Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin. 2020;70(1):7–30. https://doi.org/10.3322/caac.21590.
Article
PubMed
Google Scholar
Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer. 2015;15(6):371–81.
Article
CAS
Google Scholar
Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, et al. Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun. 2019;10(1):1388.
Article
CAS
Google Scholar
Lang UE, Yeh I, McCalmont TH. Molecular melanoma diagnosis update: gene fusion, genomic hybridization, and massively parallel short-read sequencing. Clin Lab Med. 2017;37(3):473–84.
Article
Google Scholar
Reeser JW, Martin D, Miya J, Kautto EA, Lyon E, Zhu E, et al. Validation of a targeted RNA sequencing assay for kinase fusion detection in solid tumors. J Mol Diagn. 2017;19(5):682–96.
Article
CAS
Google Scholar
Lam SW, Cleton-Jansen AM, Cleven AHG, Ruano D, van Wezel T, Szuhai K, et al. Molecular analysis of gene fusions in bone and soft tissue tumors by anchored multiplex PCR-based targeted next-generation sequencing. J Mol Diagn. 2018;20(5):653–63.
Article
CAS
Google Scholar
Benayed R, Offin M, Mullaney K, Sukhadia P, Rios K, Desmeules P, et al. High yield of RNA sequencing for targetable kinase fusions in lung adenocarcinomas with no mitogenic driver alteration detected by DNA sequencing and low tumor mutation burden. Clin Cancer Res. 2019;25(15):4712–22.
Article
CAS
Google Scholar
Cohen D, Hondelink LM, Solleveld-Westerink N, Uljee SM, Ruano D, Cleton-Jansen AM, et al. Optimizing mutation and fusion detection in NSCLC by sequential DNA and RNA sequencing. J Thorac Oncol. 2020;15(6):1000–14.
Article
CAS
Google Scholar
Cocco E, Benhamida J, Middha S, Zehir A, Mullaney K, Shia J, et al. Colorectal carcinomas containing hypermethylated MLH1 promoter and wild-type BRAF/KRAS are enriched for targetable kinase fusions. Cancer Res. 2019;79(6):1047–53.
Article
CAS
Google Scholar
Wang J, Yi Y, Xiao Y, Dong L, Liang L, Teng L, et al. Prevalence of recurrent oncogenic fusion in mismatch repair-deficient colorectal carcinoma with hypermethylated MLH1 and wild-type BRAF and KRAS. Mod Pathol. 2019;32(7):1053–64.
Article
CAS
Google Scholar
Sato K, Kawazu M, Yamamoto Y, Ueno T, Kojima S, Nagae G, et al. Fusion kinases identified by genomic analyses of sporadic microsatellite instability-high colorectal cancers. Clin Cancer Res. 2019;25(1):378–89.
Article
CAS
Google Scholar
Forbes SA, Beare D, Boutselakis H, Bamford S, Bindal N, Tate J, et al. COSMIC: somatic cancer genetics at high-resolution. Nucleic Acids Res. 2017;45(D1):D777–83.
Article
CAS
Google Scholar
Chakravarty D, Gao J, Phillips SM, Kundra R, Zhang H, Wang J, et al. OncoKB: a precision oncology knowledge base. JCO Precis Oncol. 2017. https://doi.org/10.1200/PO.17.00011.
Article
PubMed
PubMed Central
Google Scholar
Wang J, Li R, He Y, Yi Y, Wu H, Liang Z. Next-generation sequencing reveals heterogeneous genetic alterations in key signaling pathways of mismatch repair deficient colorectal carcinomas. Mod Pathol. 2020;33(12):2591–601.
Article
CAS
Google Scholar
Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884–90.
Article
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Article
CAS
Google Scholar
DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, Williams C, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012;28(11):1530–2.
Article
CAS
Google Scholar
National Comprehensive Cancer Network I. NCCN clinical practice guidelines in oncology (NCCN guidelines). Non-small cell lung cancer (version 2.2021). 2021.
Pagani F, Randon G, Guarini V, Raimondi A, Prisciandaro M, Lobefaro R, et al. The landscape of actionable gene fusions in colorectal cancer. Int J Mol Sci. 2019. https://doi.org/10.3390/ijms20215319.
Article
PubMed
PubMed Central
Google Scholar
Esteve-Codina A, Arpi O, Martinez-Garcia M, Pineda E, Mallo M, Gut M, et al. A comparison of RNA-seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples. PLoS ONE. 2017;12(1): e0170632.
Article
Google Scholar
Barua S, Wang G, Mansukhani M, Hsiao S, Fernandes H. Key considerations for comprehensive validation of an RNA fusion NGS panel. Pract Lab Med. 2020;21: e00173.
Article
Google Scholar
Parsons MT, Buchanan DD, Thompson B, Young JP, Spurdle AB. Correlation of tumour BRAF mutations and MLH1 methylation with germline mismatch repair (MMR) gene mutation status: a literature review assessing utility of tumour features for MMR variant classification. J Med Genet. 2012;49(3):151–7.
Article
CAS
Google Scholar
Prahallad A, Sun C, Huang S, Di Nicolantonio F, Salazar R, Zecchin D, et al. Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature. 2012;483(7387):100–3.
Article
CAS
Google Scholar
Corcoran RB, Ebi H, Turke AB, Coffee EM, Nishino M, Cogdill AP, et al. EGFR-mediated re-activation of MAPK signaling contributes to insensitivity of BRAF mutant colorectal cancers to RAF inhibition with vemurafenib. Cancer Discov. 2012;2(3):227–35.
