREX2 · PRF1 · PRIM2 · PRKAA1 · PRKACA · PRKACB · PRKAG1 · PRKAG2 · PRKAR1A · PRKCB · PRKCD · PRKCI · PRKCQ · PRKCZ · PRKD1 · PRKDC · PRKG1 · PRKN · PROM1 · PRPH · PRPS2 · PRRX1 · PSCA · PTCH1 · PTEN · PTGFRN · PTGS2 · PTK2 · PTK7 · PTP4A1 · PTPN1 · PTPN11 · PTPN3 · PTPN5 · PTPN6 · PTPRB · PTPRD · PTPRG · PTPRH · PTPRJ · PTPRK · PTPRQ · PTPRS · PTPRT · PVT1 · PXDNL · QKI · RAC1 · RACK1 · RAD17 · RAD21 · RAD50 · RAD51 · RAD51B · RAD51C · RAD51D · RAD54L · RAF1 · RAI14 · RAMP3 · RAN · RAP1GAP · RARA · RASA1 · RASSF1 · RB1 · RBFOX1 · RBL1 · RBL2 · RBM10 · RBM12 · RBM46 · RBPJ · RBPMS · RBX1 · RECQL4 · RELA · RET · RFX7 · RGMB · RGS7 · RHOA · RHOB · RICTOR · RIMS1 · RIPK1 · RIPK4 · RIT1 · RNF130 · RNF2 · RNF43 · RNGTT · ROBO1 · ROBO2 · ROBO3 · ROR2 · ROS1 · RP1L1 · RPL22 · RPS15 · RPS27 · RPS6KA2 · RPS6KA3 · RPS6KB1 · RPTOR · RRAS2 · RRM1 · RSF1 · RSPO2 · RSPO3 · RSPO4 · RTTN · RUNX1 · RUNX1T1 · RXRA · RYBP · RYR1 · RYR2 · RYR3 · S100A4 · S100B · S1PR2 · SAMHD1 · SBDS · SBNO2 · SCGN · SCN11A · SCN8A · SCN9A · SDHA · SDHB · SDHC · SDHD · SEC61G · SEMA3A · SEMA3C · SEMA3E · SEMA3G · SEMA5A · SEMA7A · SERPINB3 · SERPINB4 · SETBP1 · SETD1B · SETD2 · SETDB1 · SF3B1 · SFPQ · SGCE · SGK1 · SH2B3 · SHH · SHQ1 · SIK2 · SKP1 · SLC16A4 · SLC45A3 · SLC5A3 · SLC6A18 · SLC6A19 · SLCO1B3 · SLFN11 · SLIT1 · SLIT2 · SLIT3 · SLITRK6 · SLX4 · SMAD2 · SMAD3 · SMAD4 · SMAD6 · SMARCA1 · SMARCA2 · SMARCA4 · SMARCA5 · SMARCB1 · SMARCC1 · SMARCC2 · SMARCD1 · SMARCE1 · SMC1A · SMC3 · SMG1 · SMO · SMYD3 · SNAI1 · SNCAIP · SND1 · SNRPD3 · SNX25 · SNX31 · SOCS1 · SOD1 · SOS1 · SOS2 · SOX10 · SOX11 · SOX17 · SOX2 · SOX3 · SOX4 · SOX6 · SOX7 · SOX9 · SP140 · SPAG17 · SPART · SPATC1L · SPDEF · SPECC1L · SPEN · SPINK1 · SPOP · SPOPL · SPRY2 · SPTA1 · SPTAN1 · SQSTM1 · SRC · SRGAP2 · SRGAP3 · SRSF2 · SS18 · SSTR2 · SSX1 · SSX2 · STAC · STAG1 · STAG2 · STAR · STAT1 · STAT3 · STAT4 · STAT5B · STAT6 · STING1 · STK11 · STK19 · STRN · SUFU · SUZ12 · SYK · SYNE1 · SYNE2 · SYP · TACC1 · TACC3 · TAF1 · TAF15 · TAF9 · TAGLN · TAP1 · TAP2 · TAPBP · TBC1D3 · TBK1 · TBL1XR1 · TBR1 · TBX21 · TBX3 · TCF21 · TCF4 · TCF7 · TCF7L1 · TCF7L2 · TCHH · TEAD1 · TEK · TENT5C · TERC · TERT · TET1 · TET2 · TET3 · TFAP4 · TFE3 · TFEB · TFEC · TGFB1 · TGFBR1 · TGFBR2 · TGFBR3 · TGIF1 · TH · THADA · THSD7B · TIAM1 · TIGIT · TLN2 · TLR2 · TLR4 · TLX1 · TMEM106B · TMEM127 · TMEM14C · TMEM30A · TMEM71 · TMEM87B · TMPRSS2 · TMSB4X · TNF · TNFAIP3 · TNFRSF10A · TNFRSF14 · TNFRSF1B · TNFRSF4 · TNFRSF9 · TNIP2 · TNK2 · TNNT2 · TOP1 · TOP2A · TOX · TP53 · TP63 · TP73 · TPM3 · TRABD · TRAF2 · TRAF3 · TRAF3IP2 · TRAF7 · TRIM24 · TRIM28 · TRIO · TRMT10A · TRPC4AP · TRRAP · TSC1 · TSC2 · TSHR · TSPAN8 · TTC28 · TTK · TTN · TUBD1 · TWIST1 · TWIST2 · TXNIP · TYK2 · TYRP1 · U2AF1 · UBA7 · UBE2A · UBE2QL1 · UBE4B · UBR5 · UBTF · UCA1 · UCP2 · UGT1A1 · UHRF1 · UHRF2 · UPK1A · UPK2 · UQCRH · USF1 · USH2A · USP10 · USP22 · USP28 · USP34 · USP7 · USP8 · USP9X · UTY · VAV1 · VAV2 · VCAN · VEGFA · VEGFC · VGLL3 · VGLL4 · VHL · VIM · VOPP1 · VSIR · WASF2 · WASHC1 · WDR87 · WHSC1L1 · WNK1 · WNK2 · WNT11 · WNT4 · WNT5A · WNT5B · WT1 · WWOX · WWTR1 · XIAP · XPO1 · XPO4 · XRCC1 · XRCC3 · XRCC4 · XRN1 · YAP1 · YEATS4 · YES1 · YTHDF3 · YWHAZ · ZAP70 · ZBTB16 · ZBTB7A · ZC3H18 · ZEB1 · ZEB2 · ZFAT · ZFHX3 · ZFP36L1 · ZIC1 · ZIC3 · ZIM2 · ZMAT3 · ZMYM3 · ZMYND11 · ZNF217 · ZNF350 · ZNF595 · ZNF703 · ZNF717 · ZNF750 · ZNF765 · ZNF862 · ZNRF3 · ZRSR2

