Papers
| Title | Year | Journal | Cancer types | Genes |
|---|---|---|---|---|
| Radiation Oncology-Biology Integration Network (ROBIN): Bridging the gap between biological research and clinical practice | 2026 | Clin Cancer Res | PRAD, READ, BLCA, HNSC, CESC, PAAD, DMG, NBL | MYC, TP53, MDM2, CD274, PDCD1 |
| Somatic mutations in STAG2 are associated with separated megakaryocyte nuclear lobes in myelodysplastic syndromes | 2025 | Blood Advances | MDS | STAG2, ASXL1, SF3B1, SRSF2, RUNX1, SETBP1, TP53, NRAS |
| ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors | 2025 | Research | SCLC | ARID1A, MYC, PARP1, RAD51, CHEK1, ARID1B, BRD4, AKT1, PIK3CA |
| AI-driven multimodal algorithm predicts immunotherapy and targeted therapy outcomes in clear cell renal cell carcinoma | 2025 | Cell Reports Medicine | CCRCC | BAP1, SETD2, MTOR, PBRM1, KDM5C, NF2, CD274, PDCD1 |
| Distinct and convergent effects of SF3B1 mutations in human breast cancer | 2025 | Proceedings of the National Academy of Sciences | BRCA | SF3B1, TP53, PIK3CA, MKI67, MYC, DLST, GCC2, TMEM14C, ENOSF1 |
| 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 | 2025 | Journal of Extracellular Vesicles | NBL | GJC1, MYCN |
| Hepatitis B virus integration and hepatocarcinogenesis | 2025 | Liver Research | HCC | TERT, KMT2D, CCNE1, MYC, TP53, RB1, CTNNB1, GSK3B, MTOR, DNMT3A, CASP1 |
| HIFα isoform specific activities drive cell-type specificity of VHL-associated oncogenesis | 2025 | Nature Communications | CCRCC | VHL, HIF1A, EPAS1, PAX8, HNF4A, HNF1B, FOXA2, MKI67, CCND1, TP53, RB1 |
| Genomic and transcriptomic landscapes of metastatic neuroendocrine neoplasms from distinct primary sites and their clinical implications | 2025 | Scientific Reports | PANET, PANEC, LNET, LUNE, MTNN, SBWDNET, HGONEC, MNET, NETNOS | MEN1, DAXX, ATRX, RB1, TP53, RET, MYC, MYCN, KRAS, SMAD4, CDK8, FLT1, NTHL1, MSH6, MLH1, MSH3, CDKN2A, CDKN2B, TSC1, TMEM71, BRIP1, TOP2A, MGMT, CD274, PDCD1, DLL3, SSTR2, RICTOR, FGFR3, PIK3R2, MET, PDGFRA, PDGFRB |
| Molecular Profiling of Sinonasal Adenoid Cystic Carcinoma: Canonical and Noncanonical Gene Fusions and Mutation | 2025 | American Journal of Surgical Pathology | ACYC | MYB, MYBL1, NFIB, EWSR1, ACTB, ACTN4, ESRRG, DNM3, BCOR, NOTCH1, NOTCH2, NOTCH3, EP300, SMARCA4, RUNX1, KDM6A, SPEN, RIT1, MGA, RB1, PHF6, PTEN, CREBBP, DDX41, CHD2, ROS1, TAF1, CCND1, NF1, PALB2, ACVR1B, ARID1A, ARID1B, PPM1D, LZTR1, GEN1, PDGFRA, PBRM1, BRAF, FAT1, RET |
| Exploring the Diagnostic and Predictive Value of Oral Microbiome in Esophageal Cancer: A Systematic Review and Meta-Analysis | 2025 | International Journal of Molecular Sciences | ESCC, ESCA | TP53, RB1, CDKN2A, PIK3CA, NOTCH1, NFE2L2 |
| Divergent Morphologies and Common Signaling Features of Active and Inactive Oncogenic RHOA Mutants in Yeast | 2025 | Cells | AITL, ATLL, DSTAD, BL, PTCL | RHOA |
| Familial Non-Hereditary Gastric Cancer: Diagnosis, Management, Molecular Characteristics and Future Perspective | 2025 | Cancers | STAD | CDH1, CTNNA1, CTNND1, TP53, RHOA, MLH1, MSH2, MSH6, PMS2, EPCAM, APC, BMPR1A, SMAD4, MUTYH, STK11, BRCA1, BRCA2, PALB2, ATM, BRIP1, DOT1L, INSR, FBXO24, FHIT, PSCA, PLCE1, PRKAA1, MUC1, XRCC1, GSTM1, IL1B, TNF, IL10, RASSF1, LOX, KDM4B, PTGS2, CDKN1A, YAP1 |
| Novel Therapeutic Development for Nasopharyngeal Carcinoma | 2025 | Current Oncology | NPC, HNSC | EGFR, ERBB3, MET, AXL, KDR, VEGFA, PDGFRB, KIT, RET, FLT3, TEK, CDK4, CDK6, PARP1, XIAP, BIRC2, BIRC3, CD70, CD276, EPCAM, MUC1, PDCD1, CD274, CTLA4, LAG3, HAVCR2, BTLA, TNFRSF4, TNFRSF9, ADORA2A, IKZF2, FOXP3, PTCH1, RASSF1, BBC3, BCL2L11 |
| 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 | 2025 | Biology Direct | GBC | SEMA7A, ITGB1, PLXNC1, EP300, AKT1, YAP1, WWTR1, TEAD1, ACTA2, CCN2, COL1A1, COL1A2, COL4A1, COL4A2, COL8A1, FN1, MFAP5, PDGFRA, TGFBR1, TGFBR2, CDH1, VIM, EPCAM, CD44, ALDH1A1, SNAI1, ZEB1, EGFR, ERBB2, ERBB3, ERBB4 |
| EWS::FLI1 expression in human embryonic mesenchymal stem cells leads to transcriptional reprograming, defective DNA damage repair and Ewing sarcoma | 2025 | Nature Communications | ES | EWSR1, FLI1, BRCA1, ATM, ATR, PRKDC, PRKCB, CD99, EZH2, IGF1, NGFR, PADI2, DKK2, NR0B1, UCP2, BCL11B, ITM2A, RNF2, TP53, CDKN1A, RB1 |
| Chronic Liver Disease Associated Cholangiocarcinoma: Genomic Insights and Precision Therapeutic Strategies | 2025 | Cancers | IHCH, EHCH, CHOL, HCC | KRAS, TP53, ARID1A, CDKN2A, CDKN2B, EGFR, PIK3CA, BRAF, BRCA1, BRCA2, SMAD4, IDH1, IDH2, FGFR2, FGFR1, ERBB2, BAP1, PTEN, TERT, MET, ALKBH5, FAT2, NTRK1, NTRK2, NTRK3, DDX1, ALDH1A1, TGFBR2, FBXW7, MYC |
| Targeting the gut-liver axis in cholangiocarcinoma: mechanisms, therapeutic advances, and future directions | 2025 | Frontiers in Oncology | CHOL, IHCH, EHCH, PHCH, HCC, GBC | NR1H4, GPBAR1, S1PR2, IDH1, IDH2, FGFR2, EGFR, KRAS, TP53, METTL3, STAT3, BCL2L1, PTGS2, CXCL16, CXCL1, ABCB11, HNF4A, CYP7A1, FGF19, SLCO1B3, CEACAM1, TGFB1, PDCD1 |
| SF3B1 mutation accelerates the development of CLL via activation of the mTOR pathway | 2025 | JCI Insight | CLLSLL | SF3B1, NFATC1, MYC, MTOR, DLEU1, DLEU2, MIR15A, ATM, ZAP70, CD5, BRD9, PPP2R5A, AKT1 |
| Rat somatic genome editing enables ER+ breast cancer modeling | 2025 | bioRxiv | BRCA, IDC, DCIS, MBC | TP53, PIK3CA, NF1, KRAS, HRAS, ESR1, PGR |
| Mutation burden of narrowband ultraviolet B phototherapy (NB-UVB) in human skin: relevance to NB-UVB lifetime exposures and skin cancer surveillance | 2025 | British Journal of Dermatology | CSCC, BCC, SKIN | |
| A profile of lung cancer in the young population with a highlight on the Indian perspective | 2025 | Frontiers in Oncology | NSCLC, LUAD | EGFR, ALK, ROS1, KRAS, BRAF, MET, ERBB2, RET, NTRK1, NTRK2, NTRK3, TP53, BRCA1, BRCA2, ATM, CHEK2, BAP1, FANCA, FANCI, FANCM, LZTR1, XRCC3, EML4, ERC1 |
| Targeting the ATM-TRMT10A-BRCA1 axis confers synthetic lethality to PARP inhibition in metastatic castration-resistant prostate cancer | 2025 | Science Advances | PRAD | TRMT10A, USP10, BRCA1, BRCA2, ATM, ATR, RAD51, PALB2, PARP1, PARP2 |
| EWSR1::BEND2 fusion sarcoma of the urinary bladder – a case report and review of literature | 2025 | Diagnostic Pathology | BLCA, ES, ASTB | EWSR1, BEND2, PTEN, MN1, FLI1, NFATC2, PATZ1, POU2AF3, CIC, BCOR, FUS |
| Genomic landscape of endometrial polyps | 2025 | Genome Medicine | UCEC, ULM | HMGA1, HMGA2, UBE2A, PLAG1, KRAS, PIK3CA, PIK3R1, PTEN, ERBB2, PPP2R1A, FBXW7, ARHGAP35, PIEZO2, LRMDA, RAD51B, TRAF3IP2, ZMAT3, C19ORF38, MED12, JAZF1, MATR3 |
| Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus | 2025 | Nature Communications | PRAD | NOL10, USF1, TBX3, TFAP4, TMPRSS2, ERG, HNF1B, APOBEC3A, APOBEC3B, STK11 |
| Germline variants observed in pediatric cancer patients related to hereditary breast and ovarian cancer in adults | 2025 | International Journal of Cancer | BLLNOS, TLL, AML, MBL, LCH, RMS, OS, LIHB | TP53, CHEK2, ATM, NF1, NBN, BRIP1, BRCA1, BRCA2, BLM, FANCC, FANCM, MSH2, STK11 |
| CHEK1 is a synthetic lethal interactor of FBXO7 in colonic epithelial cells | 2025 | Molecular Therapy: Oncology | COADREAD | FBXO7, CHEK1, CHEK2, SOD1, BRCA1, BRCA2, PARP1, ATM, CDK2, SKP1, CUL1, RBX1, APC, KRAS, TP53 |
| A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing | 2025 | Nature Communications | COAD, UCEC, EGC, BLCA, PRAD, CUP, SBC | MLH1, MSH2, MSH6, PMS2, POLE |
| Clinicogenomic landscape of pancreatic adenocarcinoma identifies KRAS mutant dosage as prognostic of overall survival | 2025 | Nature Medicine | PAAD | KRAS, BRAF, NRAS, NF1, NTRK1, NTRK3, FGFR2, ERBB2, MAP2K1, ROS1, MET, RAF1, TP53, CDKN2A, CDKN2B, SMAD4, BRCA1, BRCA2, ATM, PALB2, CHEK2, MLH1, MSH2, MSH6, PMS2, GNAS, PIK3CA, SMARCB1, FOXP1, CREBBP, ARID1A, RNF43, AKT2, RB1, BAP1, MYC |
| Somatic mutations distinguish melanocyte subpopulations in human skin | 2025 | bioRxiv | SKIN, MEL | HMOX1, ABCC2, MC1R, HERC2, LIPA, HLA-DPA1, VCAN, FBN1, PALLD, ITM2A, TAGLN, MYL9, MYLK, SGCE, HACD1, SEMA3C, TCF4, DAAM2, RGMB, NTNG1, PMEL, TYRP1, MLANA, MITF, AXL, KRT14, KRT17, KRT5, LUM, COL1A1, S100A4 |
| Circulating Tumor DNA and Response to Cisplatin-based Chemotherapy in Patients with Metastatic Urothelial Carcinoma Enrolled in CALGB 90601 (Alliance) | 2025 | European Urology Open Science | BLCA | TERT, PIK3CA, ERBB2, ERCC2, FGFR3, ATM, BRCA1, BRCA2, KDM6A, RB1, TSC1, BRAF, KRAS, MDM2 |
| A platform-independent AI tumor lineage and site (ATLAS) classifier | 2024 | Communications Biology | CUP, NSCLC, LUAD, LUSC, SCLC, PRAD, PRNE, BRCA, MEL, PLMESO | |
| Clinical and molecular characteristics of early-onset vs average-onset esophagogastric cancer | 2024 | JNCI: Journal of the National Cancer Institute | EGC, STAD, ESCA, GEJ | ERBB2, CDKN2A, KRAS, CCNE1, PIK3CA, CDH1, ARID1A |
