Allele specific locked nucleic acid quantitative PCR (ASLNAqPCR): An accurate and cost-effective assay to diagnose and quantify KRAS and BRAF mutation

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Morandi, Luca ^a   de Biase, Dario ^a   Visani, Michela ^a   Cesari, Valentina ^a   de Maglio, Giovanna ^b   Pizzolitto, Stefano ^b   Pession, Annalisa ^a   Tallini, Giovanni ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b SANTA MARIA DELLA MISERICORDIA UNIVERSITY HOSPITAL   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; B RAF KINASE; BRAF PROTEIN, HUMAN; DIAGNOSTIC AGENT; KRAS PROTEIN, HUMAN; LOCKED NUCLEIC ACID; OLIGONUCLEOTIDE; ONCOPROTEIN; RAS PROTEIN;

ACCURACY; ALLELE SPECIFIC LOCKED NUCLEIC ACID QUANTITATIVE POLYMERASE CHAIN REACTION; ARTICLE; CANCER CELL; COST EFFECTIVENESS ANALYSIS; CYTOLOGY; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; MAJOR CLINICAL STUDY; ONCOGENE; ONCOGENE BRAF; ONCOGENE K RAS; POLYMERASE CHAIN REACTION; PREDICTIVE VALUE; SENSITIVITY AND SPECIFICITY; VALIDITY; ALLELE; BIOASSAY; COLON TUMOR; COST BENEFIT ANALYSIS; ECONOMICS; GENETICS; METHODOLOGY; MUTATION; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; STANDARD; TITRIMETRY;

ALLELES; BIOLOGICAL ASSAY; COLONIC NEOPLASMS; COST-BENEFIT ANALYSIS; DNA MUTATIONAL ANALYSIS; HUMANS; MUTATION; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TITRIMETRY;

EID: 84860456253     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0036084     Document Type: Article

References (34)

