1
|
Kallioniemi OP, Kallioniemi A, Kurisu W, Thor A, Chen LC, Smith HS, Waldman FM, Pinkel D and Gray JW: ERBB2 amplification in breast cancer analyzed by fluorescence in situ hybridization. Proc Natl Acad Sci USA. 89:5321–5325. 1992. View Article : Google Scholar : PubMed/NCBI
|
2
|
Marks JL, Broderick S, Zhou Q, Chitale D, Li AR, Zakowski MF, Kris MG, Rusch VW, Azzoli CG, Seshan VE, et al: Prognostic and therapeutic implications of EGFR and KRAS mutations in resected lung adenocarcinoma. J Thorac Oncol. 3:111–116. 2008. View Article : Google Scholar : PubMed/NCBI
|
3
|
Choi YL, Soda M, Yamashita Y, Ueno T, Takashima J, Nakajima T, Yatabe Y, Takeuchi K, Hamada T, Haruta H, et al: EML4-ALK mutations in lung cancer that confer resistance to ALK inhibitors. N Engl J Med. 363:1734–1739. 2010. View Article : Google Scholar : PubMed/NCBI
|
4
|
Nguyen-Ngoc T, Bouchaab H, Adjei AA and Peters S: BRAF alterations as therapeutic targets in non-small-cell lung cancer. J Thorac Oncol. 10:1396–1403. 2015. View Article : Google Scholar : PubMed/NCBI
|
5
|
Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, et al: Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med. 350:2129–2139. 2004. View Article : Google Scholar : PubMed/NCBI
|
6
|
Chuang JC, Stehr H, Liang Y, Das M, Huang J, Diehn M, Wakelee HA and Neal JW: ERBB2-Mutated metastatic non-small cell lung cancer: Response and resistance to targeted therapies. J Thorac Oncol. 12:833–842. 2017. View Article : Google Scholar : PubMed/NCBI
|
7
|
Skoulidis F, Li BT, Dy GK, Price TJ, Falchook GS, Wolf J, Italiano A, Schuler M, Borghaei H, Barlesi F, et al: Sotorasib for lung cancers with KRAS G12C mutation. N Engl J Med. 384:2371–2381. 2021. View Article : Google Scholar : PubMed/NCBI
|
8
|
Wolf J, Seto T, Han JY, Reguart N, Garon EB, Groen HJM, Tan DSW, Hida T, de Jonge M, Orlov SV, et al: Capmatinib in MET Exon 14-Mutated or MET-Amplified non-small-cell lung cancer. N Engl J Med. 383:944–957. 2020. View Article : Google Scholar : PubMed/NCBI
|
9
|
Sanz-Garcia E, Argiles G, Elez E and Tabernero J: BRAF mutant colorectal cancer: Prognosis, treatment, and new perspectives. Ann Oncol. 28:2648–2657. 2017. View Article : Google Scholar : PubMed/NCBI
|
10
|
Karapetis CS, Khambata-Ford S, Jonker DJ, O'Callaghan CJ, Tu D, Tebbutt NC, Simes RJ, Chalchal H, Shapiro JD, Robitaille S, et al: K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med. 359:1757–1765. 2008. View Article : Google Scholar : PubMed/NCBI
|
11
|
Douillard JY, Oliner KS, Siena S, Tabernero J, Burkes R, Barugel M, Humblet Y, Bodoky G, Cunningham D, Jassem J, et al: Panitumumab-FOLFOX4 treatment and RAS mutations in colorectal cancer. N Engl J Med. 369:1023–1034. 2013. View Article : Google Scholar : PubMed/NCBI
|
12
|
Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, O'Dwyer PJ, Lee RJ, Grippo JF, Nolop K and Chapman PB: Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med. 363:809–819. 2010. View Article : Google Scholar : PubMed/NCBI
|
13
|
Carvajal RD, Antonescu CR, Wolchok JD, Chapman PB, Roman RA, Teitcher J, Panageas KS, Busam KJ, Chmielowski B, Lutzky J, et al: KIT as a therapeutic target in metastatic melanoma. JAMA. 305:2327–2334. 2011. View Article : Google Scholar : PubMed/NCBI
|
14
|
Johnson DB and Puzanov I: Treatment of NRAS-mutant melanoma. Curr Treat Options Oncol. 16:152015. View Article : Google Scholar : PubMed/NCBI
|
15
|
Lasota J and Miettinen M: KIT and PDGFRA mutations in gastrointestinal stromal tumors (GISTs). Semin Diagn Pathol. 23:91–102. 2006. View Article : Google Scholar : PubMed/NCBI
|
16
|
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM and Sirotkin K: dbSNP: The NCBI database of genetic variation. Nucleic Acids Res. 29:308–311. 2001. View Article : Google Scholar :
|
17
|
Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 1303.3997v2. 2013.