Article
CAS
Google Scholar
Huijberts SC, van Geel RM, Bernards R, Beijnen JH, Steeghs N. Encorafenib, binimetinib and cetuximab combined therapy for patients with BRAFV600E mutant metastatic colorectal cancer. Future Oncol. 2020;16(6):161–73.
Article
CAS
Google Scholar
Kopetz S, Grothey A, Yaeger R, Van Cutsem E, Desai J, Yoshino T, et al. Encorafenib, binimetinib, and cetuximab in BRAF V600E-mutated colorectal cancer. N Engl J Med. 2019;381(17):1632–43.
Article
CAS
Google Scholar
Van Cutsem E, Huijberts S, Grothey A, Yaeger R, Cuyle PJ, Elez E, et al. Binimetinib, encorafenib, and cetuximab triplet therapy for patients with BRAF V600E-mutant metastatic colorectal cancer: safety lead-in results from the phase III BEACON colorectal cancer study. J Clin Oncol. 2019;37(17):1460–9.
Article
Google Scholar
Pietrantonio F, Di Nicolantonio F, Schrock AB, Lee J, Tejpar S, Sartore-Bianchi A, et al. ALK, ROS1, and NTRK rearrangements in metastatic colorectal cancer. J Natl Cancer Inst. 2017. https://doi.org/10.1093/jnci/djx089.
Article
PubMed
Google Scholar
Pietrantonio F, Di Nicolantonio F, Schrock AB, Lee J, Morano F, Fucà G, et al. RET fusions in a small subset of advanced colorectal cancers at risk of being neglected. Ann Oncol. 2018;29(6):1394–401.
Article
CAS
Google Scholar
Hsiao SJ, Zehir A, Sireci AN, Aisner DL. Detection of tumor NTRK gene fusions to identify patients who may benefit from tyrosine kinase (TRK) inhibitor therapy. J Mol Diagn. 2019;21(4):553–71.
Article
CAS
Google Scholar
Lasota J, Chłopek M, Lamoureux J, Christiansen J, Kowalik A, Wasąg B, et al. Colonic Adenocarcinomas harboring NTRK fusion genes: a clinicopathologic and molecular genetic study of 16 cases and review of the literature. Am J Surg Pathol. 2020;44(2):162–73.
Article
Google Scholar
Gatalica Z, Xiu J, Swensen J, Vranic S. Molecular characterization of cancers with NTRK gene fusions. Mod Pathol. 2019;32(1):147–53.
Article
CAS
Google Scholar
Hechtman JF, Benayed R, Hyman DM, Drilon A, Zehir A, Frosina D, et al. Pan-Trk immunohistochemistry Is an efficient and reliable screen for the detection of NTRK fusions. Am J Surg Pathol. 2017;41(11):1547–51.
Article
Google Scholar
Ren H, Tan ZP, Zhu X, Crosby K, Haack H, Ren JM, et al. Identification of anaplastic lymphoma kinase as a potential therapeutic target in ovarian cancer. Cancer Res. 2012;72(13):3312–23.
Article
CAS
Google Scholar
Doebele RC, Pilling AB, Aisner DL, Kutateladze TG, Le AT, Weickhardt AJ, et al. Mechanisms of resistance to crizotinib in patients with ALK gene rearranged non-small cell lung cancer. Clin Cancer Res. 2012;18(5):1472–82.
Article
CAS
Google Scholar
Penzel R, Schirmacher P, Warth A. A novel EML4-ALK variant: exon 6 of EML4 fused to exon 19 of ALK. J Thorac Oncol. 2012;7(7):1198–9.
Article
CAS
Google Scholar
Lee SJ, Lee J, Park SH, Park JO, Lim HY, Kang WK, et al. c-MET overexpression in colorectal cancer: a poor prognostic factor for survival. Clin Colorectal Cancer. 2018;17(3):165–9.
Article
Google Scholar
Botton T, Talevich E, Mishra VK, Zhang T, Shain AH, Berquet C, et al. Genetic heterogeneity of BRAF fusion kinases in melanoma affects drug responses. Cell Rep. 2019;29(3):573-88.e7.
Article
CAS
Google Scholar
Grisham RN, Sylvester BE, Won H, McDermott G, DeLair D, Ramirez R, et al. Extreme outlier analysis identifies occult mitogen-activated protein kinase pathway mutations in patients with low-grade serous ovarian cancer. J Clin Oncol. 2015;33(34):4099–105.
Article
CAS
Google Scholar
Smorodinsky-Atias K, Soudah N, Engelberg D. Mutations that confer drug-resistance, oncogenicity and intrinsic activity on the ERK MAP kinases—current state of the art. Cells. 2020. https://doi.org/10.3390/cells9010129.
Article
PubMed
PubMed Central
Google Scholar
Arena S, Corti G, Durinikova E, Montone M, Reilly NM, Russo M, et al. A subset of colorectal cancers with cross-sensitivity to olaparib and oxaliplatin. Clin Cancer Res. 2020;26(6):1372–84.
Article
CAS
Google Scholar
Loree JM, Pereira AAL, Lam M, Willauer AN, Raghav K, Dasari A, et al. Classifying colorectal cancer by tumor location rather than sidedness highlights a continuum in mutation profiles and consensus molecular subtypes. Clin Cancer Res. 2018;24(5):1062–72.
Article
CAS
Google Scholar
Stintzing S, Tejpar S, Gibbs P, Thiebach L, Lenz HJ. Understanding the role of primary tumour localisation in colorectal cancer treatment and outcomes. Eur J Cancer. 2017;84:69–80.
Article
Google Scholar