title: Next-generation sequencing analysis of lung and colon carcinomas reveals a variety of genetic alterations.
abstract: The development of targeted therapies in cancer has accelerated the development of molecular diagnosis. This new cancer discipline is booming, with an increasing number of gene alterations to analyze in a growing number of patients. To deal with this fast-developing activity, current analysis techniques (Sanger sequencing, allelic discrimination and high resolution melting) take more and more time. In recent years, next generation sequencing (NGS) technologies have appeared and given new perspectives in oncology. In this study, we analyzed FFPE lung and colon carcinomas using the Truseq Cancer Panel, which analyzes the mutation hotspots of 48 genes. We also tested the use of whole-genome amplification before NGS analysis. NGS results were compared with the data obtained from routine diagnosis. All of the alterations routinely observed were identified by NGS. Moreover, NGS revealed mutations in the KRAS and EGFR genes in patients diagnosed as wild-type by routine techniques. NGS also identified concomitant mutations in EGFR and KRAS or BRAF mutations, and a 15-nt deletion in exon 19 of EGFR in colon carcinomas. The study of the other genes sequenced in the Panel revealed 14 genes altered by 27 different mutations and three SNP with a possible role in cancer susceptibility or in the response to treatment. In conclusion, this study showed that NGS analysis could be used for the analysis of gDNA extracted from FFPE tissues. However, given the high sensitivity of this technology, high-throughput clinical trials are needed to confirm its reliability for the molecular diagnosis of cancer.
authors.affiliation: Department of Biology and Pathology of Tumors, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: Sandy
authors.initials: S
authors.lastname: Chevrier
authors.affiliation: Department of Biology and Pathology of Tumors, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Arnould
authors.affiliation: Department of Medical Oncology, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: François
authors.initials: F
authors.lastname: Ghiringhelli
authors.affiliation: Department of Medical Oncology, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: Bruno
authors.initials: B
authors.lastname: Coudert
authors.affiliation: Department of Medical Oncology, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Fumoleau
authors.affiliation: Department of Biology and Pathology of Tumors, Centre Georges-François Leclerc, 21079 Dijon, France.
authors.forename: Romain
authors.initials: R
authors.lastname: Boidot
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D000368:Aged; D000369:Aged, 80 and over; D003110:Colonic Neoplasms / Q000235:genetics*; D066246:ErbB Receptors / Q000235:genetics; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D008875:Middle Aged; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D011518:Proto-Oncogene Proteins / Q000235:genetics; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras); D017422:Sequence Analysis, DNA / Q000379:methods*; D017384:Sequence Deletion; D018631:ras Proteins / Q000235:genetics
chemical_list: C117307:KRAS protein, human; D011518:Proto-Oncogene Proteins; C512478:EGFR protein, human; D066246:ErbB Receptors; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras); D018631:ras Proteins