|
18
|
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M and DePristo MA: The genome analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20:1297–1303. 2010. View Article : Google Scholar : PubMed/NCBI
|
19
|
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, et al: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 43:491–498. 2011. View Article : Google Scholar : PubMed/NCBI
|
20
|
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, et al: From FastQ data to high confidence variant calls: The genome analysis toolkit best practices pipeline. Curr Protoc Bioinformatics. 43:11 10 11–11 10 33. 2013.
|
21
|
Toolkit Picard: Broad Institute, GitHub Repository. 2019, https://broadinstitute.github.io/picard/.
|
22
|
Muller E, Goardon N, Brault B, Rousselin A, Paimparay G, Legros A, Fouillet R, Bruet O, Tranchant A, Domin F, et al: OutLyzer: Software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Oncotarget. 7:79485–79493. 2016. View Article : Google Scholar : PubMed/NCBI
|
23
|
Wang K, Li M and Hakonarson H: ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38:e1642010. View Article : Google Scholar : PubMed/NCBI
|
24
|
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X and Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 6:80–92. 2012. View Article : Google Scholar
|
25
|
Andrews S: FastQC: A quality control tool for high thoughput sequence data. 2010, http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
|
26
|
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G and Durbin R: 1000 Genome Project Data Processing Subgroup: The sequence alignment/map format and SAMtools. Bioinformatics. 25:2078–2079. 2009. View Article : Google Scholar : PubMed/NCBI
|
27
|
Okonechnikov K, Conesa A and Garcia-Alcalde F: Qualimap 2: Advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics. 32:292–294. 2016.
|
28
|
Ewels P, Magnusson M, Lundin S and Kaller M: MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 32:3047–3048. 2016. View Article : Google Scholar : PubMed/NCBI
|
29
|
Boidot R, Végran F and Ghiringhelli F: Detection method of somatic genetic anomalies, combination of capture probes and kit of detection. EP3553182. Filed April 11, 2018 issued October 16, 2019.
|
30
|
Jennings LJ, Arcila ME, Corless C, Kamel-Reid S, Lubin IM, Pfeifer J, Temple-Smolkin RL, Voelkerding KV and Nikiforova MN: Guidelines for validation of next-generation sequencing-based oncology panels: A joint consensus recommendation of the association for molecular pathology and college of american pathologists. J Mol Diagn. 19:341–365. 2017. View Article : Google Scholar : PubMed/NCBI
|
31
|
Papadopoulou E, Tsoulos N, Tsantikidi K, Metaxa-Mariatou V, Stamou PE, Kladi-Skandali A, Kapeni E, Tsaousis G, Pentheroudakis G, Petrakis D, et al: Clinical feasibility of NGS liquid biopsy analysis in NSCLC patients. PLoS One. 14:e02268532019. View Article : Google Scholar : PubMed/NCBI
|
32
|
Esagian SM, Grigoriadou GI, Nikas IP, Boikou V, Sadow PM, Won JK and Economopoulos KP: Comparison of liquid-based to tissue-based biopsy analysis by targeted next generation sequencing in advanced non-small cell lung cancer: A comprehensive systematic review. J Cancer Res Clin Oncol. 146:2051–2066. 2020. View Article : Google Scholar : PubMed/NCBI
|
33
|
Garcia J, Kamps-Hughes N, Geiguer F, Couraud S, Sarver B, Payen L and Ionescu-Zanetti C: Sensitivity, specificity, and accuracy of a liquid biopsy approach utilizing molecular amplification pools. Sci Rep. 11:107612021. View Article : Google Scholar : PubMed/NCBI
|
34
|
Shen WD, Chen HL and Liu PF: EGFR gene copy number as a predictive biomarker for resistance to anti-EGFR mono-clonal antibodies in metastatic colorectal cancer treatment: A meta-analysis. Chin J Cancer Res. 26:59–71. 2014.PubMed/NCBI
|
35
|
Bahcall M, Awad MM, Sholl LM, Wilson FH, Xu M, Wang S, Palakurthi S, Choi J, Ivanova EV, Leonardi GC, et al: Amplification of Wild-type KRAS imparts resistance to crizotinib in MET exon 14 mutant non-small cell lung cancer. Clin Cancer Res. 24:5963–5976. 2018. View Article : Google Scholar : PubMed/NCBI
|
36
|