| Tumor Volume Growth Rates and Doubling Times during Active Surveillance of IDH-mutant Low-Grade Glioma | 2024 | Clinical Cancer Research | DIFG, ASTR, ODG | IDH1, IDH2, CDKN2A, CDKN2B, TERT, CIC, FUBP1, TP53, ATRX, MYCN, CDK4, PDGFRA, PIK3R1, PIK3CA |
| The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen | 2024 | Cancer Research | DIFG, GB, ASTR, ODG | IDH1, IDH2, HOXD13, CDKN2A, MGMT, MYB, RSPO4, CENPF, PCNA, HOXA7, MSH6, NEUROD1 |
| High-risk and silent clonal hematopoietic genotypes in patients with nonhematologic cancer | 2024 | Blood Advances | JAK2, RUNX1, XPO1, DNMT3A, TET2, ASXL1, TP53 | |
| RADCURE: An open-source head and neck cancer CT dataset for clinical radiation therapy insights | 2024 | Medical Physics | HNSC | |
| The genomic and evolutionary landscapes of anaplastic thyroid carcinoma | 2024 | Cell Reports | THAP, THPA | TP53, BRAF, NRAS, PIK3CA, USH2A, CDKN2A, BRCA1, BRCA2, RB1, ATM, ATR, NF1, EIF1AX, TERT, TET1, MET, NOTCH1, FAT1, SPEN, LRP1, CDK7, FLT3, FGF9, HMCN1, HSPG2, RECQL4, FANCF, VGLL3 |
| Developing Novel Genomic Risk Stratification Models in Soft Tissue and Uterine Leiomyosarcoma | 2024 | Clinical Cancer Research | LMS, ULMS | TP53, RB1, ATRX, PTEN, CDKN2A, MED12 |
| Integrative Molecular Analyses of the MD Anderson Prostate Cancer Patient-derived Xenograft (MDA PCa PDX) Series | 2024 | Clinical Cancer Research | PRAD, PRNE | AR, PTEN, RB1, TP53, CDK12, TMPRSS2, ERG, ETV4, ETV1, FGFR1, SPOP, FOXA1, NRAS, SPEN, RNF43, KMT2D, AURKA, MYCN, ATM, BRCA1, BRCA2, CHEK2, KDM6A |
| 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 | 2024 | Haematologica | DLBCLNOS | BCL2, BCL6, MYC, TP53, MYD88, CD79B |
| Diffuse pleural mesotheliomas with genomic near-haploidization: a newly recognized subset with distinct clinical, histologic, and molecular features | 2024 | Clinical Cancer Research | PLMESO | SETDB1, TP53, NF2, BAP1, CDKN2A, CDKN2B, MLH1 |
| Nivolumab for mismatch-repair-deficient or hypermutated gynecologic cancers: a phase 2 trial with biomarker analyses | 2024 | Nature Medicine | UCEC, OVT | MLH1, MSH2, MSH6, PMS2, PTEN, PIK3CA, ARID1A, JAK1, CTNNB1, MEGF8, SETD1B, PTCH1, KRAS, TP53, B2M, POLE, PBRM1, ARID2 |
| Genome-wide loss of heterozygosity predicts aggressive, treatment-refractory behavior in pituitary neuroendocrine tumors | 2024 | Acta Neuropathologica | PTAD | TP53, ATRX, DAXX, SF3B1, USP8, MSH2, MSH6, MLH1, GNAS, TSC2, TERT, CCND3, CDKN2A, CDKN2B |
| Intensity-Modulated Reirradiation Therapy With Nivolumab in Recurrent or Second Primary Head and Neck Squamous Cell Carcinoma: A Nonrandomized Controlled Trial | 2024 | JAMA Oncology | HNSC | CD274, PDCD1, MKI67, CD4, CD8A, FOXP3 |
| A Novel Approach to Quantify Heterogeneity of Intrahepatic Cholangiocarcinoma: the Hidden-Genome Classifier | 2024 | Clinical Cancer Research | IHCH, EHCH, GBC, HCC | KRAS, SMAD4, CDKN2A, TERT, FGFR2, IDH1 |
| Molecular effects of indoor tanning | 2024 | bioRxiv | MEL | NF1, BRAF, CDKN2A, RAC1, PPP6C, ARID2, RB1 |
| Tumor-agnostic genomic and clinical analysis of BRAF fusions identify actionable targets | 2024 | Clinical Cancer Research | ASTR, LUAD, MEL, COAD, PAAD, PRAD, THPA, BLCA, ECD | BRAF, EGFR, TP53, CDKN2A, CDKN2B, TERT, RNF43, KMT2D, MSH3, ARID1A, KIAA1549, SND1, AGK, TRIM24, KRAS, HRAS, NRAS, RAF1, MAPK1, NTRK1, FGFR3, ALK, INPPL1 |
| Microsatellite Instability, Tumor Mutational Burden, and Response to Immune Checkpoint Blockade in Patients with Prostate Cancer | 2024 | Clinical Cancer Research | PRAD | MSH2, MSH6, MLH1, PMS2, POLE, JAK1, BRCA2, BRCA1, ERG, TMPRSS2, ASXL1, MSH3 |
| A Phase II study assessing Long-Term Response to Ibrutinib Monotherapy in recurrent or refractory CNS Lymphoma | 2024 | Clinical Cancer Research | PCNSL, DLBCLNOS | TBL1XR1, MYD88, CD79B, CARD11 |
| Genetic evolution of keratinocytes to cutaneous squamous cell carcinoma | 2024 | bioRxiv | CSCC | TP53, NOTCH1, NOTCH2, CDKN2A, TERT, ARID2, CBL, FAT1 |
| DNA liquid biopsy-based prediction of cancer-associated venous thromboembolism | 2024 | Nature Medicine | NSCLC, BRCA, PAAD, MEL, PRAD, BLCA | KRAS, STK11, KEAP1, TP53, EGFR, PIK3CA, CDKN2A, CTNNB1, ERBB2, ARID1A, ATM, RB1, NF1, PTEN, BRAF, SMAD4, SF3B1, KDM6A |
| Distinct clinical outcomes and biological features of specific KRAS mutants in human pancreatic cancer | 2024 | Cancer Cell | PAAD | KRAS, TP53, CDKN2A, SMAD4, BRAF, TGFBR2, MYC |
| Real-world experience with circulating tumor DNA in cerebrospinal fluid from patients with central nervous system tumors | 2024 | Acta Neuropathologica Communications | NSCLC, LUAD, BRCA, DIFG, DMG, MEL | TP53, EGFR, KRAS, BRAF, PIK3CA, MET, ERBB2, ALK, RET, ROS1, STK11, KEAP1, IDH1, EML4, H3-3A, KIAA1549 |
| The landscape of drug sensitivity and resistance in sarcoma | 2024 | Cell Stem Cell | OS, CHDM, CHS, ES, SYNS, MPNST, RMS, LMS, MFH, EPIS, DSRCT, PECOMA, MFS, WDLS, DDCHS, ARMS, ERMS, SCSRMS, IFS, SARCNOS, FIBS, LIPO | PIK3CA, MDM2, NTRK1, NTRK2, NTRK3, ETV6, FGFR1, ARID2, CRTC1, MAP3K1, EGFR, ERBB2, CDK4 |
| Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma | 2024 | bioRxiv | HGSOC | TP53, BRCA1, BRCA2, CCNE1, HLA-A, HLA-E, STAT1, CGAS, STING1, TBK1, ISG15, IFITM1, IRF7, IRF9, TAP1, MX1, MCL1, IFNE, MYC, BANF1, KLRK1, PDCD1, LAG3, HAVCR2, CTLA4, FOXP3, CD4, CD8A, CXCL9 |
| Automated real-world data integration improves cancer outcome prediction | 2024 | Nature | NSCLC, LUAD, BRCA, COAD, READ, PRAD, PAAD, PAAC | SETD2, TP53, PTEN, RB1, EGFR, KRAS, BRAF, ARID1A, MDM2, STK11, SMARCA4, KEAP1, CDKN2A, BRCA2, MET, ESR1, CCND1, NF1, AR, CHEK2, PPM1D, CDK12, FGF19, MYC, CIC, NKX3-1, NKX2-1, FOXA1, FGFR1, ERBB2, CCNE1, CD274 |
| Molecular Characterization of Acquired Resistance to KRASG12C-EGFR Inhibition in Colorectal Cancer | 2023 | Cancer Discovery | COADREAD | KRAS, NRAS, BRAF, EGFR, MET, RET, MAP2K1, MYC, APC, TP53, PIK3CA, ERBB2, ERBB3, ERBB4, RAF1, NF1, FGFR2, PTEN, RB1 |
| Multiomics in primary and metastatic breast tumors from the AURORA US network finds microenvironment and epigenetic drivers of metastasis | 2023 | Nature Cancer | BRCA | TP53, ESR1, ERBB2, PIK3CA, PTEN, RB1, KMT2C, NF1, GATA3, MYC, MDM4, FOXA1, HLA-A, B2M, JAM3, BRCA2 |
| Expanded genetic testing of GIST patients identifies high proportion of non-syndromic patients with germline alterations | 2023 | npj Precision Oncology | GIST | KIT, PDGFRA, SDHA, SDHB, SDHC, NF1, BRAF, BRCA1, BRCA2, TP53, MLH1 |
| Molecular Evolution of Classic Hodgkin Lymphoma Revealed Through Whole-Genome Sequencing of Hodgkin and Reed Sternberg Cells | 2023 | Blood Cancer Discovery | CHL | SOCS1, TNFAIP3, B2M, ITPKB, GNA13, STAT6, BCL7A, NFKBIE, PTPN1, TP53, XPO1, TMSB4X, IL4R |
| Overcoming barriers to tumor genomic profiling through direct-to-patient outreach | 2023 | Clinical Cancer Research | LCH, ECD, OGCT, MGCT, ACYC | BRAF, MAP2K1, KRAS, NRAS, CSF1R, ALK, NTRK1, PIK3CA, PTPN11, KIT, TP53, ERBB2 |
| TP53 mutations identify high-risk events for peripheral T-cell lymphoma treated with CHOP-based chemotherapy | 2023 | Blood Advances | PTCL, AITL, ALCL, ALCLALKP, ALCLALKN, MEITL, EATL | TP53, CDKN2A, TET2, RHOA, DNMT3A, IDH2, STAT3, FAT1, TP63 |
| Genomic Mapping of Metastatic Organotropism in Lung Adenocarcinoma | 2023 | Cancer Cell | LUAD | TP53, SMARCA4, CDKN2A, KEAP1, STK11, EGFR, KRAS, NF1, MDM2, PIK3CA, ERBB2, NKX2-1, FOXA1, MET, ARID1A, MGA |
| An integrated tumor, immune and microbiome atlas of colon cancer | 2023 | Nature Medicine | COAD | IFNG, TBX21, CD8A, CD8B, IL12B, STAT1, IRF1, CCL5, CXCL9, CXCL10, GNLY, PRF1, GZMA, GZMB, GZMH, CD274, CTLA4, FOXP3, IDO1, PDCD1 |
| Extremity Rhabdomyosarcoma: An Integrated Clinicopathologic and Genomic Study to Improve Risk Stratification | 2023 | JCO Precision Oncology | RMS, ARMS, ERMS, SCRMS | FOXO1, PAX3, PAX7, MYOD1, MED12, CDK4, CDKN2A |
| Distinct genomic landscapes in radiation-associated angiosarcoma compared with other radiation-associated sarcoma histologies | 2023 | J Pathol | ANGS, MPNST, MFH, OS | MYC, FLT4, CRKL, HRAS, KMT2D, TP53, KDR, ATM, ATRX, CDKN2A, CDKN2B, NF1, SUZ12, TEK, PTPRD, RB1, PTEN, FGFR1, PTPRT, NOTCH3, KIT, PDGFRA, PTPRB, PLCG1 |
| Multi-institutional Prognostic Modeling in Head and Neck Cancer: Evaluating Impact and Generalizability of Deep Learning Approaches | 2023 | Cancer Research Communications | HNSC | |
| Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer | 2023 | Clinical Cancer Research | EGC, STAD, ESCA, GEJ | ERBB2, KRAS, MYC, CDKN2A, CDKN2B, PIK3CA, PIK3CD, MET, EGFR, TP53, FGFR3, TACC3, CCND1, MT1H, MT1E, MT2A, MSMB |
| Novel Genomic Risk Stratification Model for Primary Gastrointestinal Stromal Tumors (GIST) in the Adjuvant Therapy Era | 2023 | Clinical Cancer Research | GIST | KIT, PDGFRA, SDHB, SDHA, TP53, CDKN2A, RB1, MAX, MGA, MYC |
