Targeted next-generation sequencing for cancer-associated gene mutation and copy number detection in 206 patients with non–small-cell lung cancer

References

• Seigel R, Naishadham D, Jemal A. Cancer statistics, 2014. Ca Cancer J Clin. 2014;64(1):9–29.
   PubMed Web of Science ®Google Scholar
• Chen W, Zheng R, Baade PD, et al. Cancer statistics in China, 2015. CA Cancer J Clin. 2016;66(2):115–132.
   PubMed Web of Science ®Google Scholar
• Wang L, Zhao D, Qin K, et al. Effect and biomarker of Nivolumab for non-small-cell lung cancer. Biomed Pharmacother. 2019;117:109199.
   PubMed Web of Science ®Google Scholar
• Zappa C, Mousa SA. Non-small cell lung cancer: current treatment and future advances. Transl Lung Cancer Res. 2016;5(3):288–300.
   PubMed Web of Science ®Google Scholar
• Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31–46.
   PubMed Web of Science ®Google Scholar
• Han SW, Kim HP, Shin JY, et al. Targeted sequencing of cancer-related genes in colorectal cancer using next-generation sequencing. PLoS One. 2013;8(5):e64271.
   PubMed Web of Science ®Google Scholar
• Cai H, Jing C, Chang X, et al. Mutational landscape of gastric cancer and clinical application of genomic profiling based on target next-generation sequencing. J Transl Med. 2019;17(1):189.
   PubMed Web of Science ®Google Scholar
• Ng TS, Rajadurai P, Cheah YK. Molecular profiling of genetic alterations in selected non-small cell lung cancer. J Transdisciplin Biomed. 2017;1(1):47–52.
   Google Scholar
• Lee W, Jiang Z, Liu J, et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature. 2010;465(7297):473–477.
   PubMed Web of Science ®Google Scholar
• Hagemann IS, Devarakonda S, Lockwood CM, et al. Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer. 2015;121(4):631–639.
   PubMed Web of Science ®Google Scholar
• Araujo LH, Lammers PE, Matthews-Smith V, et al. Somatic mutation spectrum of non-small-cell lung cancer in African Americans: a pooled analysis. J Thorac Oncol. 2015;10(10):1430–1436.
   PubMed Web of Science ®Google Scholar
• Ding L, Getz G, Wheeler DA, et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature. 2008;455(7216):1069–1075.
   PubMed Web of Science ®Google Scholar
• Tsoulos N, Papadopoulou E, Metaxa-Mariatou V, et al. Tumor molecular profiling of NSCLC patients using next generation sequencing. Oncol Rep. 2017;38(6):3419–3429.
   PubMed Web of Science ®Google Scholar
• Wen S, Dai L, Wang L, et al. Genomic signature of driver genes identified by target next-generation sequencing in Chinese non-small cell lung cancer. The Oncologist. 2019;24(11):e1070–e1081.
   PubMed Web of Science ®Google Scholar
• Xiong D, Li G, Li K, et al. Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients. Carcinogenesis. 2012;33(9):1797–1805.
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–1760.
   PubMed Web of Science ®Google Scholar
• Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213–219.
   PubMed Web of Science ®Google Scholar
• Amarasinghe KC, Li J, Hunter SM, et al. Inferring copy number and genotype in tumour exome data. BMC Genomics. 2014;15(1):732.
   PubMedGoogle Scholar
• Xie C, Mao X, Huang J, et al. KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res. 2011;39( Web Server issue):W316–322.
   PubMed Web of Science ®Google Scholar
• Frank R, Scheffler M, Michels SYF, et al. KEAP1-mutations in patients with non-small cell lung cancer (NSCLC). J Clin Oncol. 2015;33(15_suppl):8097.
   Google Scholar
• Wong KM, Hudson TJ, McPherson JD. Unraveling the genetics of cancer: genome sequencing and beyond. Annu Rev Genomics Hum Genet. 2011;12(1):407–430.
   PubMed Web of Science ®Google Scholar
• Shajani-Yi Z, de Abreu FB, Peterson JD, et al. Frequency of somatic TP53 mutations in combination with known pathogenic mutations in colon adenocarcinoma, non-small cell lung carcinoma, and gliomas as identified by next-generation sequencing. Neoplasia. 2018;20(3):256–262.
   PubMed Web of Science ®Google Scholar
• Vavala T, Monica V, Lo Iacono M, et al. Precision medicine in age-specific non-small-cell-lung-cancer patients: integrating biomolecular results into clinical practice-a new approach to improve personalized translational research. Lung Cancer. 2017;107:84–90.
   PubMed Web of Science ®Google Scholar
• Hainaut P, Olivier M, Pfeifer GP. TP53 mutation spectrum in lung cancers and mutagenic signature of components of tobacco smoke: lessons from the IARC TP53 mutation database. Mutagenesis. 2001;16(6):551–553. author reply 555-556.
   PubMed Web of Science ®Google Scholar
• Li S, Li L, Zhu Y, et al. Coexistence of EGFR with KRAS, or BRAF, or PIK3CA somatic mutations in lung cancer: a comprehensive mutation profiling from 5125 Chinese cohorts. Br J Cancer. 2014;110(11):2812–2820.
   PubMed Web of Science ®Google Scholar
• Rosell R, Moran T, Queralt C, et al. Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med. 2009;361(10):958–967.
   PubMed Web of Science ®Google Scholar
• Xu J, He J, Yang H, et al. Somatic mutation analysis of EGFR, KRAS, BRAF and PIK3CA in 861 patients with non-small cell lung cancer. Cancer Biomark. 2011;10(2):63–69.
