Progress and potential of RAS mutation detection for diagnostics and companion diagnostics

References

• Su Y-H, Wang M, Brenner DE, et al. Detection of mutated K-ras DNA in urine, plasma, and serum of patients with colorectal carcinoma or adenomatous polyps. Ann NY Acad Sci. 2008;1137:197–206.
   PubMed Web of Science ®Google Scholar
• Mulcahy H, Farthing MJ. Diagnosis of pancreatico-biliary malignancy: detection of gene mutations in plasma and stool. Ann Oncol Off J Eur Soc Med Oncol /ESMO. 1999;10(Suppl 4):114–117.
   PubMed Web of Science ®Google Scholar
• Diehl F, Schmidt K, Durkee KH, et al. Analysis of mutations in DNA isolated from plasma and stool of colorectal cancer patients. Gastroenterology. 2008;135(2):489–498.
   PubMed Web of Science ®Google Scholar
• De Kok JB, Van Solinge WW, Ruers TJ, et al. Detection of tumour DNA in serum of colorectal cancer patients. Scand J Clin Lab Invest. 1997;57(7):601–604.
   PubMed Web of Science ®Google Scholar
• Sorich MJ, Wiese MD, Rowland A, et al. Extended RAS mutations and anti-EGFR monoclonal antibody survival benefit in metastatic colorectal cancer: a meta-analysis of randomized, controlled trials. Ann Oncol Off J Eur Soc Med Oncol/ESMO. 2015;26(1):13–21.
   PubMed Web of Science ®Google Scholar
• Therkildsen C, Bergmann TK, Henrichsen-Schnack T, et al. The predictive value of KRAS, NRAS, BRAF, PIK3CA and PTEN for anti-EGFR treatment in metastatic colorectal cancer: a systematic review and meta-analysis. Acta Oncol. 2014;53(7):852–864.
   Web of Science ®Google Scholar
• Benvenuti S, Sartore-Bianchi A, Di Nicolantonio F, et al. Oncogenic activation of the RAS/RAF signaling pathway impairs the response of metastatic colorectal cancers to anti-epidermal growth factor receptor antibody therapies. Cancer Res. 2007;67(6):2643–2648.
   PubMed Web of Science ®Google Scholar
• Prior IA, Hancock JF. Ras trafficking, localization and compartmentalized signalling. Semin Cell Dev Biol. 2012;23(2):145–153.
   PubMed Web of Science ®Google Scholar
• Wang JY, Hsieh JS, Chang MY, et al. Molecular detection of APC, K- ras, and p53 mutations in the serum of colorectal cancer patients as circulating biomarkers. World J Surg. 2004;28(7):721–726.
   PubMed Web of Science ®Google Scholar
• Thierry AR. A targeted Q-PCR-based method for point mutation testing by analyzing circulating DNA for cancer management care. Methods Mol Biol (Clifton, NJ). 2016;1392:1–16.
   PubMedGoogle Scholar
• Siena S, Sartore-Bianchi A, Di Nicolantonio F, et al. Biomarkers predicting clinical outcome of epidermal growth factor receptor-targeted therapy in metastatic colorectal cancer. J Natl Cancer Inst. 2009;101(19):1308–1324.
   PubMedGoogle Scholar
• Young EC, Owens MM, Adebiyi I, et al. A comparison of methods for EGFR mutation testing in non-small cell lung cancer. Diagn Mol Pathol Am J Surg Pathol B. 2013;22(4):190–195.
   PubMedGoogle Scholar
• Froyen G, Broekmans A, Hillen F, et al. Validation and application of a custom-designed targeted next-generation sequencing panel for the diagnostic mutational profiling of solid tumors. Plos One. 2016;11(4):e0154038.
   Web of Science ®Google Scholar
• Siroy AE, Boland GM, Milton DR, et al. Beyond BRAF(V600): clinical mutation panel testing by next-generation sequencing in advanced melanoma. J Invest Dermatol. 2015;135(2):508–515.
   PubMed Web of Science ®Google Scholar
• Dutton-Regester K, Irwin D, Hunt P, et al. A high-throughput panel for identifying clinically relevant mutation profiles in melanoma. Mol Cancer Ther. 2012;11(4):888–897.
   PubMed Web of Science ®Google Scholar
• Wilson MA, Zhao F, Letrero R, et al. Correlation of somatic mutations and clinical outcome in melanoma patients treated with Carboplatin, Paclitaxel, and sorafenib. Clin Cancer Res Off J Am Assoc Cancer Res. 2014;20(12):3328–3337.