| Genomic analysis and clinical correlations of non-small cell lung cancer brain metastasis | 2023 | Nature Communications | LUAD, LUSC, NSCLC | CDKN2A, CDKN2B, EGFR, MYC, TP53, KRAS, STK11, SMARCA4, RB1, ARID1A, FOXA1, NKX2-1, NF1, HLA-B, NKX3-1 |
| Assessing the Genomic Landscape of Cervical Cancers: Clinical Opportunities and Therapeutic Targets | 2023 | Clinical Cancer Research | CESC | PIK3CA, ERBB2, KMT2C, KMT2D, KRAS, TP53, PTEN, STK11, ARID1A, FBXW7, TERT, MYC, HRAS, NRAS, BRCA1, BRCA2, SMAD4, CDKN2A, ERBB3, RNF43 |
| Molecular characterization of endometrial carcinomas in Black and White patients reveals disparate drivers with therapeutic implications | 2023 | Cancer Discovery | UCEC, UCS, USC | TP53, CCNE1, ERBB2, PTEN, PIK3CA, PIK3R1, KRAS, ARID1A, CTNNB1, PPP2R1A, AKT2, POLE, POLD1, FBXW7, KMT2B, NF1, BRCA1, MED12 |
| Clinical and Genomic Landscape of FGFR3-Altered Urothelial Carcinoma and Treatment Outcomes with Erdafitinib: A Real-World Experience | 2023 | Clinical Cancer Research | BLCA, UTUC | FGFR3, FGFR2, TACC3, TP53, AKT1, PIK3CA, TSC1, ERBB2, CDKN2A, CDKN1A, CDKN2B, KDM6A, RB1 |
| Sequential genomic analysis using a multisample/multiplatform approach to better define rhabdomyosarcoma progression and relapse | 2023 | npj Precision Oncology | RMS, ARMS, ERMS | PAX3, PAX7, FOXO1, MYCN, CDKN2A, CDKN2B, CDK4, TP53, BCOR, PIK3CA, HRAS, NRAS, KRAS, MDM2, SMARCA2, AKT1, GLI1, IGF2, MED12, NCOR2, BAP1, NF1, FGFR1, RB1, MYOD1, FBXW7, DMD |
| Targeted Molecular Profiling of Circulating Cell-Free DNA in Patients With Advanced Hepatocellular Carcinoma | 2023 | JCO Precision Oncology | HCC | TERT, TP53, CTNNB1, ARID1A, TSC2, TSC1, PIK3CA, BRCA1, BRCA2, APC, CDKN2A, RB1, NF1, KRAS |
| Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer | 2022 | Nature Cancer | HGSOC | BRCA1, BRCA2, CDK12, CCNE1 |
| Molecular map of chronic lymphocytic leukemia and its impact on outcome | 2022 | Nature Genetics | CLLSLL, MBL | SF3B1, NOTCH1, ATM, TP53, BRAF, MYD88, NFKB1, RRM1, MAP2K2, DIS3, DICER1, INO80, RFX7, ARID1A, KMT2C, KMT2D, BCL2, TRAF3, ZFP36L1, FUBP1, MSL3, USP8, ZC3H18, NFKBIE, ASXL1, MYC |
| Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer | 2022 | Nature Cancer | NSCLC, LUAD, LUSC | EGFR, STK11, ERBB2, ARID1A, ALK, ROS1, RET, MET, BRAF |
| Comprehensive Molecular Characterization of Gallbladder Carcinoma and Potential Targets for Intervention | 2022 | Clinical Cancer Research | GBC | TP53, CDKN2A, CDKN2B, ERBB2, ERBB3, KRAS, SMAD4, ARID1A, ARID2, PIK3CA, ELF3, STK11, CTNNB1, KMT2C, TERT, RB1, MDM2, CCNE1, MYC, CDK4, CDK12, AKT2, AXIN1, RET, SMARCA4, FGFR3, NTRK1, BRCA1, BRCA2, ATM, TSC1, TSC2, PALB2, BRIP1, MET, RAD51D, AKT1, BRAF, EGFR, ERCC2, MAP2K1, NRAS, ROS1, NOTCH1, IDH1, BAP1 |
| Collaborative study from the Bladder Cancer Advocacy Network for the genomic analysis of metastatic urothelial cancer | 2022 | Nature Communications | BLCA | TP53, RB1, KMT2D, ARID1A, KDM6A, KMT2C, EP300, KMT2A, CREBBP, SMARCA4, BRCA2, PRKDC, ATM, ERCC2, FANCA, FANCC, FGFR3, PIK3CA, TACC3, CCND1, MDM2, ERBB2, CCNE1, EGFR, POLE, MUTYH |
| Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer | 2022 | Nature Medicine | NSCLC, LUAD, LUSC | RICTOR, PIK3CA, EGFR, KRAS, TP53 |
| Molecular Classification of Appendiceal Adenocarcinoma | 2022 | Journal of Clinical Oncology | APAD | KRAS, NRAS, GNAS, TP53 |
| Ovarian cancer mutational processes drive site-specific immune evasion | 2022 | Nature | HGSOC | BRCA1, BRCA2, TP53, CCNE1, CDK12, MYC, CD274, PDCD1, HLA-A, HLA-B, B2M |
| Genomic heterogeneity as a barrier to precision oncology in urothelial cancer | 2022 | Cell Reports | BLCA, UTUC | FGFR3, ARID1A, TP53, RB1, ERBB2, PIK3CA, TSC1, KDM6A, CREBBP, CDKN1A, TERT |
| Whole-genome characterization of myoepithelial carcinomas of the soft tissue | 2022 | Cold Spring Harbor Molecular Case Studies | MYEC | SMARCB1, EWSR1, NF1, ELK4, ASCC2, GGNBP2, KLF15, CREB1, POLE, SMARCA2 |
| A Clinically Applicable Integrative Molecular Classification of Meningiomas | 2021 | Nature | MNG | NF2, TRAF7, AKT1, KLF4, SMO, POLR2A, KDM6A, CHD2, PTEN, CREBBP, FBXW7, RB1, SMARCB1, DMD, FOXM1, MYC, S100B, SCGN, ACADL, MCM2 |
| Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors | 2021 | Nature Communications | NBL | NTRK1, NTRK2, MYCN, ALK, BRCA1, BRCA2, PHOX2A, PHOX2B, TH, DBH, CHGA, CHGB, PNMT, PRPH, ISL1, SOX6, SOX10, FOXD3, S100B, ERBB3, RTTN, BCL11A, CLDN11, ASXL3, POU6F2, TP63, PROM1, LGR5, PDGFRA, PDGFRB, PRRX1, YAP1, CHRNA7, DOCK7, MKI67, USH2A |
| Molecular therapies and precision medicine for hepatocellular carcinoma | 2018 | Nature Reviews Clinical Oncology | HCC | TERT, TP53, CTNNB1, AXIN1, ARID1A, ARID1B, ARID2, ATM, RB1, CDKN2A, APC, KMT2A, KMT2B, KMT2C, BAP1, RPS6KA3, PIK3CA, KRAS, NRAS, PDGFRA, EGFR, PTEN, NFE2L2, KEAP1, ALB, APOB, IL6ST, JAK1, ACVR2A, IGF2R, MYC, CCND1, VEGFA, FGF19, FGFR4, MET, HGF, AXL, EPCAM, IGF2, PTK2, CD274, PDCD1, CTLA4, RAF1, BRAF, KIT |
| Genetic predictors of response to systemic therapy in esophagogastric cancer | 2018 | Cancer Discovery | EGC, ESCA, STAD, GEJ, DSTAD | ERBB2, TP53, ARID1A, CDKN2A, KRAS, EGFR, ERBB3, PIK3CA, FGFR2, MET, CDH1, B2M, BRCA1, BRCA2, KMT2C, GRIN2A, PTPRD, CTNNB1, CDK4, FGFR1 |
| Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma | 2018 | Science | CCRCC | PBRM1, SMARCA4, BRD7, ARID2, VHL, B2M |
| Clinical sequencing defines the genomic landscape of metastatic colorectal cancer | 2018 | Cancer Cell | COADREAD, COAD, READ | APC, TP53, KRAS, PIK3CA, SMAD4, CTNNB1, RNF43, BRAF, NRAS, PTEN, AKT1, SMAD2, ERBB2, EGFR, POLE, MSH6, BRCA1, BRCA2, NTRK1, NTRK3, RET, MLH1, MSH2, PMS2, FBXW7, PTPRS, PIK3CG, FLT4, MAP2K4, IKZF1, JUN, TBX3, FOXP1, INHBA, CDKN1B, AGAP3, CUL1, LMNA, TPM3, ETV6, NCOA4, DNMT3B, SRC |
| 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 | 2018 | Journal of Clinical Oncology | NSCLC, LUAD, LUSC | EGFR, STK11, KRAS, TP53, B2M, JAK1, JAK2, MDM2, MDM4, ALK, BRAF, ROS1, RET, MET, ERBB2, HLA-A, POLE, JAK3, CD274, PTEN, ATR |
| HER kinase inhibition in patients with HER2- and HER3-mutant cancers | 2018 | Nature | BRCA, NSCLC, LUAD, CESC, CHOL, BLCA, COAD, SACA | ERBB2, ERBB3, TP53, EGFR, PIK3CA, GRB7, BRAF, KRAS, ALK, ROS1 |
| Mutational signatures and chromosome alteration profiles of squamous cell carcinomas of the vulva | 2018 | Experimental & Molecular Medicine | VSC | TP53, CDKN2A, HRAS, PIK3CA, BRCA2, FBXW7, FAT1, KRAS, PTEN, PPP2R1A |
| Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines | 2018 | Cell Systems | PAAD, SKCM, LUAD, LUSC, BLCA, BRCA, HNSC, COAD, READ, UCEC, ESCA, CCRCC, AML, THYM, KICH, UVM, GBM | TP53, PTEN, VHL, SETD2, PBRM1, BAP1, MTOR, ELOC, PIK3CA, ATM, ERBB4, SLITRK6, KDM5C, TERT, CIC, CRLF2, FOXP1, SF3B1 |
| The long tail of oncogenic drivers in prostate cancer | 2018 | Nature Genetics | PRAD | AR, SPOP, FOXA1, TP53, PTEN, CUL3, SPEN, SF3B1, U2AF1, PIK3R2, PIK3R1, CTNNB1, APC, KRAS, BRAF, IDH1, ZMYM3, MRE11, PALB2, CDK12, BRCA2, RB1, KMT2C, KMT2D, ARID1A, ARID2, ARID4A, SMARCA1, USP28, USP7, ERG, TMPRSS2 |
| Driver Fusions and Their Implications in the Development and Treatment of Human Cancers | 2018 | Cell Reports | PANCAN, PRAD, THCA, BLCA, CESC, LUSC, LUAD, CHOL, LAML, BRCA, GBM, LIHC, HNSC, UCEC, COAD, ESCA, SARC, LGG, KICH, KIRC, KIRP, MESO, PCPG, TGCT, THYM, UVM, DLBCL, FLC, PAAD, READ, OV, STAD, SKCM, ACC, UCS | TMPRSS2, ERG, FGFR3, TACC3, EML4, ALK, CCDC6, RET, FGFR2, BICC1, EGFR, ERBB2, PPP1R1B, IKZF3, CBFB, MYH11, DNAJB1, PRKACA, NTRK1, NTRK3, BRAF, WNK1, WNK2, ERC1, FGR, WASF2, TRABD, DDR2, MERTK, TMEM87B, ESR1, TP53, BCR, ABL1, PML, RARA, NUP98, NSD1, EWSR1, FLI1, IGH |
| Genomic and Functional Approaches to Understanding Cancer Aneuploidy | 2018 | Cancer Cell | LUSC, GBM, LGG, HNSC, CESC, ESCC, LUAD, BRCA, HCC, COAD, READ, STAD, PAAD, UCEC, UCS, UVM, TGCT, AML, THYM, BLCA | TP53, POLE, IDH1, SOX2, PIK3CA, TERC, TERT, STAC, ROBO1, UBA7, LMCD1, ISG15 |
| Imaging and clinical data archive for head and neck squamous cell carcinoma patients treated with radiotherapy | 2018 | Scientific Data | HNSC | |
| A radiogenomic dataset of non-small cell lung cancer | 2018 | Scientific Data | NSCLC, LUAD, LUSC | EGFR, KRAS, ALK, EML4 |
| The Molecular Landscape of Recurrent and Metastatic Head and Neck Cancers: Insights From a Precision Oncology Sequencing Platform | 2017 | JAMA Oncology | HNSC, ACYC, OPHSC, HNSCUP, CSCC, BCC, NPC, SDCA, ACCC, MASC, MUCC, SACA, HNNE, ONBL, AMBL, CCOC, ES, CESC | TP53, TERT, NOTCH1, PIK3CA, CDKN2A, PTEN, HRAS, RB1, MAPK1, SMARCB1, FGFR3, PIK3R1, MDM2, PDGFRA, KDR, KIT, ERBB2, AR, NF1, ROS1, PTCH1, MLH1, MSH2, MSH6, POLD1, ETV6, NTRK3, EWSR1, FLI1, ATF1, FANCA |