Randon G, Yaeger R, Hechtman JF, Manca P, Fucà G, Walch H, Lee J, Élez E, Seligmann J, Mussolin B, et al: EGFR amplification in metastatic colorectal cancer. J Natl Cancer Inst. 113:1561–1569. 2021. View Article : Google Scholar : PubMed/NCBI
|
37
|
Suryavanshi M, Shah A, Kumar D, Panigrahi MK, Metha A and Batra U: MET amplification and response to MET inhibitors in stage IV lung adenocarcinoma. Oncol Res Treat. 40:198–202. 2017. View Article : Google Scholar : PubMed/NCBI
|
38
|
Chen D, Zhang LQ, Huang JF, Liu K, Chuai ZR, Yang Z, Wang YX, Shi DC, Liu Q, Huang Q and Fu WL: BRAF mutations in patients with non-small cell lung cancer: A systematic review and meta-analysis. PLoS One. 9:e1013542014. View Article : Google Scholar : PubMed/NCBI
|
39
|
Lohinai Z, Klikovits T, Moldvay J, Ostoros G, Raso E, Timar J, Fabian K, Kovalszky I, Kenessey I, Aigner C, et al: KRAS-mutation incidence and prognostic value are metastatic site-specific in lung adenocarcinoma: Poor prognosis in patients with KRAS mutation and bone metastasis. Sci Rep. 7:397212017. View Article : Google Scholar : PubMed/NCBI
|
40
|
Arcila ME, Drilon A, Sylvester BE, Lovly CM, Borsu L, Reva B, Kris MG, Solit DB and Ladanyi M: MAP2K1 (MEK1) mutations define a distinct subset of lung adenocarcinoma associated with smoking. Clin Cancer Res. 21:1935–1943. 2015. View Article : Google Scholar :
|
41
|
Barlesi F, Mazieres J, Merlio JP, Debieuvre D, Mosser J, Lena H, Ouafik L, Besse B, Rouquette I, Westeel V, et al: Routine molecular profiling of patients with advanced non-small-cell lung cancer: Results of a 1-year nationwide programme of the French cooperative thoracic intergroup (IFCT). Lancet. 387:1415–1426. 2016. View Article : Google Scholar : PubMed/NCBI
|
42
|
Zhang YL, Yuan JQ, Wang KF, Fu XH, Han XR, Threapleton D, Yang ZY, Mao C and Tang JL: The prevalence of EGFR mutation in patients with non-small cell lung cancer: A systematic review and meta-analysis. Oncotarget. 7:78985–78993. 2016. View Article : Google Scholar : PubMed/NCBI
|
43
|
Bellio H, Fumet JD and Ghiringhelli F: Targeting BRAF and RAS in colorectal cancer. Cancers (Basel). 13:22012021. View Article : Google Scholar
|
44
|
Chuang J, Wang C, Guo Y, Valenzuela V, Wu J and Fakih M: MAP2K1 mutations in advanced colorectal cancer predict poor response to anti-EGFR therapy and to vertical targeting of MAPK pathway. Clin Colorectal Cancer. 20:72–78. 2021. View Article : Google Scholar : PubMed/NCBI
|
45
|
Ross JS, Fakih M, Ali SM, Elvin JA, Schrock AB, Suh J, Vergilio JA, Ramkissoon S, Severson E, Daniel S, et al: Targeting HER2 in colorectal cancer: The landscape of amplification and short variant mutations in ERBB2 and ERBB3. Cancer. 124:1358–1373. 2018. View Article : Google Scholar : PubMed/NCBI
|
46
|
Gutierrez-Castaneda LD, Nova JA and Tovar-Parra JD: Frequency of mutations in BRAF, NRAS, and KIT in different populations and histological subtypes of melanoma: A systemic review. Melanoma Res. 30:62–70. 2020. View Article : Google Scholar :
|
47
|
Mei L, Smith SC, Faber AC, Trent J, Grossman SR, Stratakis CA and Boikos SA: Gastrointestinal stromal tumors: The GIST of precision medicine. Trends Cancer. 4:74–91. 2018. View Article : Google Scholar : PubMed/NCBI
|
48
|
Heinrich MC, Corless CL, Duensing A, McGreevey L, Chen CJ, Joseph N, Singer S, Griffith DJ, Haley A, Town A, et al: PDGFRA activating mutations in gastrointestinal stromal tumors. Science. 299:708–710. 2003. View Article : Google Scholar : PubMed/NCBI
|
49
|
Sen B, Peng S, Tang X, Erickson HS, Galindo H, Mazumdar T, Stewart DJ, Wistuba I and Johnson FM: Kinase-impaired BRAF mutations in lung cancer confer sensitivity to dasatinib. Sci Transl Med. 4:136ra702012. View Article : Google Scholar : PubMed/NCBI
|
50
|
Robert NJ, Nwokeji ED, Espirito JL, Chen L, Karhade M, Evangelist MC, Spira AI, Neubauer MA, Bullock SA, Coleman RL, et al: Biomarker tissue journey among patients (pts) with untreated metastatic non-small cell lung cancer (mNSCLC) in the U.S. Oncology Network community practices. J Clin Oncol. 39(Suppl 15)9004:2021. View Article : Google Scholar
|