   PubMed Web of Science ®Google Scholar
• Carlino MS, Haydu LE, Kakavand H, et al. Correlation of BRAF and NRAS mutation status with outcome, site of distant metastasis and response to chemotherapy in metastatic melanoma. Br J Cancer. 2014;111(2):292–299.
   PubMed Web of Science ®Google Scholar
• Siravegna G, Mussolin B, Buscarino M, et al. Clonal evolution and resistance to EGFR blockade in the blood of colorectal cancer patients. Nat Med. 2015;21(7):795–801.
   PubMed Web of Science ®Google Scholar
• Morelli MP, Overman MJ, Dasari A, et al. Characterizing the patterns of clonal selection in circulating tumor DNA from patients with colorectal cancer refractory to anti-EGFR treatment. Ann Oncol Off J Eur Soc Med Oncol /ESMO. 2015;26(4):731–736.
   PubMed Web of Science ®Google Scholar
• Allegra CJ, Rumble RB, Hamilton SR, et al. Extended RAS gene mutation testing in metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy: American Society of Clinical Oncology Provisional Clinical Opinion Update 2015. J Clin Oncol Off J Am Soc Clin Oncol. 2016;34(2):179–185.
   PubMed Web of Science ®Google Scholar
• Perrone F, Lampis A, Bertan C, et al. Circulating free DNA in a screening program for early colorectal cancer detection. Tumori. 2014;100(2):115–121.
   PubMed Web of Science ®Google Scholar
• Imperiale TF, Ransohoff DF, Itzkowitz SH, et al. Multitarget stool DNA testing for colorectal-cancer screening. N Engl J Med. 2014;370(14):1287–1297.
   PubMed Web of Science ®Google Scholar
• Sidransky D, Tokino T, Hamilton SR, et al. Identification of ras oncogene mutations in the stool of patients with curable colorectal tumors. Science. 1992;256(5053):102–105.
   PubMed Web of Science ®Google Scholar
• Mead R, Duku M, Bhandari P, et al. Circulating tumour markers can define patients with normal colons, benign polyps, and cancers. Br J Cancer. 2011;105(2):239–245.
   PubMed Web of Science ®Google Scholar
• Cree IA. Liquid biopsy for cancer patients: principles and practice. Pathogenesis. 2015;2(1–2):1–4.
   Google Scholar
• Gonzalez De Castro D, Angulo B, Gomez B, et al. A comparison of three methods for detecting KRAS mutations in formalin-fixed colorectal cancer specimens. Br J Cancer. 2012;107(2):345–351.
   PubMed Web of Science ®Google Scholar
• Tops B, Normanno N, Kurth H, et al. Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium. BMC Cancer. 2015;15(1):26.
   PubMed Web of Science ®Google Scholar
• Bolton L, Reiman A, Lucas K, et al. KRAS mutation analysis by PCR: a comparison of two methods. Plos One. 2015;10(1):e0115672.
   Web of Science ®Google Scholar
• Whitehall V, Tran K, Umapathy A, et al. A multicenter blinded study to evaluate KRAS mutation testing methodologies in the clinical setting. JMD. 2009;11(6):543–552.
   PubMed Web of Science ®Google Scholar
• Dijkstra JR, Heideman DA, Meijer GA, et al. KRAS mutation analysis on low percentage of colon cancer cells: the importance of quality assurance. Virchows Arch Int J Pathol. 2013;462(1):39–46.
   PubMed Web of Science ®Google Scholar
• Bando I, Cillero L, Sanz-Ortega J, et al. Study of KRAS new predictive marker in a clinical laboratory. Clin Transll Onco Off Publ Fed Spanish Oncol Soc Natl Cancer Inst Mexico. 2012;14(12):937–942.
   Google Scholar
• Cree IA, Deans Z, Ligtenberg MJ, et al. Guidance for laboratories performing molecular pathology for cancer patients. J Clin Pathol. 2014;67(11):923–931.
   PubMed Web of Science ®Google Scholar
• Cree IA. Diagnostic RAS mutation analysis by polymerase chain reaction (PCR). Biomol Detect Quantif. 2016;8:29–32.
   PubMedGoogle Scholar
• Kikuchi HRA, Nyoni J, Lloyd K, et al. Development and validation of a TaqMan array for cancer mutation analysis. Pathogenesis. 2016;3(1):1–8.
   Google Scholar
• Price TJ, Bruhn MA, Lee CK, et al. Correlation of extended RAS and PIK3CA gene mutation status with outcomes from the phase III AGITG MAX STUDY involving capecitabine alone or in combination with bevacizumab plus or minus mitomycin C in advanced colorectal cancer. Br J Cancer. 2015;112(6):963–970.