| Altering the Natural History of Oligometastatic Prostate Cancer With Local Therapies: Reality Versus Illusion | 2017 | Journal of Oncology Practice | PRAD, NSCLC | |
| Integrated genomic characterization of oesophageal carcinoma | 2017 | Nature | ESCA, ESCC, STAD, GEJ, HNSC | TP53, NFE2L2, KMT2D, ZNF750, NOTCH1, TGFBR2, CDKN2A, ARID1A, SMAD4, ERBB2, CCND1, SOX2, TP63, VEGFA, GATA4, GATA6, CCNE1, TERT, FGFR1, MDM2, NKX2-1, RB1, VGLL4, ATG7, CDK6, EGFR, PIK3CA, PTEN, PIK3R1, KRAS, IGF1R, JUP, PTCH1, CDH1, CTNNB1, KEAP1, CUL3, YAP1, SMARCA4, PBRM1, KMT2C, KDM6A, BST2, RUNX1, APC, FHIT, WWOX, MYC, MGMT, CHFR, ALDH2, ADH1B |
| Comprehensive molecular characterization of pheochromocytoma and paraganglioma | 2017 | Cancer Cell | PHC, PGNG | HRAS, RET, EPAS1, NF1, CSDE1, MAML3, BRAF, NGFR, VHL, SDHB, SDHD, MAX, EGLN1, TMEM127, IDH1, FGFR1, ATRX, TP53, SETD2, ARNT, UBTF, TCF4, CHGA, PNMT, WNT4, WNT11, WNT5A, NKD1, GLI2, DVL3, GSK3B, CTNNB1, FZD8, PRKAR1A, PRKACA, CYP11B1, CYP21A2, STAR |
| Chemosensitive Relapse in Small Cell Lung Cancer Proceeds through an EZH2-SLFN11 Axis | 2017 | Cancer Cell | SCLC | SLFN11, EZH2, TWIST1, TP53, RB1, RBL2, SOX2, MYC |
| Prospective comprehensive molecular characterization of lung adenocarcinomas for efficient patient matching to approved and emerging therapies | 2017 | Cancer Discovery | LUAD | EGFR, KRAS, ALK, ROS1, RET, MET, BRAF, ERBB2, ERBB3, ERBB4, NF1, NRAS, HRAS, MAP2K1, ARAF, RAF1, PIK3CA, PTEN, TSC1, TSC2, AKT1, MTOR, BRCA1, BRCA2, KIT, CD74, NRG1, FGFR3, TACC3, SND1, TP53, STK11, KEAP1, NFE2L2, KMT2D, KMT2C, SETD2, CREBBP, PDGFRA, MRE11, CDKN2A, ERRFI1, KDM5C, RIT1 |
| Integrated genomic analyses reveal frequent aberrations in acral melanoma | 2017 | Genome Research | ACRM, SKCM | TERT, PAK1, BRAF, NRAS, NF1, KIT, CCND1, CDK4, CDKN2A, GAB2, MDM2, TP53, PTEN, EGFR, KRAS, ERBB3, PREX2, CLPTM1L, ADCY2, PDCD1LG2, NIPBL, FER, PAK2, MAP3K8, DEK, HECTD4, UBE2QL1, TRIO, RAI14, PDZD2, MITF |
| Phylogenetic ctDNA analysis depicts early stage lung cancer evolution | 2017 | Nature | NSCLC, LUAD, LUSC | KRAS, EGFR, TP53, ERBB2, ARID1A |
| Multicenter phase II study of temozolomide and myeloablative chemotherapy with autologous stem cell transplant for newly diagnosed anaplastic oligodendroglioma | 2017 | Neuro-Oncology | ODG3, ODG | IDH1, IDH2, TERT, CIC, FUBP1, NOTCH1, NOTCH2, EGFR, NF1, MDM2, PTEN, CDKN2A, CDKN2B, CDK4, TSC1, PIK3CA, PIK3R1, KRAS, SMARCA4, FBXW7, APC, ARID1A, ATRX, BCOR, CCND1, ETV1, FAT1, GLI1, KDM6A, MSH2, PBRM1, RASA1, SETD2, TP53 |
| Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients | 2017 | Nature Medicine | PRAD, BRCA, LUAD, SCLC, COAD, READ, PAAD, HGSOC, STAD, ESCA, EGC, UCEC, GB, MEL, BLCA, THYC, CHRCC, GIST, ES, FLC | TP53, KRAS, PIK3CA, BRAF, EGFR, TERT, AR, ESR1, VHL, APC, IDH1, ALK, RET, ROS1, MET, TMPRSS2, ERG, EML4, EWSR1, FLI1, DNAJB1, PRKACA, POLE, CDK5RAP2 |
| Somatic mutation profiles of clear cell endometrial tumors revealed by whole exome and targeted gene sequencing | 2017 | Cancer | UCCC, UCEC, USC, UEC | TP53, PIK3CA, PIK3R1, ARID1A, PPP2R1A, SPOP, TAF1, FBXW7, KMT2C, PTEN, KRAS, POLE, MSH6 |
| Next-generation Sequencing of Nonmuscle Invasive Bladder Cancer Reveals Potential Biomarkers and Rational Therapeutic Targets | 2017 | European Urology | BLCA | TERT, FGFR3, KDM6A, PIK3CA, STAG2, ARID1A, TP53, ERBB2, ERCC2, ATM, BRCA1, BRCA2, ERCC4, PALB2, CHEK2, FANCC, MSH6, POLE, MDM2, RB1, CCND1, CDKN1A, CDKN2A, TACC3, TNIP2 |
| Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma | 2017 | Cancer Discovery | CHOL, IHCH, EHCH, PHCH | ERBB2, TP53, ARID1A, BRCA1, BRCA2, CTNNB1, WNT5B, AKT1, BAP1, IDH1, IDH2, FGFR2, FGFR3, TACC3, BICC1, PRKACB, RASA1, STK11, MAP2K4, SF3B1, KRAS, TERT, FBXW7, SMAD4, MYC, MDM2, EGFR, CCND1, CDKN2A, UTY, KDM5D, TTC28, POLE, PDCD1, PDCD1LG2, BTLA, TET1, EZH2 |
| The whole-genome landscape of medulloblastoma subtypes | 2017 | Nature | MBL | KBTBD4, PRDM6, SNCAIP, CTNNB1, PTCH1, DDX3X, KMT2D, SMARCA4, KMT2C, KDM6A, TP53, SUFU, APC, CSNK2B, EPHA7, ARID1A, ARID2, CREBBP, EP300, KAT6B, BRPF1, KANSL1, IDH1, SMO, TERT, MYC, MYCN, GFI1, GFI1B, OTX2, ZMYM3, CTDNEP1, ZIC1, GSE1, TCF4, FBXW7, BCOR, CHD7, CDK6, MED12, STAG2, GLI2, PTEN, PVT1, POLE, MLH1, BRCA2, FLG |
| Integrative Clinical Genomics of Metastatic Cancer | 2017 | Nature | MIXED, PRAD, BRCA, SARCNOS, CUP, ULMS | TP53, CDKN2A, PTEN, RB1, PIK3CA, AR, KRAS, GNAS, NF1, BRCA1, BRCA2, MUTYH, CHEK2, APC, MITF, HOXB13, MLH1, NBN, ALK, BRAF, GREB1, NR4A3, POC5, PRKD1, CITED1, SPAG17, PARS2 |
| Prospective Genomic Profiling of Prostate Cancer Across Disease States Reveals Germline and Somatic Alterations That May Affect Clinical Decision Making | 2017 | JCO Precision Oncology | PRAD | AR, TP53, PTEN, RB1, BRCA2, BRCA1, ATM, CHEK2, FANCA, CDK12, PALB2, RAD50, MSH2, MLH1, MSH6, PMS2, BRIP1, NBN, FH, APC, CTNNB1, RNF43, SPOP, FOXA1, PIK3CA, PIK3R1, AKT1, AKT3, BRAF, HRAS, KRAS, MAP2K1, EP300, KDM5A, KMT2D, ARID5B |
| Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features | 2017 | Scientific Data | GB, DIFG | |
| Genetic and Functional Drivers of Diffuse Large B Cell Lymphoma | 2017 | Cell | DLBCLNOS, BL | MYC, BCL2, BCL6, CARD11, IRF4, SPEN, CDKN2A, TNFAIP3, EZH2, SGK1, GNA13, SOCS1, STAT6, TNFRSF14, ETV6, MYD88, PIM1, TBL1XR1, TP53, KLHL6, KMT2D, RHOA, SF3B1, MTOR, MGA, PTEN, NCOR1, EBF1, IKBKB, ZBTB7A, XPO1, TGFBR2, PTPN6, CD79B, ZFAT, NF1, KLHL14, BTG1, PAX5, CREBBP, NFKBIA, ARID5B, PIK3R1, PIM2, BTK, CHD8, POU2F2, YY1, H1-4, NOTCH2, PIK3CD, JAK2, RB1, CD70 |
| Comprehensive molecular characterization of muscle invasive bladder cancer | 2017 | Cell | BLCA | FGFR3, TACC3, TP53, RB1, ERCC2, PPARG, CDKN2A, CDKN1A, ATM, ERBB2, PIK3CA, KRAS, MDM2, KMT2C, KMT2A, KMT2D, KDM6A, CREBBP, EP300, KANSL1, ARID1A, ASXL1, ASXL2, STAG2, FAT1, CASP8, CDH1, SPTAN1, E2F3, SOX4, POLE, RAD51B, APOBEC3A, APOBEC3B, GATA3, FOXA1, EGFR, CD274, PDCD1, CTLA4, TP63, KLF4, BRD4, EZH2, MYCL, NECTIN4, CCND1, CCNE1, AHR, TERT, YWHAZ, ZNF703, BCL2L1, MALAT1, NEAT1, UCA1, LXN, PARP6, NAPRT, UPK2, UPK1A, KRT20, KRT5, KRT6A, KRT14, CD44 |
| Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab | 2017 | Cell | SKCM | B2M, CDKN2A, JAK1, JAK2, SERPINB3, SERPINB4, NF1, PTEN, PDCD1, CD274, CTLA4, CD80, CD86, CD28, CD247, CD3D, CD3E, CD3G, PTPN6, ICOS, LAG3, TNFRSF9, TNFRSF4, TIGIT, HAVCR2, VSIR, GZMA, PRF1, FGFR3, IL17RE, IL17RC, FOXP3 |
| Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas | 2017 | Cell | SARCNOS, DDLS, LMS, ULMS, USARC, MFS, MPNST, SS | TP53, ATRX, RB1, MDM2, CDK4, CDKN2A, HMGA2, FRS2, NAV3, JUN, DDIT3, PTPRQ, YAP1, CEBPA, NF1, NF2, PRKDC, TERT, TRIO, FGFR3, SS18, SSX1, SSX2, PTEN, AKT3, MTOR, IGF1R, RICTOR, MYOCD, VGLL3, CCNE1, CCNE2, MCM2, FANCI, CD274, ESR1, MSH6, MSH2, MYLK, MYH11 |
| Novel MYBL1 gene rearrangements with recurrent MYBL1-NFIB fusions in salivary adenoid cystic carcinomas lacking t(6;9) translocations | 2016 | Clinical Cancer Research | ACYC | MYBL1, MYB, NFIB, YTHDF3, XRCC4, NKAIN2, PTPRD, AIG1, RAD51B, NOTCH1, SPEN, MUC16, MUC12, TFAP4, MAP10 |
| Deep sequencing of uveal melanoma identifies a recurrent mutation in PLCB4 | 2016 | Oncotarget | UM | PLCB4, PLCB3, GNAQ, GNA11, BAP1, SF3B1, EIF1AX, LLGL1, MUC3A, TCHH, TTN, GSPT1, HSD17B3, FAM135B, PDSS2 |
| Divergent clonal selection dominates medulloblastoma at recurrence | 2016 | Nature | MBL | TP53, PTCH1, DYNC1H1, SMO, MYC, TERT, CDKN2A, CDKN2B, CREBBP, ARID1B, TCF4 |
| Ampullary cancers harbor ELF3 tumor suppressor gene mutations and exhibit frequent WNT dysregulation | 2016 | Cell Reports | AMPCA, DA, EHCH | ELF3, TP53, KRAS, SMAD4, CDKN2A, APC, SOX9, TGFBR2, PBRM1, RECQL4, KDM6A, ARID1A, ARID2, PMS2, KDM4C, UHRF2, CTNNB1, MET, SLC45A3, ELK4, IDH1, BAP1 |
| Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma | 2016 | Cell | DIFG, GBM, ASTR, ODG, PAST | IDH1, IDH2, TERT, ATRX, TP53, EGFR, PTEN, CIC, FUBP1, SETD2, ARID2, DNMT3A, KRAS, NRAS, CDK4, CDKN2A, CDKN2B, BRAF, NF1, NTRK1, NTRK2, FGFR1, FGFR2, STAG2, NIPBL, TRIM28, CACNG6, DAXX, H3-3A, SOX2, OLIG2 |
| An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma | 2016 | Nature Genetics | ACYC | MYB, NFIB, TGFBR3, RAD51B, TP63, NOTCH1, SPEN, ARID1A, BRD4, JAG1, JAG2, EN1, RBPJ, KIT, MYC, BCL2, CDK6 |
| Divergent clonal evolution of castration resistant neuroendocrine prostate cancer | 2016 | Nature Medicine | PRAD | AR, RB1, TP53, BRCA2, MYCN, CYLD, DEK, SBDS, FOXA1, NCOR1, NCOR2, ZBTB16, EZH2, SPDEF, AURKA, NCAM1, PEG10, DKK1, NKD1, TMPRSS2, ERG |
| Whole-Genome Sequencing of Salivary Gland Adenoid Cystic Carcinoma | 2016 | Cancer Prevention Research | ACYC | NFIB, MYB, MYBL1, MAP3K5, RIMS1, MYO6, RPS6KA2, NOTCH1, NOTCH2, KMT2D, KMT2C, EP300, SMARCA2, SMARCC1, KDM6A, RHOA, ARHGEF3, ARHGEF5, ARHGEF18, CDH2, CDH13, ACTB, PLXNB1, PLXNA1, PRKD1, SLIT1, SRGAP2, SRGAP3, SEMA3G, SEMA5A, NTNG1, ADAM2, ADAMTS5, ADAMTS13, DUX4 |
| Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers | 2016 | Journal of Clinical Investigation | THPD, THAP, THPA | BRAF, NRAS, HRAS, KRAS, TERT, TP53, EIF1AX, PIK3CA, PTEN, NF1, NF2, ATM, PIK3C2G, PIK3CG, PIK3C3, PIK3R1, PIK3R2, AKT3, TSC1, TSC2, MTOR, ARID1A, ARID1B, ARID2, ARID5B, SMARCB1, PBRM1, ATRX, KMT2A, KMT2C, KMT2D, SETD2, MSH2, MSH6, MLH1, CTNNB1, AXIN1, APC, CDKN1B, CDKN2C, CDKN2A, ERBB2, PTCH1, DAXX, RB1, MEN1, TSHR, STK11, RET, CCDC6, NCOA4, PAX8, PPARG, ALK, STRN, EML4, CCDC149, NUTM1, BRD4, EPHA3, EGFR, FLT1, FLT4, KDR, NOTCH1, NOTCH2, NOTCH3, NOTCH4, CREBBP, EP300, BCOR, BCL6, DIS3, FAT1, POLE, RBM10, RAD54L, RECQL4, SF3B1 |
| Frequent somatic CDH1 loss-of-function mutations in plasmacytoid-variant bladder cancer | 2016 | Nature Genetics | SRCBC, BLCA | CDH1, TP53, RB1, ARID1A, ERBB2, PIK3CA, CDKN1A, PIK3C2G, PTEN, NOTCH2, FAT4, TSC1 |
| Substantial inter-individual and limited intra-individual genomic diversity among tumors from men with metastatic prostate cancer | 2016 | Nature Medicine | PRAD | AR, ERG, TP53, RB1, SPOP, CHD1, ZBTB16, MYC, FOXA2, MSH2, MSH6, TMPRSS2, NR3C1, PGR, ESR1, E2F1, FANCA, FANCI, FANCD2, BRCA1, BRCA2, PALB2, ATM, FANCB, FANCC, FANCE, FANCF, FANCG, BRIP1, FANCL, FANCM, SLX4, PTEN, CSMD1, NCOR2 |
| Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways | 2016 | Cancer Cell | MRT, MRTL | SMARCB1, SMARCA4, DSCAM, SPECC1L, KCNJ3, NF2, LIF, SMARCE1, HOTAIR, BMP4, WNT5A, STAT3, FLT3LG, ZIC3, SOX3, DLK1, MEOX2, PCDH18, TCF21, MEIS1 |
| Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma | 2016 | Cell | SKCM, MEL | BRCA2, AXL, ROR2, WNT5A, LOXL2, TWIST2, TAGLN, FAP, IL10, VEGFA, VEGFC, CCL2, CCL7, CCL8, CCL13, CDH1, PTEN, PDCD1, CD274, PDCD1LG2, CTLA4, LAG3, IFNG, GZMA, PRF1, BRAF |
| Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma | 2016 | Cell Reports | COADREAD | BCL9L, RBM10, RBM12, CTCF, KLF5, TGIF1, TCF7, PRKCQ, MAP2K1, MAP2K7, PTEN, RB1, RNF43, KRAS, NRAS, POLE, B2M, CALR, CANX, HSPA5, PDIA3, TAP1, TAP2, TAPBP |
| Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas | 2016 | Nature Genetics | LUAD, LUSC, NSCLC | TP53, RB1, ARID1A, CDKN2A, PIK3CA, NF1, STK11, RBM10, KEAP1, RAF1, RIT1, MET, EGFR, KRAS, ERBB2, ALK, ROS1, BRAF, NTRK1, NTRK2, NFE2L2, KDM6A, RASA1, NOTCH1, HRAS, AKT1, CDK4, DNMT3A, PPP3CA, DOT1L, KMT2C, SETD2, CMTR2, SF3B1, SNRPD3, SMARCA4, CUL3, KLF5, FBXW7, EP300, CREBBP, NKX2-1, MYC, TERT, MCL1, MDM2, SOX2, CCND1, WHSC1L1, FGFR1, KAT6A, ZNF217, MYCL, IGF1R, KDM5A, PTP4A1, PHF3, CCND3, MIR21, TUBD1, YES1, MIR205, MAPK1, ARID2, ZMYND11, ROBO1, USP22, B2M, TRAF3, MAP2K1, CAPZA2, KIF5B, TRIM24, TP63, PDGFRA, KIT, KDR, SOS1, VAV1, ARHGAP35, U2AF1, PASK, MLH1, MB21D2, HLA-A, HLA-B, PDCD1, CD274 |
| The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes | 2016 | Nature Communications | BRCA | PIK3CA, TP53, MUC16, AHNAK2, SYNE1, KMT2C, GATA3, BRCA1, BRCA2, CHEK2, TBX3, CBFB, RUNX1, SF3B1, AGTR2, ARID1A, PBRM1, CDKN2A, KDM6A, AFDN, FOXO3, CTNNA1, FOXP1, MEN1, KRAS, HRAS, BRAF, SMAD4, ERBB2, PTEN, AKT1, PIK3R1, RB1, CDH1, MAP3K1, NCOR1, CTCF, MAP2K4, BAP1, CDKN1B, GPS2, ZFP36L1, TBL1XR1, USP9X, NF1, CCND1, PAK1, ZNF703, MYC, JAK1, NT5E |
| Genomic Classification and Prognosis in Acute Myeloid Leukemia | 2016 | New England Journal of Medicine | AML | NPM1, DNMT3A, FLT3, NRAS, TP53, IDH1, IDH2, TET2, ASXL1, SRSF2, SF3B1, U2AF1, ZRSR2, STAG2, BCOR, KMT2A, EZH2, PHF6, RUNX1, CEBPA, BRAF, MYC, PTPN11, WT1, KIT, GATA2, RAD21, MECOM, PML, RARA, CBFB, MYH11, RUNX1T1, DEK, NUP214, MLLT3 |
| Genetic Determinants of Cisplatin Resistance in Patients With Advanced Germ Cell Tumors | 2016 | Journal of Clinical Oncology | GCT, NSGCT, SEM, MGCT, TT | TP53, MDM2, MYCN, KRAS, NRAS, BRAF, KIT, RAC1, CBL, GNAQ, KDR, MET, PIK3CA, PTEN, AKT1, MTOR, TSC1, TSC2, APC, FAT1, AXIN1, EP300, SETD2, PTPRD, BRCA2, MAX, MCL1, CCND3 |
| Anti-tubulin drugs conjugated to anti-ErbB antibodies selectively radiosensitize | 2016 | Nature Communications | HNSC, NSCLC, ESCA, BRCA, STAD, COAD, GB | EGFR, ERBB2 |
| Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets | 2016 | Nature Communications | URCC, RCC, NCCRCC, CCRCC, PRCC, CHRCC, TRCC | NF2, SETD2, BAP1, KMT2C, MTOR, TSC1, TSC2, PTEN, FH, ALK, TPM3, KMT2D, ATRX, DNMT3A, SMARCB1, KLF6, NOTCH2, TP53, PBRM1, CHEK2, BRCA2, KMT2A, MET, BRAF, VHL, YAP1, WWTR1 |
| Clonal Evolution of Chemotherapy-resistant Urothelial Carcinoma | 2016 | Nature Genetics | BLCA | TP53, PIK3CA, KMT2D, ATM, TSC1, CDKN2A, CDKN2B, MTAP, RB1, FANCC, ERCC2, L1CAM, APOBEC3A, APOBEC3B, E2F3, SETDB1, MLLT11, TSPAN8, RYR2, ANKRD62, NCOA3, LSS, POLD2, FOXP1, FGFR4, TRRAP, EGFR |
| Deregulation of DUX4 and ERG in acute lymphoblastic leukemia | 2016 | Nature Genetics | BLL | DUX4, ERG, IKZF1, PAX5, MYC, MYCBP2, MGA, ZEB2, KMT2D, SETD2, ARID2, NCOR1, NRAS, NSD1, RNGTT |
| Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma | 2016 | Nature | ODG | IDH1, IDH2, CIC, OLIG1, OLIG2, OMG, APOE, ALDOC, SOX9, SOX4, SOX11, SOX2, NFIB, ASCL1, CHD7, CD24, BOC, TCF4, CCND2, CCND1, CCND3, ETV1, ETV5, GFAP, MKI67 |
| A current perspective on stereotactic body radiation therapy for pancreatic cancer | 2016 | OncoTargets and Therapy | PAAD | SMAD4, TGFB1, TGFBR2 |
| TP53 and Decitabine in Acute Myeloid Leukemia and Myelodysplastic Syndromes | 2016 | New England Journal of Medicine | AML, MDS | TP53, DNMT3A, IDH1, IDH2, ASXL1, SRSF2, U2AF1, SF3B1, TET2, PPM1D, RUNX1 |
| Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations | 2016 | Genome Medicine | AML, JMML, AMKL, CML, BLL, BLLNOS, TLL, ALCL, HL, PTLD, NBL, OS, ES, ARMS, ERMS, IFS, ASPS, DSRCT, MBL, EPM, EPMT, HGGNOS, DIFG, PXA, ATRT, MRT, MRTL, LIHB, HCC, WT, RCC, ACC, PB, PPB, IMT, PINT | TP53, KRAS, NRAS, KIT, TET2, FLT3, JAK1, JAK3, IDH1, PTPN11, SETBP1, CEBPA, STAT5B, PIK3CA, TSC1, SMARCA4, SMARCB1, SMARCC2, PTCH1, SUFU, ZIC3, FGFR1, FGFR4, H3-3A, CDK2, CDK4, MDM2, MCL1, CCNE1, CUL4A, RAD51C, PDGFRA, PDGFRB, KDR, MYC, MYCN, CCND1, ATRX, KDM6A, DICER1, VHL, APC, ATM, BRCA1, PMS2, C1QA, XIAP, RUNX1, GATA2, KMT2A, KMT2C, KMT2D, AFF1, NUP98, NSD1, NUP214, ABL1, BCR, FOXP1, NT5C2, PAX7, FOXO1, EWSR1, FLI1, WT1, ASPSCR1, TFE3, CBFB, MYH11, CBFA2T3, GLIS2, EML4, NTRK3, VCAN, IL23R, TMEM106B, BRAF, RELA, RB1, TNNT2, RYR1, ITK, SDHC, ALK, UGT1A1, ASCL1 |
| Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis | 2016 | PLOS Medicine | BRCA, IDC, ILC | TP53, PIK3CA, GATA3, ESR1, MAP3K1, CDH1, AKT1, MAP2K4, RB1, PTEN, CBFB, CDKN2A, FSIP2, FRAS1, OSBPL3, EDC4, PALB2, IGFN1, AGRN, TSC1, TSC2, ERBB4, NOTCH3, ALK, EZH2, BRAF, ERBB2, CCND1, MYC, APOBEC3B |
| Genomic Predictors of Survival in Patients with High-Grade Urothelial Carcinoma of the Bladder | 2015 | European Urology | BLCA | PIK3CA, TP53, CDKN2A, KDM6A, ARID1A, STAG2, KMT2D, SMARCA4, CREBBP, EP300, PTEN, AKT1, TSC1 |
| Spectrum of diverse genomic alterations define non–clear cell renal carcinoma subtypes | 2015 | Nature Genetics | PRCC, CHRCC, TRCC, ROCY | MET, NF2, SLC5A3, PNKD, CPQ, LRP2, CHD3, NHERF1, SETD2, CRTC1, TP53, PTEN, FAAH2, PDHB, PDXDC1, ZNF765, PRKAG2, PRKAG1, TSC1, TSC2, MTOR, ARID1A, ERCC2, C2CD4C, IDH2, JAK2, ACTG1, MITF, TFE3, TFEB, TFEC, ASPSCR1, CLTC, MIDN, SBNO2, BIRC7, FH, VHL, FLCN, SDHB, SDHC, SDHD, BAP1, HIF1A, APEX1 |
| Dynamics of genomic clones in breast cancer patient xenografts at single cell resolution | 2015 | Nature | BRCA | TP53 |
| Mutational landscape of gastric adenocarcinoma in Chinese: Implications for prognosis and therapy | 2015 | Proceedings of the National Academy of Sciences (PNAS) | STAD | TP53, ARID1A, NRG1, ERBB4, ERBB2, BRCA2, BRCA1, CDH1, APC, RHOA, PIK3CA, SMAD4, MYC, KRAS, MSH6, TGFBR2, KMT2D, KDM5A, SETBP1, AKAP9, CDK6, CACNA1D |
| Novel recurrently mutated genes in African American colon cancers | 2015 | Proceedings of the National Academy of Sciences | COAD | EPHA6, FLCN, MAGEB10, CPT1C, HTR1F, ANKRD36, MGAT4C, ZNF717, ZNF862, CP, CCDC74A, EML6, ATP8B2, JAK1, CHD5, WASHC1, GPR149, CDK8, WDR87, APC, TP53, KRAS, PIK3CA, SMAD4, BRAF, FBXW7, EPHA3, EPHB6 |
| Genomic analysis of metastatic cutaneous squamous cell carcinoma | 2015 | Clinical Cancer Research | CSCC | TP53, CDKN2A, CDKN2B, NOTCH1, NOTCH2, NOTCH4, RIPK4, SMAD4, BRAF, KRAS, HRAS, EGFR, FGFR3, KIT, ERBB4, PIK3CA, HGF, MTOR, STK11, PTEN, NF1, EZH2, CARD11, CREBBP, EP300, KMT2D, ARID1A, ARID2, ARID5B, SMARCA4, SMARCB1, NF2, TP63, MYC, CCND1, CDK4, CDK6, RB1, ATR, NFKBIA, LAMA5, FANCC, SDHB, SOX2, KNSTRN, STK19, VEGFA |