Cancer types

ACBC · ACC · ACCC · ACML · ACRM · ACYC · AITL · ALCL · ALCLALKN · ALCLALKP · AMBL · AMKL · AML · AMPCA · ANGS · APAD · APLPMLRARA · ARMS · ASPS · ASTB · ASTR · ATLL · ATRT · BCC · BL · BLCA · BLL · BLLKMT2A · BLLNOS · BRCA · CCOC · CCRCC · CESC · CHDM · CHL · CHOL · CHRCC · CHS · CLLSLL · CML · CMML · COAD · COADREAD · CSCC · CUP · DA · DCIS · DDCHS · DDLS · DESM · DIFG · DLBCLNOS · DMG · DSRCT · DSTAD · EATL · ECD · EGC · EHCH · EPIS · EPM · EPMT · ERMS · ES · ESCA · ESCC · ET · FIBS · FL · FLC · GB · GBC · GBM · GCT · GEJ · GIST · HCC · HGGNOS · HGONEC · HGSOC · HL · HNNE · HNSC · HNSCUP · HPHSC · IDC · IFS · IHCH · ILC · IMT · IPMN · JMML · KICH · KIRC · KIRP · LAML · LCH · LGG · LIAD · LIHB · LIHC · LIPO · LMS · LNET · LUAD · LUNE · LUSC · LXSC · MASC · MBC · MBL · MCL · MCN · MDS · MEITL · MEL · MESO · MF · MFH · MFS · MGCT · MIXED · MNET · MNG · MPN · MPNST · MPNU · MRLS · MRT · MRTL · MTNN · MUCC · MXOV · MYCF · MYEC · NBL · NCCRCC · NETNOS · NPC · NSCLC · NSGCT · OCSC · ODG · ODG3 · OGCT · ONBL · OPHSC · OS · OV · OVT · PAAC · PAAD · PAASC · PANCAN · PANEC · PANET · PAST · PB · PCM · PCNSL · PCPG · PECOMA · PGNG · PHC · PHCH · PINT · PLLS · PLMESO · PPB · PRAD · PRCC · PRNE · PTAD · PTCL · PTLD · PV · PXA · RCC · READ · RMS · ROCY · SACA · SARC · SARCNOS · SBC · SBWDNET · SCCO · SCLC · SCRMS · SCSRMS · SDCA · SEM · SKCM · SKIN · SPN · SRCBC · SS · STAD · SYNS · TET · TGCT · THAP · THCA · THPA · THPD · THYC · THYM · TLL · TRCC · TT · UCCC · UCEC · UCS · UEC · ULM · ULMS · UM · URCC · USARC · USC · UTUC · UVM · VSC · WDLS · WT

