title: Comprehensive profiling and quantitation of oncogenic mutations in non small-cell lung carcinoma using single molecule amplification and re-sequencing technology.
abstract: Activating and resistance mutations in the tyrosine kinase domain of several oncogenes are frequently associated with non-small cell lung carcinoma (NSCLC). In this study we assessed the frequency, type and abundance of EGFR, KRAS, BRAF, TP53 and ALK mutations in tumour specimens from 184 patients with early and late stage disease using single molecule amplification and re-sequencing technology (SMART). Based on modelling of EGFR mutations, the detection sensitivity of the SMART assay was at least 0.1%. Benchmarking EGFR mutation detection against the gold standard ARMS-PCR assay, SMART assay had a sensitivity and specificity of 98.7% and 99.0%. Amongst the 184 samples, EGFR mutations were the most prevalent (59.9%), followed by KRAS (16.9%), TP53 (12.7%), EML4-ALK fusions (6.3%) and BRAF (4.2%) mutations. The abundance and types of mutations in tumour specimens were extremely heterogeneous, involving either monoclonal (51.6%) or polyclonal (12.6%) mutation events. At the clinical level, although the spectrum of tumour mutation(s) was unique to each patient, the overall patterns in early or advanced stage disease were relatively similar. Based on these findings, we propose that personalized profiling and quantitation of clinically significant oncogenic mutations will allow better classification of patients according to tumour characteristics and provide clinicians with important ancillary information for treatment decision-making.
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Shirong
authors.initials: S
authors.lastname: Zhang
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Xia
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Jiang
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Limin
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Rujun
authors.initials: R
authors.lastname: Xu
authors.affiliation: Berry Genomics Corporation, Beijing 100015, China.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Shi
authors.affiliation: Berry Genomics Corporation, Beijing 100015, China.
authors.forename: Jianguang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Berry Genomics Corporation, Beijing 100015, China.
authors.forename: Mengnan
authors.initials: M
authors.lastname: Xu
authors.affiliation: Berry Genomics Corporation, Beijing 100015, China.
authors.forename: David S
authors.initials: DS
authors.lastname: Cram
authors.affiliation: Department of Oncology, Hangzhou First People's Hospital, Nanjing Medical University, Zhejiang, Hangzhou 310006, China.
authors.forename: Shenglin
authors.initials: S
authors.lastname: Ma
mesh_terms: D000368:Aged; D000077548:Anaplastic Lymphoma Kinase; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics* / Q000378:metabolism; D004252:DNA Mutational Analysis; D020000:Decision Support Systems, Clinical; D066246:ErbB Receptors / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics* / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D009154:Mutation; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D016896:Treatment Outcome; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: C117307:KRAS protein, human; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; C512478:EGFR protein, human; D066246:ErbB Receptors; D020794:Receptor Protein-Tyrosine Kinases; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras)
keywords: allele-specific amplification refractory mutation system; non small-cell lung carcinoma; oncogenic mutations; single molecule amplification and re-sequencing technology