| Comprehensive genomic characterization of head and neck squamous cell carcinomas | 2015 | Nature | HNSC, OCSC, OPHSC, LXSC, HPHSC | TP53, PIK3CA, CDKN2A, TRAF3, E2F1, HRAS, CASP8, NOTCH1, AJUBA, FAT1, NSD1, NFE2L2, KEAP1, CUL3, CCND1, FADD, CTTN, BIRC2, YAP1, EGFR, ERBB2, FGFR1, FGFR2, FGFR3, IGF1R, DDR2, EPHA2, MET, MYC, PTEN, PIK3R1, RB1, KMT2D, HLA-A, TGFBR2, FBXW7, SOX2, TP63, ZNF750, SMAD4, NF1, CDK6, PLK1, HMGA2, B2M, CTNNB1, PTCH1, CHEK2, SCN9A |
| The landscape of somatic mutations in Infant MLL rearranged acute lymphoblastic leukemias | 2015 | Nat Genet | BLLKMT2A, TLL | KMT2A, FLT3, KRAS, NRAS, CREBBP, NT5C2, TP53 |
| Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer | 2015 | Science | NSCLC | POLD1, POLE, MSH2, PRKDC, RAD17, POLR2A, KEAP1, KRAS, CD274, HERC1, PAPPA2, PXDNL, RYR1, SCN8A, SLIT3 |
| Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets | 2015 | Nature Genetics | HCC | TP53, CTNNB1, AXIN1, ALB, ARID1A, ARID2, ACVR2A, NFE2L2, RPS6KA3, KEAP1, RPL22, CDKN2A, CDKN1A, RB1, TERT, FGF3, FGF4, FGF19, CCND1, VEGFA, MET, MYC, JAK3, CCNE1, CFH, IRF2, PTPN3, PTEN, ZNRF3, USP34, MACF1, APOB, FGA, HNF1A, IL6ST, NQO1, HGF, SMARCA2, BRAF, ERBB2, JAK1, KDR, MTOR, EGFR, KIT, TEK, EPHA4, IL6R, PIK3CA, KRAS |
| Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets | 2015 | Nature Communications | PAAD, PAASC, PAAC, IPMN | KRAS, TP53, SMAD4, CDKN2A, CDKN2B, BRAF, PIK3CA, ARID1A, ARID1B, RBM10, MYC, RNF43, GNAS, ATM, BRCA1, BRCA2, CCND1, CDK4, RB1, AXIN1, AXIN2, APC, CTNNB1, GLI2, GLI3, SMO, PTCH1, LRP2, BCLAF1, IRF6, FLG, FANCF, FANCA, FANCD2, FANCM, ACVR1B, ACVR1C, TGFBR1, TGFBR2, TGFB1, SMAD3, SMAD6, NOTCH1, NOTCH2, NOTCH3, NOTCH4, JAG1, JAG2, MAML1, MAML2, MAML3, STK11, CHEK2, ATXN1, COL14A1, RP1L1, ITGAE, SPTA1, NIN, HDAC2, PABPC1, USP10, CDH13, MSH2, MSH6, MLH1, MLH3, PMS2, POLE, EXO1, SMARCA2, SMARCA4, SMARCC1, SMARCC2, PBRM1, TERT, PDGFA |
| Genome-wide analysis uncovers novel recurrent alterations in primary central nervous system lymphomas | 2015 | Clinical Cancer Research | PCNSL, DLBCLNOS | PRKCD, TOX, MYD88, CDKN2A, CDKN2B, TNFAIP3, PRDM1, TMEM30A, TBL1XR1, B2M, CD58, CD79B, CARD11, BCL6, FOXP1, GNA13, PIM1, BTG2, BRAF, BCL10, BCL7A, ETV6, TCF4, TNFRSF10A |
| Integrative clinical genomics of advanced prostate cancer | 2015 | Cell | PRAD | AR, TP53, PTEN, ETV1, ERG, FLI1, ETV4, ETV5, PIK3CA, PIK3CB, AKT1, BRAF, RAF1, APC, CTNNB1, RNF43, ZNRF3, RSPO2, ZBTB16, BRCA1, BRCA2, ATM, CDK12, FANCA, RAD51B, RAD51C, MLH1, MSH2, MSH6, SPOP, FOXA1, NCOR1, NCOR2, RB1, CCND1, CDKN2A, CDKN2B, CDKN1B, CDK4, MYC, CHD1, KMT2D, GNAS |
| Genomic Classification of Cutaneous Melanoma | 2015 | Cell | SKCM | BRAF, NRAS, HRAS, KRAS, NF1, CDKN2A, CDKN2B, TP53, PTEN, RAC1, MAP2K1, MAP2K2, PPP6C, ARID2, IDH1, RB1, DDX3X, MRPS31, RPS27, KIT, PDGFRA, KDR, CDK4, CCND1, MDM2, TERT, MITF, CD274, PDCD1, AKT1, AKT3, PIK3CA, GNAQ, GNA11, CTNNB1, EZH2, SF3B1, BAP1, BCL2, LCK, SYK, RAF1, HMGA2, MAPK1, MAPK3, IGFBP2, FOXP1 |
| Genomic landscape of adenoid cystic carcinoma of the breast | 2015 | J Pathol | ACBC, BRCA | MYB, NFIB, TLN2, BRAF, FBXW7, SF3B1, FGFR2, SMARCA5, MTOR, RASA1, PTPN11, PRKD1, ARAF, CDH1, KMT2D, TP53, PIK3CA |
| Comprehensive genomic profiles of small cell lung cancer | 2015 | Nature | SCLC | TP53, RB1, TP73, NOTCH1, NOTCH2, NOTCH3, NOTCH4, CREBBP, EP300, RBL1, RBL2, PTEN, BRAF, KIT, PIK3CA, CCND1, CDKN2A, FHIT, ROBO1, MYC, MYCN, MYCL, FGFR1, IRS2, ASCL1, DLK1, CHGA, GRP, SYP, NCAM1, HES1, COL22A1, RGS7, FPR1, ASPM, ALMS1, PDE4DIP, XRN1, PTGFRN, FMN2, TTC28, CDKAL1, CRACDL |
| Genomic Characterization of Upper Tract Urothelial Carcinoma | 2015 | European Urology | UTUC, BLCA | FGFR3, HRAS, TP53, RB1, CDKN2B, CDKN2A, KDM6A, KMT2D, ARID1A, TSC1, CREBBP, PIK3CA, TACC3, POLE, MDM2, KRAS, CCND1, ERBB2, ERBB3, STAG2, KMT2A, KMT2C, EP300, SMARCA4, INPP4A |
| Exome sequencing of desmoplastic melanoma identifies recurrent NFKBIE promoter mutations and diverse activating mutations in the MAPK pathway | 2015 | Nature Genetics | DESM, MEL | NFKBIE, NF1, CBL, ERBB2, MAP2K1, MAP3K1, BRAF, EGFR, PTPN11, MET, RAC1, SOS2, NRAS, PIK3CA, TP53, CDKN2A, FBXW7, ARID2, RB1, ARID1A, CDK4, MDM2, TERT, YAP1, CCND1, MYC, EZH2, IDH1, PPP6C, FSIP1, CDH2, IL36A, PAK3, CCNE1 |
| Genomic correlates of response to CTLA-4 blockade in metastatic melanoma | 2015 | Science | SKCM, MEL | BRAF, NRAS, CTLA4, PDCD1LG2, GZMA, PRF1 |
| Comprehensive molecular portraits of invasive lobular breast cancer | 2015 | Cell | BRCA, ILC, IDC, MIXED | CDH1, PTEN, TBX3, FOXA1, GATA3, PIK3CA, RUNX1, TP53, MYC, CCNE1, ERBB2, EGFR, ESR1, AKT1, MET, KIT, PDGFRA, IDO1, IFNG, EP300, MAPK3, RB1, JAK2, TYK2, BRCA2 |
| Telomerase activation by genomic rearrangements in high-risk neuroblastoma | 2015 | Nature | NBL | TERT, MYCN, ATRX, ALK, SLC6A18, SLC6A19, CLPTM1L |
| Mutations driving CLL and their evolution in progression and relapse | 2015 | Nature | CLLSLL | RPS15, IKZF3, MGA, BRAF, TP53, ATM, SF3B1, NRAS, KRAS, MAP2K1, BIRC3, MYD88, CHD2, DDX3X, BCOR, PTPN11, FUBP1, XPO4, EWSR1, NXF1, CHEK2, BRCC3, ELF4, DYRK1A, ASXL1, H1-5, BAZ2B, TRAF2, TRAF3, CARD11, POT1, EGR2, XPO1 |
| The Molecular Taxonomy of Primary Prostate Cancer | 2015 | Cell | PRAD | ERG, ETV1, ETV4, FLI1, SPOP, FOXA1, IDH1, TMPRSS2, SLC45A3, NDRG1, TP53, PTEN, CHD1, MED12, CDKN1B, BRAF, HRAS, AKT1, PIK3CA, PIK3CB, CTNNB1, ATM, BRCA1, BRCA2, CDK12, FANCD2, RAD51C, KDM6A, KMT2C, KMT2D, APC, NKX3-1, ZMYM3, MYC, CCND1, FGFR1, WHSC1L1, MAP3K1, MAP3K7, RB1, SPINK1, AR, SPOPL, FOXP1, RYBP, SHQ1, MTOR, RAC1, RRAS2 |
| The mutational landscape of cutaneous T-cell lymphoma and Sézary syndrome | 2015 | Nature Genetics | SS, MYCF | TP53, RB1, PTEN, DNMT3A, CDKN1B, TET2, CREBBP, KMT2D, KMT2C, BRD9, SMARCA4, CHD3, MAPK1, BRAF, CARD11, PRKG1, JAK3, SH2B3, STAT3, PREX2, PLCG1, TNFRSF1B |
| The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma | 2014 | Cancer Discovery | SKCM | BRAF, NRAS, MAP2K1, MAP2K2, MITF, NF1, PTEN, PIK3CA, PIK3R1, RAC1, HOXD8 |
| Whole exome sequencing of pancreatic neoplasms with acinar differentiation | 2014 | Journal of Pathology | PAAC, PB | SMAD4, TP53, GNAS, RNF43, MEN1, ATM, BRCA2, PALB2, JAK1, BRAF, RB1, APC, PTEN, ARID1A, KMT2C, BAP1, CDKN2A, KRAS, CTNNB1, MSH2, MSH3, MLH1, MLH3, PMS2, BRCA1 |
| Mutational Analysis Reveals the Origin and Therapy-driven Evolution of Recurrent Glioma | 2014 | Science | ASTR, GBM, DIFG | IDH1, TP53, ATRX, SMARCA4, BRAF, RB1, CDKN2A, CDK4, PIK3CA, PTEN, MTOR, MSH6, MGMT |
| Widespread genetic heterogeneity in multiple myeloma: implications for targeted therapy | 2014 | Cancer Cell | PCM | KRAS, NRAS, BRAF, TENT5C, TP53, DIS3, TRAF3, CYLD, RB1, PRDM1, IRF4, SP140, EGR1, CDKN2C, BIRC2, BIRC3, PTPRD, BLK, MSRA, PINX1, SOX7, MAX, MYC, CCND1, CDKN1B, FGFR3, MYD88, CARD11, BCL2 |
| Comprehensive genomic analysis of rhabdomyosarcoma reveals a landscape of alterations affecting a common genetic axis in fusion-positive and fusion-negative tumors | 2014 | Cancer Discovery | RMS, ARMS, ERMS | PAX3, PAX7, FOXO1, NCOA1, INO80D, NRAS, KRAS, HRAS, NF1, BRAF, PIK3CA, PIK3CD, PTEN, FGFR4, PDGFRA, ERBB2, ERBB4, FBXW7, BCOR, CTNNB1, TP53, BUB1B, FOXM1, CCND1, CCND2, PTPN11, ATM, ZNF350, TRPC4AP, ARID1A, IGF1R, IGF2, CDK4, MDM2, FRS2, MYCN, CDKN2A, MIR17HG, MYOD1, MET, CNR1, RPTOR, CACNA1A, NRG1, FOXP2 |
| Comprehensive molecular characterization of urothelial bladder carcinoma | 2014 | Nature | BLCA | TP53, ARID1A, KMT2D, KDM6A, PIK3CA, EP300, CDKN1A, RB1, ERCC2, FGFR3, STAG2, ERBB3, FBXW7, RXRA, ELF3, NFE2L2, TSC1, KLF5, TXNIP, FOXQ1, CDKN2A, FOXA1, PAIP1, HRAS, ZFP36L1, CCND3, ERBB2, ATM, CTNNB1, TACC3, MDM2, PPARG, E2F3, CCND1, EGFR, NECTIN4, BCL2L1, ZNF703, CCNE1, AKT3, TSC2, CREBBP, APOBEC3B, RHOB, BTG2, GATA3 |
| Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing | 2014 | Nature Genetics | CCRCC | VHL, PBRM1, BAP1, SETD2, KDM5C, PTEN, MTOR, TP53, PIK3CA, ARID1A, SMARCA4, ELOC |
| Recurrent SMARCA4 mutations in small cell carcinoma of the ovary | 2014 | Nature Genetics | SCCO, LUAD, BLCA, STAD | SMARCA4, SMARCA2, ARID1A, ARID1B, PBRM1, TP53 |
| Genomic and molecular characterization of esophageal squamous cell carcinoma | 2014 | Nature Genetics | ESCC | FAT1, FAT2, FAT3, ZNF750, KMT2D, KMT2C, KDM6A, ARID2, PBRM1, XPO1, FBXW7, IL7R, JAK1, SOX2, FGFR1, MAP3K13, MAP3K15, ERBB4, PTEN, PIK3CA, TP53, NOTCH1, CCND1, EGFR, MYC, KRAS, CDKN2A, APOBEC3B |
| Molecular Profiling of Liver Tumors: Classification and Clinical Translation for Decision Making | 2014 | Seminars in Liver Disease | HCC, LIAD | TERT, TP53, CTNNB1, AXIN1, ARID1A, ARID2, RPS6KA3, PIK3CA, IRF2, NFE2L2, KEAP1, CDKN2A, MET, FGF19, VEGFA, MYC, IGF2, IGF2R, IGF1R, EGF, EGFR, BRAF, RAF1, ERBB2, BCR, ABL1, ALK, EML4, EPCAM, KRT19, GPC3, HSPA1A, GLUL, MICA, DEPDC5, KIF1B, UBE4B, PGD, DLC1, STAT4, ABCB11, LRP2, TAF9, RAN, RAMP3, JPT1 |
| Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach | 2014 | Nature Communications | NSCLC, HNSC | |