Datasets

Drugs

abiraterone · acitretin · adagrasib · adg106 · ado-trastuzumab-emtansine · afatinib · aldesleukin · alpelisib · alvespimycin · amg-232 · amoxicillin · anlotinib · apalutamide · apatinib · aspirin · atezolizumab · avelumab · axitinib · azacitidine · azd8055 · bat6026 · becotatug-vedotin · belzutifan · bevacizumab · bez235 · bgb-a445 · binimetinib · bintrafusp-alfa · bl-b01d1 · bleomycin · blu-554 · bortezomib · brd-k98645985 · brentuximab-vedotin · brivanib · brontictuzumab · buparlisib · busulfan · c646 · cabozantinib · cadonilimab · camrelizumab · capecitabine · capmatinib · carboplatin · caspofungin · cdca · cediranib · ceralasertib · cetuximab · cisplatin · cladribine · cobimetinib · crenolanib · crizotinib · cyclophosphamide · cytarabine · dabrafenib · dacomitinib · dalpiciclib · dasatinib · daunorubicin · decitabine · degarelix · disitamab-vedotin · dky709 · docetaxel · donafenib · dostarlimab · dovitinib · doxorubicin · durvalumab · dutasteride · encorafenib · enfortumab-vedotin · entrectinib · envafolimab · enzalutamide · erdafitinib · erlotinib · etoposide · etrumadenant · everolimus · fgf401 · fludarabine · fluorouracil · flutamide · folfirinox · folfox · fulvestrant · futibatinib · fuzuloparib · galunisertib · gdc-0941 · gefitinib · gemcitabine · gen1160 · gen1286 · gsk-690693 · gw4064 · h3b-6527 · h3b-8800 · hlx10 · ibi-310 · ibrutinib · idarubicin · ifosfamide · ilb-2109 · imatinib · inc-b099280 · infigratinib · int-777 · interferon-alpha · ipilimumab · irinotecan · ivosidenib · jq1 · jte-013 · ku-55933 · lanreotide · lapatinib · larotrectinib · lbl-007 · lenalidomide · lenvatinib · letrozole · leucovorin · leuprolide · linifanib · linsitinib · lomustine · lorlatinib · ly294002 · melphalan · mertansine · methotrexate · methoxsalen · metronidazole · mg-132 · mitomycin-c · mk-2206 · mocetinostat · monalizumab · monomethyl-auristatin-e · mva-eb-na1-lmp2 · myriocin · nab-paclitaxel · nanatinostat · navitoclax · neomycin · neratinib · nimotuzumab · niraparib · nivolumab · nutlin-3 · nutlin-3a · obeticholic-acid · octreotide · olaparib · osimertinib · oxaliplatin · paclitaxel · palbociclib · panitumumab · panobinostat · pazopanib · pembrolizumab · pemetrexed · pemigatinib · penpulimab · pertuzumab · pimurutamab · plx-4545 · plx4720 · prednisone · prexasertib · procarbazine · ql1706 · ramucirumab · refametinib · regorafenib · relatlimab · retlirafusp-alfa · ribociclib · rituximab · rmc-6236 · rucaparib · ruxolitinib · sacituzumab-govitecan · saridegib · sbi-115 · selinexor · selpercatinib · selumetinib · serplulimab · shr-1701 · si-b003 · sintilimab · sirolimus · sorafenib · sotorasib · spartalizumab · spautin-1 · sunitinib · surufatinib · tabelecleucel · tagitanlimab · tak-500 · taladegib · talazoparib · tamoxifen · tanespimycin · tazemetostat · telomerase-inhibitor-ix · temozolomide · temsirolimus · tepotinib · thiotepa · tifcemalimab · tirabrutinib · tislelizumab · tivantinib · tofacitinib · tolinapant · topotecan · toripalimab · tqb2618 · tqb2858 · trametinib · trastuzumab · trastuzumab-deruxtecan · tremelimumab · tretinoin · valganciclovir · vancomycin · vandetanib · veliparib · vemurafenib · venetoclax · verteporfin · vincristine · vinorelbine · vk-2019 · vorinostat · vudalimab · wgc-043 · yl201 · zimberelimab

