Targeted RNA-sequencing for the evaluation of gene fusions in lung tumors: current status and future prospects

References

• Siemanowski J, Heydt C, Merkelbach-Bruse S. Predictive molecular pathology of lung cancer in Germany with focus on gene fusion testing: methods and quality assurance. Cancer Cytopathol. 2020 Sep;128(9):611–621. PubMed PMID: 32885916; eng.
   PubMed Web of Science ®Google Scholar
• Hong M, Tao S, Zhang L, et al. RNA sequencing: new technologies and applications in cancer research. J Hematol Oncol. 2020 Dec 4;13(1):166. PubMed PMID: 33276803; PubMed Central PMCID: PMCPMC7716291. eng.
   PubMed Web of Science ®Google Scholar
• Mosele F, Remon J, Mateo J, et al. Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO precision medicine working group. Ann Oncol. 2020 Nov;31(11):1491–1505. PubMed PMID: 32853681; eng.
   PubMed Web of Science ®Google Scholar
• Barr FG. Fusion genes in solid tumors: the possibilities and the pitfalls. Expert Rev Mol Diagn. 2016 Sep;16(9):921–923. PubMed PMID: 27550633; PubMed Central PMCID: PMCPMC6699740.
   PubMed Web of Science ®Google Scholar
• Heydt C, Ruesseler V, Pappesch R, et al. Comparison of in situ and extraction-based methods for the detection of ROS1 rearrangements in solid tumors. J Mol Diagn. 2019 Nov;21(6):971–984. PubMed PMID: 31382035.
   PubMed Web of Science ®Google Scholar
• Childress MA, Himmelberg SM, Chen H, et al. ALK fusion partners impact response to ALK inhibition: differential effects on sensitivity, cellular phenotypes, and biochemical properties. Mol Cancer Res. 2018 Nov;16(11):1724–1736. PubMed PMID: 30002191; PubMed Central PMCID: PMCPMC6214753.
   PubMed Web of Science ®Google Scholar
• De Luca A, Esposito Abate R, Rachiglio AM, et al. FGFR fusions in cancer: from diagnostic approaches to therapeutic intervention. Int J Mol Sci. 2020 Sep 18;21(18):6856. PubMed PMID: 32962091; PubMed Central PMCID: PMCPMC7555921. eng.
   Web of Science ®Google Scholar
• Schroder J, Kumar A, Wong SQ. Overview of fusion detection strategies using next-generation sequencing. Methods Mol Biol. 2019;1908:125–138. PubMed PMID: 30649725.
   PubMedGoogle Scholar
• Stengel A, Shahswar R, Haferlach T, et al. Whole transcriptome sequencing detects a large number of novel fusion transcripts in patients with AML and MDS. Blood Adv. 2020 Nov 10;4(21):5393–5401. PubMed PMID: 33147338; PubMed Central PMCID: PMCPMC7656918.
   PubMed Web of Science ®Google Scholar
• Heyer EE, Deveson IW, Wooi D, et al. Author correction: diagnosis of fusion genes using targeted RNA sequencing. Nat Commun. 2020 Apr 8;11(1):1810. PubMed PMID: 32269228; PubMed Central PMCID: PMCPMC7142116.
   PubMed Web of Science ®Google Scholar
• Davies KD, Lomboy A, Lawrence CA, et al. DNA-based versus RNA-based detection of MET Exon 14 skipping events in lung cancer. J Thorac Oncol. 2019 Apr;14(4):737–741. PubMed PMID: 30639620.
   PubMed Web of Science ®Google Scholar
• Heydt C, Wölwer CB, Velazquez Camacho O, et al. Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation. BMC Med Genomics. 2021 Feb 27;14(1):62. PubMed PMID: 33639937; PubMed Central PMCID: PMCPMC7912891. eng.
   PubMed Web of Science ®Google Scholar
• Wei H, Smith Z, Doh J, et al. Simultaneously DNA and RNA extraction from formalin-fixed paraffin embedded (FFPE) tissue. J Biomol Tech. 2019;30(Suppl):S37–S37. PubMed PMID: PMC6938039; eng.