| A specific missense mutation in GTF2I occurs at high frequency in thymic epithelial tumors | 2014 | Nature Genetics | TET, THYM, THYC | GTF2I, TP53, CYLD, CDKN2A, BAP1, PBRM1, BCL2, KIT, BRD4, NUTM1, FOS |
| Copy number alteration burden predicts prostate cancer relapse | 2014 | Proceedings of the National Academy of Sciences | PRAD | PTEN, MYC, TP53, RB1, FOXP1, RYBP, SHQ1 |
| Comprehensive molecular characterization of gastric adenocarcinoma | 2014 | Nature | STAD | PIK3CA, JAK2, CD274, PDCD1LG2, ARID1A, BCOR, TP53, KRAS, ERBB2, ERBB3, EGFR, MLH1, CDKN2A, RHOA, CDH1, CLDN18, ARHGAP26, ARHGAP6, RNF43, B2M, NF1, APC, CTNNB1, SMAD4, SMAD2, RASA1, FGFR2, MET, CCNE1, CCND1, CDK6, MYC, PTEN, PIK3R1, HLA-B, GATA4, GATA6, AURKA, AURKB, ZNF217, CD44, VEGFA, POLE |
| Comprehensive molecular profiling of lung adenocarcinoma | 2014 | Nature | LUAD | EGFR, KRAS, TP53, BRAF, PIK3CA, MET, RIT1, STK11, KEAP1, NF1, RB1, CDKN2A, SETD2, ARID1A, SMARCA4, RBM10, U2AF1, MGA, MYC, ERBB2, ALK, ROS1, RET, NKX2-1, TERT, MDM2, CCNE1, CCND1, CCND3, TERC, MECOM, MAP2K1, NRAS, HRAS, CTNNB1 |
| Somatic ERCC2 mutations correlate with cisplatin sensitivity in muscle-invasive urothelial carcinoma | 2014 | Cancer Discovery | BLCA | ERCC2, TP53, RB1, KDM6A, ARID1A, BRCA1, BRCA2 |
| The somatic genomic landscape of chromophobe renal cell carcinoma | 2014 | Cancer Cell | CHRCC, CCRCC | TP53, PTEN, TERT, MTOR, NRAS, TSC1, TSC2, FLCN, CDKN2A, PPARGC1A, APOBEC3B, PDCD6, NEK5, SDHB, NDUFS1, PBRM1 |
| Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions | 2014 | Genome Biology | COADREAD, COAD, READ | KRAS, NRAS, BRAF, APC, TP53, PIK3CA, SMAD4, SMAD3, MAP2K1, EGFR, CARD11, ETV1, IKZF1, PTK7, RASA1, CDK8, AMER1, FBXW7, CTNNB1, PIK3CD, PIK3CG, PIK3C2G, PIK3R1, PTEN, RUNX1T1 |
| Organoid cultures derived from patients with advanced prostate cancer | 2014 | Cell | PRAD | AR, ATRX, CDK12, CDKN2A, CHD1, CHEK2, ERG, FOXA1, FOXP1, KDM4C, KDM4D, KMT2D, MED1, PIK3R1, PTEN, RB1, RYBP, SETD2, SETDB1, SHQ1, SPINK1, SPOP, TMPRSS2, TP53, TSC2 |
| Genomic landscape of Ewing sarcoma defines an aggressive subtype with co-association of STAG2 and TP53 mutations | 2014 | Cancer Discovery | ES | STAG2, TP53, CDKN2A, EZH2, BCOR, ZMYM3, EWSR1, FLI1, ERG, ETV1, FEV, TAF15, FUS, SETD2, KMT2D, KMT2C, PRDM9, STAG1, CTCF |
| Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes | 2014 | Nature Communications | UCS, MXOV | TP53, KRAS, ARID1A, ARID1B, KMT2C, KMT2D, SPOP, BAZ1A, PIK3CA, PIK3R1, PTEN, CTNNB1, FBXW7, PPP2R1A, ERBB3, BRCA1, BRCA2, FANCM, MLH1, MSH6 |
| PRC2 is recurrently inactivated through EED or SUZ12 loss in malignant peripheral nerve sheath tumors | 2014 | Nature Genetics | MPNST | EED, SUZ12, NF1, CDKN2A, TP53, EZH1, EZH2, IGF2, FOXN4, PAX2, TLX1 |
| Mutational landscape of aggressive cutaneous squamous cell carcinoma | 2014 | Clinical Cancer Research | CSCC | TP53, CDKN2A, NOTCH1, NOTCH2, AJUBA, HRAS, CASP8, FAT1, KMT2C, KMT2D, PARD3, RASA1, RIPK4, RAC1, PIK3CA, NFE2L2, BRAF, NRAS, PTCH1, CCND1, POLE, EGFR, SNX25, EIF2D, RBM46, DCLK1 |
| Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma | 2014 | New England Journal of Medicine | SKCM, MEL | CTLA4, BRAF, NRAS, FAM3C, CSMD1 |
| Integrated Genomic Characterization of Papillary Thyroid Carcinoma | 2014 | Cell | THPA | BRAF, NRAS, HRAS, KRAS, EIF1AX, PPM1D, CHEK2, TERT, RET, NTRK1, NTRK3, ALK, PPARG, PAX8, ETV6, EML4, SND1, MKRN1, RBPMS, THADA, FGFR2, MET, LTK, PTEN, PIK3CA, AKT1, AKT2, TP53, RB1, NF1, NF2, MEN1, APC, ATM, SPOP, KMT2A, KMT2C, ARID1B, ZFHX3, RAP1GAP, TSHR, FANCA, FGFR3 |
| The genetic landscape of high-risk neuroblastoma | 2013 | Nature Genetics | NBL | ALK, PTPN11, ATRX, MYCN, NRAS, CHEK2, BARD1, PINK1, TP53, PALB2, MLH1, PHOX2B, ARID1A, ARID1B |
| The genomic landscape of hypodiploid acute lymphoblastic leukemia | 2013 | Nature Genetics | BLL | TP53, NF1, NRAS, KRAS, FLT3, PTPN11, IKZF2, IKZF3, IKZF1, RB1, CREBBP, EZH2, PAG1, CDKN2A, CDKN2B, MAPK1, CBL, ETV6 |
| Evolution and impact of subclonal mutations in chronic lymphocytic leukemia | 2013 | Cell | CLLSLL | TP53, ATM, MYD88, SF3B1, NOTCH1, DDX3X, ZMYM3, FBXW7, XPO1, CHD2, POT1, NRAS, KRAS, BCOR, EGR2, MED12, RIPK1, SAMHD1, ITPKB, H1-4 |
| Exome and whole genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity | 2013 | Nature Genetics | ESCA, GEJ | TP53, CDKN2A, SMAD4, PIK3CA, ARID1A, ARID2, SMARCA4, PBRM1, JARID2, ELMO1, DOCK2, RAC1, PAK1, TRIO, TIAM1, VAV2, ECT2, SPART, TLR4, AKAP6, HECW1, AJAP1, NUAK1, KAT6A, KRAS, ERBB2, EGFR, PIK3R1, PTEN, NF1, BRAF, APC, CDH1, AXIN1, CTNNB1, MSH6, MSH3, DNM2, GALNT7, CCND1, CCNE1, CDK6 |
| Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers | 2013 | Cancer Discovery | OCSC, HNSC | NOTCH1, CASP8, FAT1, TP53, TP63, HRAS, PIK3CA, BRAF, EGFR, AKT1, CCND1, CDKN2A, MYC, CDKN1A, FHIT, CSMD1, NFIB, JAG1, JAG2, NUMB, MAML1, FADD, BIRC2, BIRC3, IKBKB, LTO1, RPS6KB1, TNK2, PTK2, SRC, LYN, YES1, AURKA, AURKC, TERC, PRKCI |
| Punctuated Evolution of Prostate Cancer Genomes | 2013 | Cell | PRAD, PRNE | TMPRSS2, ERG, ETV1, ETV3, ETV6, SMAD4, SPOP, FOXA1, FOXP1, NKX3-1, NRF1, BRAF, CRKL, MAPK1, MAGI2, GSK3B, FOXO1, PIK3R1, PTEN, TP53, CDKN1B, RB1, CHEK2, CHD1 |
| Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia | 2013 | N Engl J Med | AML | FLT3, NPM1, DNMT3A, IDH1, IDH2, TP53, RUNX1, CEBPA, TET2, KIT, WT1, PHF6, EZH2, U2AF1, SMC1A, SMC3, RAD21, STAG2, ASXL1, KRAS, NRAS, PTPN11, KDM6A, SF3B1, SRSF2, PML, RARA, CBFB, MYH11, RUNX1T1, KMT2A, MLLT3, MLLT10, NUP98, NSD1, PICALM, BCR, ABL1, KMT2C |
| Integrated genomic characterization of endometrial carcinoma | 2013 | Nature | UCEC, UEC, USC | TP53, PTEN, PIK3CA, PIK3R1, KRAS, CTNNB1, ARID1A, ARID5B, POLE, POLD1, FBXW7, PPP2R1A, MLH1, RPL22, SOX17, ERBB2, MYC, CCNE1, FGFR1, FGFR2, FGFR3, IGF1R, LRP1B, AKT3, CDKN2A, AURKA, CCNB1, ASNS, PGR, FOXA1, RAD50, CTCF, BCL2, BCL2L11, BCL7A, BCL9 |
| The mutational landscape of adenoid cystic carcinoma | 2013 | Nature Genetics | ACYC | MYB, NFIB, SMARCA2, SMARCE1, ARID1A, ATRX, CREBBP, EP300, KDM6A, KMT2C, ARID5B, PIK3CA, PTEN, FOXO3, FGF16, FGFR2, FGFR4, IGFBP2, IL17RD, TP53, UHRF1, TXNIP, ATM, BRCA1, NOTCH1, FBXW7, FOXP2, RYR2, RYR3, PTPRG, PTPRH, PTPRJ, PTPRK, HSPG2, IDH1, FAT3, FAT4, MGA |
| Whole exome sequencing of adenoid cystic carcinoma | 2013 | The Journal of Clinical Investigation | ACYC | MYB, NFIB, PIK3CA, ATM, CDKN2A, SF3B1, SUFU, TSC1, CYLD, NOTCH1, NOTCH2, SPEN, FGFR2, ARID1A, ARID1B, ARID5B, CREBBP, EP300, KDM6A, KDM5A, KMT2C, SMARCA2, CHD2, BRD2 |
| Comprehensive molecular characterization of clear cell renal cell carcinoma | 2013 | Nature | CCRCC | VHL, PBRM1, SETD2, BAP1, KDM5C, PTEN, MTOR, TP53, ARID1A, SMARCA4, HIF1A, CDKN2A, MYC, MDM4, JAK2, PRKCI, MECOM, TFE3, SFPQ, EGFR, GRB10, TSC2, SQSTM1, RACK1, UQCRH, FASN, G6PD, CTNNB1, TGFBR2, NEGR1, QKI, CADM2, PTPRD, NRXN3 |
| Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma | 2013 | Nature Genetics | PAST, GB, DMG | FGFR1, NTRK2, BRAF, KRAS, PTPN11, NF1, H3-3A, FGF2, KIAA1549, FAM131B, RNF130, CLCN6, MKRN1, GNAI1, QKI, NACC2, TP53, FGFR2, FGFR3, RAF1, NTRK1, NTRK3, TACC1, TACC3, FLT3 |
| Prevalence and Co-Occurrence of Actionable Genomic Alterations in High-Grade Bladder Cancer | 2013 | Journal of Clinical Oncology | BLCA | TP53, RB1, FGFR3, FGFR1, PIK3CA, ERBB2, MDM2, CDKN2A, CDKN2B, CCND1, CCNE1, E2F3, KRAS, BRAF, HRAS, NF1, MET, RAF1, AKT1, PTEN, TSC1, MTOR |
| New cast for a new era: preclinical cancer drug development revisited | 2013 | The Journal of Clinical Investigation | LUAD, PAAD, APLPMLRARA, NSCLC | KRAS, STK11, SMO, TP53 |
| The Somatic Genomic Landscape of Glioblastoma | 2013 | Cell | GBM | EGFR, PDGFRA, PTEN, TP53, PIK3CA, PIK3R1, NF1, RB1, IDH1, LZTR1, SPTA1, ATRX, GABRA6, KEL, BRAF, TERT, QKI, LRP1B, NPAS3, LSAMP, SMYD3, MET, FGFR1, FGFR2, FGFR3, TACC3, MDM2, MDM4, CDK4, CDK6, CDKN2A, CCND1, CCND2, CCNE2, SOX2, MYC, MYCN, MGMT, IDH2, H3-3A, SEC61G, LANCL2, VOPP1, BRIP1, CPM, PRIM2, BCL11A |
| Whole-genome and whole-exome sequencing of bladder cancer identifies frequent alterations in genes involved in sister chromatid cohesion and segregation | 2013 | Nature Genetics | BLCA | STAG2, ESPL1, FGFR3, TACC3, NIPBL, SMC1A, SMC3, TP53, HRAS, KRAS, PIK3CA, RB1, TSC1, KDM6A, UTY, ARID1A, ARID4A, KMT2A, KMT2C, KMT2E, EP300, EP400, CREBBP, NCOR1, CHD6, SMARCA4, KDM5A, KDM5B, ERCC2, TRRAP, FAT4, MDM2, MYC, E2F1, E2F3, CCND1, CCNE1, ERBB2, CEBPA, MUC1, TRIO, DHFR, CDKN2A, CDKN2B, BRCA1, BRCA2, ATM, ATR, BUB1 |
| Landscape of somatic mutations and clonal evolution in mantle cell lymphoma | 2013 | Proceedings of the National Academy of Sciences USA | MCL | ATM, CCND1, TP53, NSD2, KMT2D, BIRC3, MEF2B, TLR2, NOTCH1, NOTCH2, SOX11, UBR5, B2M, CDKN2A |