Methods

16s-rrna-seq · 3prime-rna-seq · 450k-methylation-array · 89zr-trastuzumab-pet · ACCESS129 · Bait_UCSF500 · DFCI-ONCOPANEL-1 · DFCI-ONCOPANEL-3 · IMPACT341 · IMPACT410 · IMPACT468 · IMPACT505 · aav-crispr-somatic-editing · absolute · acmg-variant-classification · affymetrix-250k-snp-array · affymetrix-snp6 · affymetrix-u133-plus2 · agfusion · agilent-244k · alphamissense · aml-264-gene-panel · aml-8-gene-ampliseq-panel · amplicon-sequencing · ampliseq-childhood-cancer-panel · annovar · archer-fusionplex · array-cgh-agilent-1m · ascat · bambam · bayesian-nmf · bile-acid-metabolomics · body-composition-ct · brain-tumor-methylation-classifier · brats-challenge · breakdancer · breakfast · breakpointer · bwa · cadd · calmorph · captk · cbct-delta-radiomics · cellminer · chainfinder · chip-qpcr · chip-seq · chromosome-arm-aneuploidy-score · cibersortx · clanc · clinical-longformer · clinicalbert · clonet · clonogenic-survival-assay · clumps · cms-classifier · cnvkit · co-immunoprecipitation · coca · columbia-comprehensive-cancer-panel · comet-assay · cone-beam-ct-igrt · consensus-hierarchical-clustering · consensus-tme · contest · cosmx-smi · crest · crispr-base-editing · crispr-cas9-arm-deletion · crispri · ct-imaging · ct-radiomics · ctdna-dynamics · ctdx-lung · cwl-docker-workflow · cyberknife · cycif · defuse · delly · depo · dicom-rt-planning · dicom-rt-struct · dna-methylation-array · dranger · droplet-digital-pcr · dynamut · edger · elastic-net · elisa · emsa · endoscopic-fiducial-placement · epic-methylation-array · ericscript · estimate · exact-1 · excavator-cnv · expands · facets · fdg-pet-ct · firefly · fish · fish-1p19q · four-dimensional-ct-simulation · fusionmap · gatk-cocleaning · gatk-somatic-indel-detector · genome-music · genome-wide-association-study · geomx-wta · germline-burden-test · gistic · glistrboost · gnomad-non-cancer-controls · gsea · guardant360 · hm27-methylation-array · hm450-methylation-array · hmmcopy · hr-nhej-gfp-reporter-assay · ichorcna · icluster · icr-signature · igcaller · illumina-goldengate · illumina-microarray · immunoediting-quantification · immunohistochemistry · imrt-reirradiation · indelocator · ingenuity-pathway-analysis · integrative-genomics-viewer · intensity-modulated-radiotherapy · intraductal-aav-delivery · intramuscular-xenograft · invex · isopure · its2-rdna-seq · joint-longitudinal-survival-model · karyotyping · lc-ms-ms-proteomics · linac-sbrt · log-linear-mixed-effects-model · luciferase-reporter-assay · lymphgen · masson-trichrome-staining · mate-pair-seq · math-score · mc3 · mc3-pipeline · meerkat · memo · mendelian-randomization · metabric-targeted-sequencing · microarray-gene-expression · mimsi · mirna-seq · msi-pcr-pentaplex · msisensor · msk-access · msk-fusion · msk-hemepact · msk-impact-panel · mtdna-long-range-pcr · mtlr · multimodal-late-fusion · multiparameter-flow-cytometry · multiplexed-immunofluorescence · multiregion-exome-seq · muse · mutation-validator · mutational-signatures · mutationalpatterns · mutcomfocal · mutect · mutsig · n250-targeted-panel · nanoseq · netmhc4 · netmhcpan · nextgene-aligner · nexus-copy-number · nlp-prissmm · oncocast · oncocast-mpm · oncodriveclust · oncokb · oncokb-annotation · oncoscan-snp-array · oncosign · oncotator · organoid-drug-screening · oxog-filter · panel-of-normals-filter · paradigm · patient-derived-xenograft · pd-l1-ihc-22c3 · pet-ct-imaging · phylogenetic-tree-reconstruction · phylogicndt · pindel · polyacrylamide-hydrogel-stiffness-assay · polygenic-risk-score · polysolver · prada · prostate-organoid-pten-lkb1 · protein-binding-microarray · proton-beam-therapy · pycerr · pyclone · pyradiomics · qmsp · quantitative-imaging-microscopy · quantitative-rt-pcr · radia · radiomic-signature-4-feature · radiomics · radlongformer · random-forest-classifier · random-survival-forest · revel · rna-seq · rnascope-ish · rppa · rrbs · rsem · sanger-sequencing · sarcoma-methylation-classifier · scrna-seq · sequenom-genotyping · sequenza · shatterseek · shrna-rnai-screen · sigma-mutational-signatures · sigprofiler · single-cell-dna-seq · single-cell-genotyping · sleeping-beauty-transposon-screen · smart-seq2 · snapshot-pcr · snps-seq · snrna-seq · somatic-signatures · somatic-sniper · spatial-transcriptomics · splice-ai · star · star-aligner · star-fusion · stardist-nuclei · stereotactic-body-radiation-therapy · strelka · subcutaneous-xenograft · synergyfinder-hsa · targeted-deep-amplicon-seq · targeted-dna-seq · tcr-seq · teratoma-assay · titan-cna · tophat-cufflinks · tophat-fusion · transwell-invasion-assay · trusight-oncology-500 · trusight-pan-cancer-rna-panel · tsne · tukey-outlier-detection · tumor-map · tumorsphere-formation-assay · variantdx · varscan · vcf2maf · vep · viper · visium-hd · vogelstein-ratiometric · volumetric-mri-segmentation · whole-exome-seq · whole-genome-bisulfite-seq · whole-genome-seq · xenium · xgboost · yeast-complementation-assay

Themes

open_questions · radiation-biology

How to read a page

Paper pages follow a fixed template — start with TL;DR, then Cohort & data, Key findings, Clinical implications, and Limitations & open questions. Every section cites back to the source PMID.
Entity pages (genes, cancer types, drugs, etc.) aggregate everything the corpus says about that entity, with every claim tied to the paper it came from. If an entity has only one citing paper, the page will be short — that is expected.
Unverified flags. When an entity couldn’t be validated against OncoTree, HUGO, or cBioPortal’s study/panel catalogs, its page carries an unverified: true flag. Treat those pages as provisional.

About this site

This site is built from a Markdown vault that lives in a git repository. The content is maintained by a small set of sub-agents (paper compiler, entity writer, crosslinker, linter) that read raw paper text and write into the wiki. The rendering, search, and navigation you see here are from Quarto. For the full pipeline and engineering details, see the project repository.