1. Pao W, Kris MG, Iafrate AJ, Ladanyi M, Janne PA, et al. (2009) Integration of molecular profiling into the lung cancer clinic. Clin Cancer Res 15: 5317-5322.
2. Hoshino R, Chatani Y, Yamori T, Tsuruo T, Oka H, et al. (1999) Constitutive activation of the 41-/43-kDa mitogen-activated protein kinase signaling pathway in human tumors. Oncogene 18: 813-822.
3. Karapetis CS, Khambata-Ford S, Jonker DJ, O'Callaghan CJ, Tu D, et al. (2008) K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 359: 1757-1765.
4. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, et al. (2004) The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 91: 355-358.
5. Linardou H, Dahabreh IJ, Kanaloupiti D, Siannis F, Bafaloukos D, et al. (2008) Assessment of somatic k-RAS mutations as a mechanism associated with resistance to EGFR-targeted agents: a systematic review and meta-analysis of studies in advanced non-small-cell lung cancer and metastatic colorectal cancer. Lancet Oncol 9: 962-972.
6. Pao W, Wang TY, Riely GJ, Miller VA, Pan Q, et al. (2005) KRAS mutations and primary resistance of lung adenocarcinomas to gefitinib or erlotinib. PLoS Med 2: e17.
7. Allegra CJ, Jessup JM, Somerfield MR, Hamilton SR, Hammond EH, et al. (2009) American Society of Clinical Oncology provisional clinical opinion: testing for KRAS gene mutations in patients with metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy. J Clin Oncol 27: 2091-2096.
8. van Krieken JH, Jung A, Kirchner T, Carneiro F, Seruca R, et al. (2008) KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program. Virchows Arch 453: 417-431.
9. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, et al. (2002) Mutations of the BRAF gene in human cancer. Nature 417: 949-954.
10. Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, et al. (2005) Distinct sets of genetic alterations in melanoma. N Engl J Med 353: 2135-2147.
11. Xing M, Vasko V, Tallini G, Larin A, Wu G, et al. (2004) BRAF T1796A transversion mutation in various thyroid neoplasms. J Clin Endocrinol Metab 89: 1365-1368.
12. Paik PK, Arcila ME, Fara M, Sima CS, Miller VA, et al. (2011) Clinical characteristics of patients with lung adenocarcinomas harboring BRAF mutations. J Clin Oncol 29: 2046-2051.
13. Deng G, Bell I, Crawley S, Gum J, Terdiman JP, et al. (2004) BRAF mutation is frequently present in sporadic colorectal cancer with methylated hMLH1, but not in hereditary nonpolyposis colorectal cancer. Clin Cancer Res 10: 191-195.
14. Di Nicolantonio F, Martini M, Molinari F, Sartore-Bianchi A, Arena S, et al. (2008) Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol 26: 5705-5712.
15. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, et al. (2011) Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 364: 2507-2516.
16. Hruban RH, van Mansfeld AD, Offerhaus GJ, van Weering DH, Allison DC, et al. (1993) K-ras oncogene activation in adenocarcinoma of the human pancreas. A study of 82 carcinomas using a combination of mutant-enriched polymerase chain reaction analysis and allele-specific oligonucleotide hybridization. Am J Pathol 143: 545-554.
17. James MR, Dumeni T, Stark MS, Duffy DL, Montgomery GW, et al. (2006) Rapid screening of 4000 individuals for germ-line variations in the BRAF gene. Clin Chem 52: 1675-1678.
18. Kim IJ, Kang HC, Jang SG, Ahn SA, Yoon HJ, et al. (2007) Development and applications of a BRAF oligonucleotide microarray. J Mol Diagn 9: 55-63.
19. Leboeuf R, Baumgartner JE, Benezra M, Malaguarnera R, Solit D, et al. (2008) BRAFV600E mutation is associated with preferential sensitivity to mitogen-activated protein kinase kinase inhibition in thyroid cancer cell lines. J Clin Endocrinol Metab 93: 2194-2201.
20. Morandi L, Franceschi E, de Biase D, Marucci G, Tosoni A, et al. (2010) Promoter methylation analysis of O6-methylguanine-DNA methyltransferase in glioblastoma: detection by locked nucleic acid based quantitative PCR using an imprinted gene (SNURF) as a reference. BMC Cancer 10: 48.
21. Latorra D, Campbell K, Wolter A, Hurley JM, (2003) Enhanced allele-specific PCR discrimination in SNP genotyping using 3′ locked nucleic acid (LNA) primers. Hum Mutat 22: 79-85.
22. Xing M, Tufano RP, Tufaro AP, Basaria S, Ewertz M, et al. (2004) Detection of BRAF mutation on fine needle aspiration biopsy specimens: a new diagnostic tool for papillary thyroid cancer. J Clin Endocrinol Metab 89: 2867-2872.
23. Livak KJ, Schmittgen TD, (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25: 402-408.
24. Zhou X-H, Obuchowski NA, McClish DK, (2011) Statistical Methods in Diagnostic Medicine: Wiley & Sons.
25. Murray A, Lawrence GP, (1993) How should the repeatability of clinical measurements be analysed? An assessment of analysis techniques with data from cardiovascular autonomic function tests. Q J Med 86: 831-836.
26. Liikanen E, (2002) Common technical specification for in vitro diagnostic medical devices. Off J Eur Commun L131: 17-30.
27. Neumann J, Zeindl-Eberhart E, Kirchner T, Jung A, (2009) Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer. Pathol Res Pract 205: 858-862.
28. Kubota K, Ohashi A, Imachi H, Harada H, (2006) Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes. Appl Environ Microbiol 72: 5311-5317.
29. Sun Z, Chen Z, Hou X, Li S, Zhu H, et al. (2008) Locked nucleic acid pentamers as universal PCR primers for genomic DNA amplification. PLoS One 3: e3701.
30. Arcila M, Lau C, Nafa K, Ladanyi M, (2010) Detection of KRAS and BRAF mutations in colorectal carcinoma roles for high-sensitivity locked nucleic acid-PCR sequencing and broad-spectrum mass spectrometry genotyping. J Mol Diagn 13: 64-73.
31. Sundstrom M, Edlund K, Lindell M, Glimelius B, Birgisson H, et al. (2010) KRAS analysis in colorectal carcinoma: analytical aspects of Pyrosequencing and allele-specific PCR in clinical practice. BMC Cancer 10: 660.
32. Goranova TE, Ohue M, Shimoharu Y, Kato K, (2011) Dynamics of cancer cell subpopulations in primary and metastatic colorectal tumors. Clin Exp Metastasis 28: 427-435.
33. Farber L, Efrati E, Elkin H, Peerless Y, Sabo E, et al. (2011) Molecular morphometric analysis shows relative intra-tumoural homogeneity for KRAS mutations in colorectal cancer. Virchows Arch 459: 487-493.
34. Marchetti A, Milella M, Felicioni L, Cappuzzo F, Irtelli L, et al. (2009) Clinical implications of KRAS mutations in lung cancer patients treated with tyrosine kinase inhibitors: an important role for mutations in minor clones. Neoplasia 11: 1084-1092.