Asian Pacific Journal of Cancer Prevention

Asian Pacific Journal of Cancer Prevention (아시아태평양암예방학회)
권호 표지
DOI QR코드

DOI QR Code

Sensitive High-Resolution Melting Analysis for Screening of KRAS and BRAF Mutations in Iranian Human Metastatic Colorectal Cancers

  • Niya, Mohammad Hadi Karbalaie (Department of Virology, Faculty of Medicine, Iran University of Medical Sciences) ;
  • Basi, Ali (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Koochak, Aghigh (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Tameshkel, Fahimeh Safarnezhad (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Rakhshani, Nasser (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Zamani, Farhad (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Imanzade, Farid (Department of Pediatrics, Shahid Beheshti University of Medical Sciences) ;
  • Rezvani, Hamid (Department of Oncology, Shahid Beheshti University of Medical Sciences) ;
  • Adib sereshki, Mohammad Mahdi (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences) ;
  • Sohrabi, Masoud Reza (Gastrointestinal and Liver Diseases Research Center, Firoozgar Hospital, Iran University of Medical Sciences)
  • Published : 2016.12.01
⟨ Previous Next ⟩

Abstract

Background: Investigations of methods for detection of mutations have uncovered major weaknesses of direct sequencing and pyrosequencing, with their high costs and low sensitivity in screening for both known and unknown mutations. High resolution melting (HRM) analysis is an alternative tool for the rapid detection of mutations. Here we describe the accuracy of HRM in screening for KRAS and BRAF mutations in metastatic colorectal cancer (mCRCs) samples. Materials and Methods: A total of 1000 mCRC patients in Mehr Hospital, Tehran, Iran, from Feb 2008 to May 2012 were examined for KRAS mutations and 242 of them were selected for further assessment of BRAF mutations by HRM analysis. In order to calculate the sensitivity and specificity, HRM results were checked by pyrosequencing as the golden standard and Dxs Therascreen as a further method. Results: In the total of 1,000 participants, there were 664 (66.4%) with wild type and 336 (33.6%) with mutant codons 12 and/or 13 of the KRAS gene. Among 242 samples randomly checked for the BRAF gene, all were wild type by HRM. Pyrosequencing and Dxs Therascreen results were in line with those of the HRM. In this regard, the sensitivity and specificity of HRM were evaluated as 100%. Conclusion: The findings suggest that the HRM, in comparison with DNA sequencing, is a more appropriate method for precise scanning of KRAS and BRAF mutations. It is also possible to state that HRM may be an attractive technique for the detection of known or unknown somatic mutations in other genes.