   PubMed Web of Science ®Google Scholar
• Maemondo M, Inoue A, Kobayashi K, et al. Gefitinib or chemotherapy for non-small-cell lung cancer with mutated EGFR. N Engl J Med. 2010;362(25):2380–2388.
   PubMed Web of Science ®Google Scholar
• Mitsudomi T, Morita S, Yatabe Y, et al. Gefitinib versus cisplatin plus docetaxel in patients with non-small-cell lung cancer harbouring mutations of the epidermal growth factor receptor (WJTOG3405): an open label, randomised phase 3 trial. Lancet Oncol. 2010;11(2):121–128.
   PubMed Web of Science ®Google Scholar
• Shi Y, Au JS, Thongprasert S, et al. A prospective, molecular epidemiology study of EGFR mutations in Asian patients with advanced non-small-cell lung cancer of adenocarcinoma histology (PIONEER). J Thorac Oncol. 2014;9(2):154–162.
   PubMed Web of Science ®Google Scholar
• Labbé C, Cabanero M, Korpanty GJ, et al. Prognostic and predictive effects of TP53 co-mutation in patients with EGFR-mutated non-small cell lung cancer (NSCLC). Lung Cancer. 2017;111:23–29.
   PubMed Web of Science ®Google Scholar
• Wang R, Zhang Y, Pan Y, et al. Comprehensive investigation of oncogenic driver mutations in Chinese non-small cell lung cancer patients. Oncotarget. 2015;6(33):34300–34308.
   PubMedGoogle Scholar
• Wang J, Li C, Wan F, et al. The rs1550117 A>G variant in DNMT3A gene promoter significantly increases non-small cell lung cancer susceptibility in a Han Chinese population. Oncotarget. 2017;8(14):23470–23478.
   PubMedGoogle Scholar
• Yang B, Li J, Li F, et al. Comprehensive analysis of age-related somatic mutation profiles in Chinese young lung adenocarcinoma patients. Cancer Med. 2019;8(4):1350–1358.
   PubMed Web of Science ®Google Scholar
• Zhou Q, Peng X, Wang W, et al. P2. 04-20 TP53/KMT2C co-mutation as a novel biomarker for immunotherapy in non-small cell lung cancer patients. J Thoracic Oncol. 2019;14(10):S716.
   Google Scholar
• Lee T, Lee B, Choi YL, et al. Non-small cell lung cancer with concomitant EGFR, KRAS, and ALK mutation: clinicopathologic features of 12 cases. J Pathol Transl Med. 2016;50(3):197–203.
   PubMed Web of Science ®Google Scholar
• Jabs V, Edlund K, Konig H, et al. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer. PLoS One. 2017;12(11):e0187246.
   PubMed Web of Science ®Google Scholar
• Zhu XH, Tian J. The expression of BCL6 co-inhibitory factor-like protein 1 in the tissues of elderly patients with non-small cell lung cancer and its effect on long-term prognosis. Chin J Gerontol. 2018;12:27.
   Google Scholar
• Bechara EG, Sebestyen E, Bernardis I, et al. RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Mol Cell. 2013;52(5):720–733.
   PubMed Web of Science ®Google Scholar
• Yuan X, Wu H, Xu H, et al. Meta-analysis reveals the correlation of Notch signaling with non-small cell lung cancer progression and prognosis. Sci Rep. 2015;5(1):10338.
   PubMed Web of Science ®Google Scholar
• Galluzzo P, Bocchetta M. Notch signaling in lung cancer. Expert Rev Anticancer Ther. 2011;11(4):533–540.
   PubMed Web of Science ®Google Scholar
• Zhang C, Lan T, Hou J, et al. NOX4 promotes non-small cell lung cancer cell proliferation and metastasis through positive feedback regulation of PI3K/Akt signaling. Oncotarget. 2014;5(12):4392–4405.
   PubMedGoogle Scholar
• Lai S, Wang G, Cao X, et al. EMP-1 promotes tumorigenesis of NSCLC through PI3K/AKT pathway. J Huazhong Univ Sci Technolog Med Sci. 2012;32(6):834–838.
   PubMedGoogle Scholar
• Zhang X, Tang N, Hadden TJ, et al. Akt, FoxO and regulation of apoptosis. Biochim Biophys Acta. 2011;1813(11):1978–1986.
   PubMed Web of Science ®Google Scholar
• Chen G, Yu L, Dong H, et al. MiR‐182 enhances radioresistance in non‐small cell lung cancer cells by regulating FOXO 3. Clin Exp Pharmacol Physiol. 2019;46(2):137–143.
   PubMed Web of Science ®Google Scholar
• Liu H, Zhou BH, Qiu X, et al. T63, a new 4-arylidene curcumin analogue, induces cell cycle arrest and apoptosis through activation of the reactive oxygen species-FOXO3a pathway in lung cancer cells. Free Radic Biol Med. 2012;53(12):2204–2217.
   PubMed Web of Science ®Google Scholar
• Wu D, Zhao B, Qi X, et al. Nogo-B receptor promotes epithelial-mesenchymal transition in non-small cell lung cancer cells through the Ras/ERK/Snail1 pathway. Cancer Lett. 2018;418:135–146.
   PubMed Web of Science ®Google Scholar
• Zheng G, Shen Z, Chen H, et al. Metapristone suppresses non-small cell lung cancer proliferation and metastasis via modulating RAS/RAF/MEK/MAPK signaling pathway. Biomed Pharmacother. 2017;90:437–445.
   PubMed Web of Science ®Google Scholar
• Sun W, Ping W, Tian Y, et al. MiR-202 enhances the anti-tumor effect of cisplatin on non-small cell lung cancer by targeting the Ras/MAPK pathway. Cell Physiol Biochem. 2018;51(5):2160–2171.
   PubMedGoogle Scholar