   Google Scholar
• Kresse SH, Namløs HM, Lorenz S, et al. Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples. PloS One. 2018;13(5):e0197456.
   PubMed Web of Science ®Google Scholar
• Pennock ND, Jindal S, Horton W, et al. RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery. BMC Med Genomics. 2019 Dec 19;12(1):195.
   PubMed Web of Science ®Google Scholar
• Newton Y, Sedgewick AJ, Cisneros L, et al. Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Sci Rep. 2020 Oct 19;10(1):17597.
   PubMed Web of Science ®Google Scholar
• Esteve-Codina A, Arpi O, Martinez-García 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. PubMed PMID: 28122052; PubMed Central PMCID: PMCPMC5266269. eng.
   PubMed Web of Science ®Google Scholar
• Awad MM, Oxnard GR, Jackman DM, et al. MET Exon 14 mutations in non-small-cell lung cancer are associated with advanced age and stage-dependent MET genomic amplification and c-met overexpression. J Clin Oncol. 2016 Mar 1;34(7):721–730. PubMed PMID: 26729443; eng.
   PubMed Web of Science ®Google Scholar
• Frampton GM, Ali SM, Rosenzweig M, et al. Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. Cancer Discov. 2015 Aug 5;(8):850–859. DOI:10.1158/2159-8290.cd-15-0285. PubMed PMID: 25971938; eng.
   PubMed Web of Science ®Google Scholar
• Wolf J, Seto T, Han JY, et al. Capmatinib in MET Exon 14-mutated or MET-amplified non-small-cell lung cancer. N Engl J Med. 2020 Sep 3;383(10):944–957. PubMed PMID: 32877583; eng.
   PubMed Web of Science ®Google Scholar
• Montera M, Piaggio F, Marchese C, et al. A silent mutation in exon 14 of the APC gene is associated with exon skipping in a FAP family. J Med Genet. 2001 Dec;38(12):863–867. PubMed PMID: 11768390; PubMed Central PMCID: PMCPMC1734788. eng.
   PubMed Web of Science ®Google Scholar
• Wegert J, Vokuhl C, Collord G, et al. Recurrent intragenic rearrangements of EGFR and BRAF in soft tissue tumors of infants. Nat Commun. 2018 June 18;9(1):2378.
   PubMedGoogle Scholar
• Gallant JN, Sheehan JH, Shaver TM, et al. EGFR Kinase Domain Duplication (EGFR-KDD) is a novel oncogenic driver in lung cancer that is clinically responsive to afatinib. Cancer Discov. 2015 Nov 5;(11):1155–1163. DOI:10.1158/2159-8290.cd-15-0654. PubMed PMID: 26286086; PubMed Central PMCID: PMCPMC4631701. eng.
   PubMed Web of Science ®Google Scholar
• Rutkowska A, Stoczyńska-Fidelus E, Janik K, et al. EGFR(vIII): an oncogene with ambiguous role. J Oncol. 2019;2019:1092587. PubMed PMID: 32089685; PubMed Central PMCID: PMCPMC7024087 publication of this paper. eng
   PubMed Web of Science ®Google Scholar
• An Z, Aksoy O, Zheng T, et al. Epidermal growth factor receptor and EGFRvIII in glioblastoma: signaling pathways and targeted therapies. Oncogene. 2018 Mar;37(12):1561–1575. PubMed PMID: 29321659; PubMed Central PMCID: PMCPMC5860944. eng.
   PubMed Web of Science ®Google Scholar
• Lin JJ, Zhu VW, Yoda S, et al. Impact of EML4-ALK variant on resistance mechanisms and clinical outcomes in ALK-positive lung cancer. J Clin Oncol. 2018 Apr 20;36(12):1199–1206. PubMed PMID: 29373100; PubMed Central PMCID: PMCPMC5903999. eng.
   PubMed Web of Science ®Google Scholar
• Li Z, Shen L, Ding D, et al. Efficacy of crizotinib among different types of ROS1 fusion partners in patients with ros1-rearranged non-small cell lung cancer. J Thorac Oncol. 2018 Jul;13(7):987–995. PubMed PMID: 29704675; eng.
   PubMed Web of Science ®Google Scholar