Keywords

Acknowledgement

Supported by : Iran University of Medical Sciences

References

  1. Andreyev HJ, Norman AR, Cunningham D, et al (2001). Kirsten ras mutations in patients with colorectal cancer: the 'RASCAL II' study. Br J Cancer, 85, 692-6. https://doi.org/10.1054/bjoc.2001.1964
  2. Andreyev HJ, Norman AR, Cunningham D, Oates JR, Clarke PA (1998). Kirsten ras mutations in patients with colorectal cancer: the multicenter "RASCAL" study. J Natl Cancer Inst, 90, 675-84. https://doi.org/10.1093/jnci/90.9.675
  3. Allegra CJ, Jessup JM, Somerfield MR, 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, 2091-6. https://doi.org/10.1200/JCO.2009.21.9170
  4. Borras E, Jurado I, Hernan I, et al (2011). Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing. BMC Cancer, 11, 406. https://doi.org/10.1186/1471-2407-11-406
  5. Boyd EM, Bench AJ, van 't Veer MB, et al (2011). High resolution melting analysis for detection of BRAF exon 15 mutations in hairy cell leukaemia and other lymphoid malignancies. Br J Haematol, 155, 609-12. https://doi.org/10.1111/j.1365-2141.2011.08868.x
  6. Chateigner-Boutin AL, Small I (2007). A rapid high-throughput method for the detection and quantification of RNA editing based on high-resolution melting of amplicons. Nucleic Acids Res, 35, e114. https://doi.org/10.1093/nar/gkm640
  7. Chen D, Wang YY, Chuai ZR, et al (2014). High-resolution melting analysis for accurate detection of BRAF mutations: a systematic review and meta-analysis. Sci Rep, 4, 4168.
  8. De Roock W, De Vriendt V, Normanno N, Ciardiello F, Tejpar S (2011). KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer. Lancet Oncol, 12, 594-603. https://doi.org/10.1016/S1470-2045(10)70209-6
  9. Di Nicolantonio F, Martini M, Molinari F, et al (2008). Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol, 26, 5705-12. https://doi.org/10.1200/JCO.2008.18.0786
  10. Fransen K, Klintenas M, Osterstrom A, et al (2004). Mutation analysis of the BRAF, ARAF and RAF-1 genes in human colorectal adenocarcinomas. Carcinogenesis, 25, 527-33.
  11. Guedes JG, Veiga I, Rocha P, et al (2013). High resolution melting analysis of KRAS, BRAF and PIK3CA in KRAS exon 2 wild-type metastatic colorectal cancer. BMC Cancer, 13, 169. https://doi.org/10.1186/1471-2407-13-169
  12. Janakiraman M, Vakiani E, Zeng Z, et al (2010). Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res, 70, 5901-11. https://doi.org/10.1158/0008-5472.CAN-10-0192
  13. Ji H, Wang Z, Perera SA, et al (2007). Mutations in BRAF and KRAS converge on activation of the mitogen-activated protein kinase pathway in lung cancer mouse models. Cancer Res, 67, 4933-9. https://doi.org/10.1158/0008-5472.CAN-06-4592
  14. Katsanis SH, Katsanis N (2013). Molecular genetic testing and the future of clinical genomics. Nat Rev Genet, 14, 415-26.
  15. Koochak A, Rakhshani N, Karbalaie Niya MH, et al (2016). Mutation Analysis of KRAS and BRAF Genes in Metastatic Colorectal Cancer: a First Large Scale Study from Iran. Asian Pac J Cancer Prev, 17, 603-8. https://doi.org/10.7314/APJCP.2016.17.2.603
  16. Krypuy M, Newnham GM, Thomas DM, Conron M, Dobrovic A (2006). High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer. BMC Cancer, 6, 295. https://doi.org/10.1186/1471-2407-6-295
  17. Li BS, Wang XY, Xu AG, et al (2012). High-resolution melting assay (HRMA) is a simple and sensitive stool-based DNA Test for the detection of mutations in colorectal neoplasms. Clin Colorectal Cancer, 11, 280-90. https://doi.org/10.1016/j.clcc.2012.04.001
  18. Mader E, Lukas B, Novak J (2008). A strategy to setup codominant microsatellite analysis for high-resolutionmelting- curve-analysis (HRM). BMC Genet, 9, 69.
  19. Minoo P, Moyer MP, Jass JR (2007). Role of BRAF-V600E in the serrated pathway of colorectal tumourigenesis. J Pathol, 212, 124-33. https://doi.org/10.1002/path.2160
  20. Montgomery JL, Sanford LN, Wittwer CT (2010). Highresolution DNA melting analysis in clinical research and diagnostics. Expert Rev Mol Diagn, 10, 219-40. https://doi.org/10.1586/erm.09.84
  21. Morandi L, de Biase D, Visani M, et al (2012). Allele specific locked nucleic acid quantitative PCR (ASLNAqPCR): an accurate and cost-effective assay to diagnose and quantify KRAS and BRAF mutation. PloS One, 7, e36084. https://doi.org/10.1371/journal.pone.0036084
  22. Negru S, Papadopoulou E, Apessos A, et al (2014). KRAS, NRAS and BRAF mutations in Greek and Romanian patients with colorectal cancer: a cohort study. BMJ, 4, e004652.
  23. Packham D, Ward RL, Ap Lin V, Hawkins NJ, Hitchins MP (2009). Implementation of novel pyrosequencing assays to screen for common mutations of BRAF and KRAS in a cohort of sporadic colorectal cancers. Diagn Mol Pathol, 18, 62-71. https://doi.org/10.1097/PDM.0b013e318182af52
  24. Pinto P, Rocha P, Veiga I, et al (2011). Comparison of methodologies for KRAS mutation detection in metastatic colorectal cancer. Cancer Genet, 204, 439-46. https://doi.org/10.1016/j.cancergen.2011.07.003
  25. Popovici V, Budinska E, Tejpar S, et al (2012). Identification of a poor-prognosis BRAF-mutant-like population of patients with colon cancer. J Clin Oncol, 30, 1288-95. https://doi.org/10.1200/JCO.2011.39.5814
  26. Reed GH,Wittwer CT (2004). Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem, 50, 1748-54. https://doi.org/10.1373/clinchem.2003.029751
  27. Roth AD, Tejpar S, Delorenzi M, et al (2010). Prognostic role of KRAS and BRAF in stage II and III resected colon cancer: results of the translational study on the PETACC-3, EORTC 40993, SAKK 60-00 trial. J Clin Oncol, 28, 466-74. https://doi.org/10.1200/JCO.2009.23.3452
  28. Simi L, Pratesi N, Vignoli M, et al (2008). High-resolution melting analysis for rapid detection of KRAS, BRAF, and PIK3CA gene mutations in colorectal cancer. Am J Clin Pathol, 130, 247-53. https://doi.org/10.1309/LWDY1AXHXUULNVHQ
  29. Sundstrom M, Edlund K, Lindell M, et al (2004). KRAS analysis in colorectal carcinoma: analytical aspects of Pyrosequencing and allele-specific PCR in clinical practice. BMC Cancer, 10, 660.
  30. Takano T, Ohe Y, Tsuta K, et al (2007). Epidermal growth factor receptor mutation detection using high-resolution melting analysis predicts outcomes in patients with advanced non small cell lung cancer treated with gefitinib. Clin Cancer Res, 13, 5385-90. https://doi.org/10.1158/1078-0432.CCR-07-0627
  31. Tan YH, Liu Y, Eu KW, et al (2008). Detection of BRAF V600E mutation by pyrosequencing. Pathology, 40, 295-8. https://doi.org/10.1080/00313020801911512
  32. Taylor CF (2009). Mutation scanning using high-resolution melting. Biochem Soc Trans, 37, 433-7. https://doi.org/10.1042/BST0370433
  33. Wittwer CT (2009). High-resolution DNA melting analysis: advancements and limitations. Hum Mutat, 30, 857-9. https://doi.org/10.1002/humu.20951
  34. Wooster R, Futreal AP, Stratton MR (2006). Sequencing analysis of BRAF mutations in human cancers. Methods Enzymol, 407, 218-24.
  35. Vakil L, Najafipour R, Rakhshani N, et al (2016). Investigation of FIH-1 and SOCS3 expression in KRAS mutant and wild-type patients with colorectal cancer. Tumour Biol, 37, 8841-8. https://doi.org/10.1007/s13277-015-4723-1