| Exome sequencing identifies frequent inactivating mutations in BAP1, ARID1A and PBRM1 in intrahepatic cholangiocarcinomas | 2013 | Nature Genetics | IHCH, GBC | BAP1, ARID1A, PBRM1, IDH1, IDH2, FGFR2, TP53, KRAS, NRAS, PIK3CA, PTEN, PIK3C2A, PIK3C2G, AKT1, CDKN2A, SMAD4, CTNNB1, TGFBR2, KMT2C |
| Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2 | 2013 | New England Journal of Medicine | MPN, ET, PV, MF, MPNU, MDS, CMML, ACML, AML | CALR, JAK2, MPL, TET2, DNMT3A, ASXL1, EZH2, IDH1, IDH2, U2AF1, SF3B1, SRSF2, CBL, NFE2, SH2B3, CHEK2 |
| Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing | 2012 | Proceedings of the National Academy of Sciences | DLBCLNOS | MYD88, CARD11, EZH2, CREBBP, CD79B, TP53, KMT2D, TNFRSF14, BTG1, MEF2B, GNA13, BCL2, KRAS, BRAF, NOTCH1, PIM1, ACTB, P2RY8, CCND3, SOCS1, B2M, HLA-A, STAT3, SGK1, STAT6, CD58, NFKBIA, SYK, ETV6, TBL1XR1 |
| The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity | 2012 | Nature | MEL, PCM, ES, NBL | BRAF, NRAS, KRAS, EGFR, ERBB2, MET, ALK, MDM2, AHR, SLFN11, NQO1, IGF1R, IGF1, PTEN, TP53, HGF, EXT2, MITF, SOX10, CYP1A1, TOP1, SPRY2, PTPN5 |
| The clonal and mutational evolution spectrum of primary triple negative breast cancers | 2012 | Nature | BRCA | TP53, PIK3CA, PTEN, RB1, EGFR, BRCA2, BRAF, NRAS, ERBB2, ERBB3, KRAS, IDH1, ETV6, PRKN, USH2A, MYO3A, ATR, UBR5, COL6A3, PIK3R1, ATM, SYNE1, SYNE2, PRPS2, NR3C1, PRKCZ, GH1 |
| The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups | 2012 | Nature | BRCA | PPP2R2A, MTAP, MAP2K4, ZNF703, PTEN, MYC, CCND1, MDM2, ERBB2, CCNE1, MDM4, CDK4, NCOR1, PAK1, RSF1, EMSY, IGF1R, KRAS, EGFR, CDKN2A, CDKN2B, BRCA2, RB1, ATM, SMAD4, TP53, AURKB, BUB1, FOXM1, TTK, CHEK1 |
| Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer | 2012 | Nature Genetics | PRAD | SPOP, FOXA1, MED12, TP53, PTEN, PIK3CA, CDKN1B, CHD1, TMPRSS2, ERG, AR, NKX3-1, MSH6, THSD7B, SCN11A, ZNF595, FOXO3, PRDM1 |
| Melanoma genome sequencing reveals frequent PREX2 mutations | 2012 | Nature | SKCM, MEL | PREX2, BRAF, NRAS, PTEN, KIT, ETV1, MITF, MAGI2, FHIT, MACROD2, CSMD1, RBFOX1 |
| The landscape of cancer genes and mutational processes in breast cancer | 2012 | Nature | BRCA | TP53, PIK3CA, AKT1, AKT2, ERBB2, MYC, FGFR1, ZNF703, GATA3, CCND1, CDH1, PTEN, RB1, BRCA1, MAP3K1, MAP2K4, MAP3K13, NCOR1, SMARCD1, ARID1B, CDKN1B, CASP8, TBX3, KRAS, NF1, APC, ARID1A, ARID2, ASXL1, BAP1, SETD2, SF3B1, SMAD4, STK11, MDM2 |
| Sequence analysis of mutations and translocations across breast cancer subtypes | 2012 | Nature | BRCA | PIK3CA, TP53, AKT1, GATA3, MAP3K1, CBFB, RUNX1, ERBB2, AKT3, MAGI3, PTEN |
| Novel mutations target distinct subgroups of medulloblastoma | 2012 | Nature | MBL | KDM6A, EZH2, DDX3X, PIK3CA, CTNNB1, SMARCA4, CREBBP, CHD7, ZMYM3, CDH1, MYC, MYCN, OTX2, TP53, PTCH1, PTEN, APC, SUFU, KMT2D, TRRAP, MED13 |
| The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer | 2012 | Nature | PRAD | AR, TP53, PTEN, RB1, CHD1, FOXA1, KMT2D, CDK12, ERG, TMPRSS2, ETS2, ETV3, ETV1, ETV5, KDM6A, ASXL1, ASH2L, KMT2A, ZFHX3, APC, OR5L1, PRKDC, EZH2, SPINK1, KLK3 |
| CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set | 2012 | Cancer Research | COAD | ABCB1, EGFR, CDH1, MYC, TOP1, CHEK2, ZEB1, RNF43 |
| Comprehensive molecular characterization of human colon and rectal cancer | 2012 | Nature | COADREAD | APC, TP53, KRAS, PIK3CA, FBXW7, SMAD4, TCF7L2, NRAS, CTNNB1, SMAD2, AMER1, SOX9, ARID1A, BRAF, ERBB2, ERBB3, IGF2, PTEN, PIK3R1, MLH1, MSH2, MSH3, MSH6, PMS2, POLE, TGFBR2, ACVR2A, MYC, NAV2, TCF7L1, IRS2 |
| A Landscape of Driver Mutations in Melanoma | 2012 | Cell | MEL, SKCM | BRAF, NRAS, PTEN, TP53, CDKN2A, MAP2K1, PPP6C, RAC1, SNX31, TACC1, ARID2, NF1, CTNNB1, PIK3CA, EZH2, IDH1, GNA11, KIT, HRAS, RB1, CDK4, CCND1, MITF, TERT, ARID1A, ARID1B, SMARCA4, FBXW7 |
| Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations | 2012 | Nature | MBL | DDX3X, CTNNB1, PTCH1, KMT2D, KMT2C, SMARCA4, TP53, GPS2, BCOR, LDB1, KDM6A, CTDNEP1, SUFU, CSNK2B, NCOR2 |
| Dissecting the genomic complexity underlying medulloblastoma | 2012 | Nature | MBL | CTNNB1, DDX3X, PTCH1, SMARCA4, KMT2D, TP53, KDM6A, CTDNEP1, MYCN, SMO, BCOR, TBR1, EOMES, ERBB4, DNAJB6, SHH |
| Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma | 2012 | Nature Genetics | MEL, SKCM, UM | RAC1, BRAF, NRAS, PPP6C, NF1, TP53, ARID2, PTEN, CDKN2A, DCC, PTPRK, PTPRD, PAK1, CDK4, CCND1, RICTOR, BAP1 |
| Recurrent R-spondin fusions in colon cancer | 2012 | Nature | COAD, COADREAD | RSPO2, RSPO3, APC, KRAS, TP53, SMAD4, FBXW7, PIK3CA, ATM, TCF7L2, TET2, TET3, ERBB3, IGF2, MYC, BRAF, CTNNB1, PTEN |
| Integrative genome analyses identify key somatic driver mutations of small cell lung cancer | 2012 | Nature Genetics | SCLC | TP53, RB1, CREBBP, EP300, KMT2A, PTEN, SLIT2, EPHA7, FGFR1, MYCL, MYCN, MYC, SOX2, CCNE1, NFIB, COBL, PIK3CA |
| Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer | 2012 | Nature Genetics | SCLC | SOX2, TP53, RB1, MYCL, PIK3CA, PTEN, MYC, KIT, NOTCH1, EP300, CDKN2A |
| Comprehensive genomic characterization of squamous cell lung cancers | 2012 | Nature | LUSC | TP53, CDKN2A, PTEN, PIK3CA, KEAP1, KMT2D, HLA-A, NFE2L2, NOTCH1, RB1, EGFR, KRAS, SOX2, TP63, FGFR1, NSD3, PDGFRA, KIT, CCND1, MYC, CDK6, MDM2, BCL2L1, FOXP1, NF1, CUL3, NOTCH2, ASCL4, DDR2, HRAS, FBXW7, SMARCA4, SMAD4, APC, TSC1, BRAF, TNFAIP3, CREBBP, AMER1, AKT3 |
| Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing | 2012 | Cell | LUAD | TP53, KRAS, EGFR, STK11, KEAP1, NF1, BRAF, SMAD4, U2AF1, RBM10, ARID1A, SETD2, BRD3, SMARCA4, PIK3CA, CTNNB1, FGFR3, ATM, CBL, PTEN, FBXW7, RB1, CDKN2A, NKX2-1, TERT, MYC, ERBB2, SIK2 |
| Comprehensive molecular portraits of human breast tumors | 2012 | Nature | BRCA, HGSOC | TP53, PIK3CA, GATA3, MAP3K1, MAP2K4, CDH1, PTEN, AKT1, RB1, ERBB2, EGFR, BRCA1, BRCA2, PIK3R1, NF1, SF3B1, TBX3, RUNX1, CBFB, FOXA1, MYC, CCND1, CCNE1, INPP4B, KRAS, BRAF, MDM2, ATM, FGFR1, FGFR2, FGFR4, KIT, MET, PDGFRA, IGF1R, CDK4 |
| Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes | 2012 | Nature | PAAD | KRAS, TP53, CDKN2A, SMAD4, KMT2C, TGFBR2, ARID1A, SF3B1, EPC1, ARID2, ATM, ZIM2, MAP2K4, NALCN, SLC16A4, MAGEA6, SLIT2, ROBO1, ROBO2, ROBO3, SEMA3A, SEMA3E, PLXNA1 |
| DAXX/ATRX, MEN1 and mTOR Pathway Genes are Frequently Altered in Pancreatic Neuroendocrine Tumors | 2011 | Science | PANET | MEN1, DAXX, ATRX, PTEN, TSC2, PIK3CA, TP53, KRAS |
| Integrated Genomic Analyses of Ovarian Carcinoma | 2011 | Nature | HGSOC | TP53, BRCA1, BRCA2, NF1, RB1, CDK12, CCNE1, MYC, MECOM, KRAS, NRAS, BRAF, PIK3CA, PTEN, FOXM1, CSMD3, FAT3, GABRA6, CREBBP, RAD51C |
| Frequent mutation of histone modifying genes in non-Hodgkin lymphoma | 2011 | Nature | DLBCLNOS, FL | KMT2D, MEF2B, EZH2, CREBBP, EP300, GNA13, SGK1, TP53, MYD88, CARD11, CD79B, BCL2, TNFAIP3, TNFRSF14, BTG1, B2M, FOXO1, CCND3, BCL10 |
| The Mutational Landscape of Head and Neck Squamous Cell Carcinoma | 2011 | Science | HNSC | TP53, CDKN2A, PTEN, PIK3CA, HRAS, NOTCH1, NOTCH2, NOTCH3, IRF6, TP63, CCND1, EGFR, ERBB2, CCNE1, MYC, SYNE1, SYNE2, CASP8, DDX3X, EZH2, PRDM9, CDH1, KMT2D, DICER1 |
| Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 | 2011 | Science | HNSC | NOTCH1, TP53, CDKN2A, PIK3CA, HRAS, FBXW7, EGFR, CCND1 |
| Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways | 2011 | Proceedings of the National Academy of Sciences | IPMN, MCN, SPN, PAAD | VHL, RNF43, CTNNB1, KRAS, GNAS, TP53, APC, TBC1D3, MUC4 |
| Integrative genomic profiling of human prostate cancer | 2010 | Cancer Cell | PRAD | NCOA2, ERG, TMPRSS2, PTEN, RB1, TP53, AR, MYC, PIK3CA, PIK3R1, KRAS, BRAF, FOXP1, RYBP, SHQ1, NKX3-1, INPP4B, ETV6, CDKN1B, NCOR2, MSH6, IDH2 |
| Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy | 2010 | Nature Genetics | DDLS, MRLS, PLLS, LMS, GIST, MFS, SYNS, MPNST | TP53, NF1, PIK3CA, CDK4, YEATS4, MDM2, KIT, PDGFRA, CDH1, ERBB4, PTEN, RB1, AKT1 |
| Phase 3 Randomized Trial on Larynx Preservation Comparing Sequential vs Alternating Chemotherapy and Radiotherapy | 2009 | Journal of the National Cancer Institute | HNSC, LXSC, HPHSC | |
| Comprehensive genomic characterization defines human glioblastoma genes and core pathways | 2008 | GB | EGFR, ERBB2, NF1, TP53, PIK3R1, PIK3CA, PTEN, RB1, CDKN2A, CDKN2B, CDK4, CDK6, MDM2, MDM4, MLH1, MSH2, MSH6, PMS2, MGMT | |
| Somatic mutations affect key pathways in lung adenocarcinoma | 2008 | Nature | LUAD | TP53, KRAS, EGFR, STK11, CDKN2A, NF1, ATM, RB1, APC, LRP1B, PTPRD, ERBB4, EPHA3, KDR, NTRK1, NTRK2, NTRK3, ERBB2, ERBB3, FGFR4, NRAS, PTEN, BRAF, PIK3CA, AKT1, CTNNB1, PRKDC, SMG1, PDGFRA, EPHA7, EPHB1, MDM2, TERT, CDK4, CDK6, CCND1, CCNE1, CDKN2B, TSC1, TSC2, SMAD2, SMAD4, GSK3B, HCK, PIK3C3, INHBA, FLT4 |
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