   PubMed Web of Science ®Google Scholar
• Tsiatis AC, Norris-Kirby A, Rich RG, et al. Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implications. JMD. 2010;12(4):425–432.
   PubMed Web of Science ®Google Scholar
• Altimari A, De Biase D, De Maglio G, et al. 454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples. Oncotargets Therapy. 2013;6:1057–1064.
   PubMed Web of Science ®Google Scholar
• Vakiani E, Janakiraman M, Shen R, et al. Comparative genomic analysis of primary versus metastatic colorectal carcinomas. J Clin Oncol Off J Am Soc Clin Oncol. 2012;30(24):2956–2962.
   PubMed Web of Science ®Google Scholar
• Rechsteiner M, Von Teichman A, Ruschoff JH, et al. KRAS, BRAF, and TP53 deep sequencing for colorectal carcinoma patient diagnostics. JMD. 2013;15(3):299–311.
   PubMed Web of Science ®Google Scholar
• Kothari N, Schell MJ, Teer JK, et al. Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing. J Clin Pathol. 2014;67(9):764–767.
   PubMed Web of Science ®Google Scholar
• Milbury CA, Correll M, Quackenbush J, et al. COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing. Clin Chem. 2012;58(3):580–589.
   PubMed Web of Science ®Google Scholar
• Piton N, Borrini F, Bolognese A, et al. KRAS and BRAF mutation detection: is immunohistochemistry a possible alternative to molecular biology in colorectal cancer? Gastroenterol Res Pract. 2015;2015:753903.
   PubMed Web of Science ®Google Scholar
• Uguen A, Gueguen P, Legoupil D, et al. Dual NRASQ61R and BRAFV600E mutation-specific immunohistochemistry completes molecular screening in melanoma samples in a routine practice. Hum Pathol. 2015;46(11):1582–1591.
   PubMed Web of Science ®Google Scholar
• Thiel A, Moza M, Kytola S, et al. Prospective immunohistochemical analysis of BRAF V600E mutation in melanoma. Human Pathology. 2015;46(2):169–175.
   PubMed Web of Science ®Google Scholar
• Dijkstra JR, Tops BB, Nagtegaal ID, et al. The homogeneous mutation status of a 22 gene panel justifies the use of serial sections of colorectal cancer tissue for external quality assessment. Virchows Arch Int J Pathol. 2015;467(3):273–278.
   PubMed Web of Science ®Google Scholar
• Normanno N, Rachiglio AM, Lambiase M, et al. Heterogeneity of KRAS, NRAS, BRAF and PIK3CA mutations in metastatic colorectal cancer and potential effects on therapy in the CAPRI GOIM trial. Ann Oncol Off J Eur Soc Med Oncol /ESMO. 2015;26(8):1710–1714.
   PubMed Web of Science ®Google Scholar
• Nakayama Y, Yamaguchi H, Einaga N, et al. Pitfalls of DNA quantification using DNA-binding fluorescent dyes and suggested solutions. Plos One. 2016;11(3):e0150528.
   Web of Science ®Google Scholar
• Kapp JR, Diss T, Spicer J, et al. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. J Clin Pathol. 2015;68(2):111–118.
   PubMed Web of Science ®Google Scholar
• Simbolo M, Gottardi M, Corbo V, et al. DNA qualification workflow for next generation sequencing of histopathological samples. Plos One. 2013;8(6):e62692.
   PubMed Web of Science ®Google Scholar
• Di Nicolantonio F, Mercer SJ, Knight LA, et al. Cancer cell adaptation to chemotherapy. BMC Cancer. 2005;5:78.
   PubMed Web of Science ®Google Scholar
• Glaysher S, Yiannakis D, Gabriel FG, et al. Resistance gene expression determines the in vitro chemosensitivity of non-small cell lung cancer (NSCLC). BMC Cancer. 2009;9:300.
   PubMed Web of Science ®Google Scholar
• El Messaoudi S, Mouliere F, Du Manoir S, et al. Circulating DNA as a strong multi-marker prognostic tool for metastatic colorectal cancer patient management care. Clin Cancer Res. 2016;22(12):3067–3077.
   PubMed Web of Science ®Google Scholar
• Diaz LA Jr., Williams RT, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012;486(7404):537–540.
   PubMed Web of Science ®Google Scholar
• Varada S, Mahalingam M. Mutation stability in primary and metastatic melanoma: what we know and what we don’t. Histol Histopathol. 2015;30(7):763–770.
   PubMed Web of Science ®Google Scholar