Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing

BMC Cancer

Volumn 11, Issue , 2011, Pages

  Borràs, Emma ^a   Jurado, Ismael ^a   Hernan, Imma ^a   Gamundi, María J ^a   Dias, Miguel ^a   Martí, Isabel ^a   Mañé, Begoña ^a   Arcusa, Àngels ^a   Agúndez, José A G ^b   Blanca, Miguel ^c   Carballo, Miguel ^a  

^a HOSPITAL DE TERRASSA   (Spain)

^b UNIVERSITY OF EXTREMADURA   (Spain)

^c HOSPITAL REGIONAL UNIVERSITARIO DE MÁLAGA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR; GENOMIC DNA; K RAS PROTEIN; BRAF PROTEIN, HUMAN; EGFR PROTEIN, HUMAN; KRAS PROTEIN, HUMAN; ONCOPROTEIN; RAS PROTEIN;

ACCURACY; AMINO ACID SUBSTITUTION; AMPLICON; ARTICLE; BRAF GENE; CANCER TISSUE; CODON; COLORECTAL CANCER; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; EPIDERMAL GROWTH FACTOR RECEPTOR GENE; EXON; GENE DELETION; GENE MUTATION; GENETIC VARIABILITY; HIGH RESOLUTION MELTING ANALYSIS; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN TISSUE; LUNG CANCER; MAJOR CLINICAL STUDY; MUTATION RATE; MUTATIONAL ANALYSIS; ONCOGENE; ONCOGENE K RAS; PHARMACOGENOMICS; PYROSEQUENCING; QUANTITATIVE ANALYSIS; SENSITIVITY ANALYSIS; SOMATIC MUTATION; ULTRA DEEP PYROSEQUENCING; VALIDATION PROCESS; GENETICS; METHODOLOGY; MOLECULAR GENETICS; MOLECULARLY TARGETED THERAPY; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOLECULAR SEQUENCE DATA; MOLECULAR TARGETED THERAPY; MUTATION; NEOPLASMS; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; RECEPTOR, EPIDERMAL GROWTH FACTOR; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

EID: 80053174701     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-11-406     Document Type: Article

References (35)

1. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, Louis DN, Christiani DC, Settleman J, Haber DA. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 2004, 350(21):2129-2139. 10.1056/NEJMoa040938, 15118073.
2. Paez JG, Jänne PA, Lee JC, Tracy S, Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, Naoki K, Sasaki H, Fujii Y, Eck MJ, Sellers WR, Johnson BE, Meyerson M. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science 2004, 304(5676):1497-1500. 10.1126/science.1099314, 15118125.
3. Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, Singh B, Heelan R, Rusch V, Fulton L, Mardis E, Kupfer D, Wilson R, Kris M, Varmus H. EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci USA 2004, 101(36):13306-13311. 10.1073/pnas.0405220101, 516528, 15329413.
4. Shigematsu H, Lin L, Takahashi T, Nomura M, Suzuki M, Wistuba II, Fong KM, Lee H, Toyooka S, Shimizu N, Fujisawa T, Feng Z, Roth JA, Herz J, Minna JD, Gazdar AF. Clinical and biological features associated with epidermal growth factor receptor gene mutations in lung cancers. J Natl Cancer Inst 2005, 97(5):339-346. 10.1093/jnci/dji055, 15741570.
5. Rosell R, Moran T, Queralt C, Porta R, Cardenal F, Camps C, Majem M, Lopez-Vivanco G, Isla D, Provencio M, Insa A, Massuti B, Gonzalez-Larriba JL, Paz-Ares L, Bover I, Garcia-Campelo R, Moreno MA, Catot S, Rolfo C, Reguart N, Palmero R, Sánchez JM, Bastus R, Mayo C, Bertran-Alamillo J, Molina MA, Sanchez JJ, Taron M, . Spanish Lung Cancer Group Screening for epidermal growth factor receptor mutations in lung cancer. N Engl J Med 2009, 361(10):958-967. 10.1056/NEJMoa0904554, 19692684, Spanish Lung Cancer Group.
6. Balak MN, Gong Y, Riely GJ, Somwar R, Li AR, Zakowski MF, Chiang A, Yang G, Ouerfelli O, Kris MG, Ladanyi M, Miller VA, Pao W. Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors. Clin Cancer Res 2006, 12:6494-6501. 10.1158/1078-0432.CCR-06-1570, 17085664.
7. Kobayashi S, Boggon TJ, Dayaram T, Jänne PA, Kocher O, Meyerson M, Johnson BE, Eck MJ, Tenen DG, Halmos B. EGFR mutation and resistance of non-small-cell lung cancer to gefitinib. N Engl J Med 2005, 352:786-792. 10.1056/NEJMoa044238, 15728811.
8. Adjei AA. Blocking oncogenic Ras signaling for cancer therapy. J Natl Cancer Inst 2001, 93(14):1062-1074. 10.1093/jnci/93.14.1062, 11459867.
9. Bos JL. ras oncogenes in human cancer: a review. Cancer Res 1989, 49(17):4682-4689.
10. Linardou H, Dahabreh IJ, Kanaloupiti D, Siannis F, Bafaloukos D, Kosmidis P, Papadimitriou CA, Murray S. 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 2008, 9(10):962-972. 10.1016/S1470-2045(08)70206-7, 18804418.
11. Marchetti A, Martella C, Felicioni L, Barassi F, Salvatore S, Chella A, Camplese PP, Iarussi T, Mucilli F, Mezzetti A, Cuccurullo F, Sacco R, Buttitta F. EGFR mutations in non-small-cell lung cancer: analysis of a large series of cases and development of a rapid and sensitive method for diagnostic screening with potential implications on pharmacologic treatment. J Clin Oncol 2005, 23(4):857-865. 10.1200/JCO.2005.08.043, 15681531.
12. Pollock PM, Harper UL, Hansen KS, Yudt LM, Stark M, Robbins CM, Moses TY, Hostetter G, Wagner U, Kakareka J, Salem G, Pohida T, Heenan P, Duray P, Kallioniemi O, Hayward NK, Trent JM, Meltzer PS. High frequency of BRAF mutations in nevi. Nat Genet 2003, 33:19-20. 10.1038/ng1054, 12447372.
13. Hingorani SR, Jacobtz MA, Robertson GP, Herlyn M, Tuveson DA. Suppression of BRAF V599E in human melanoma abrogates transformation. Cancer Res 2003, 63:5198-5202.
14. Di Nicolantonio F, Martini M, Molinari F, Sartore-Bianchi A, Arena S, Saletti P. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol 2008, 26(35):5705-5712. 10.1200/JCO.2008.18.0786, 19001320.
15. Loupakis F, Ruzzo A, Cremolini C, Vincenzi B, Salvatore L, Santini D, Masi G, Stasi I, Canestrari E, Rulli E, Floriani I, Bencardino K, Galluccio N, Catalano V, Tonini G, Magnani M, Fontanini G, Basolo F, Falcone A, Graziano F. KRAS codon 61, 146 and BRAF mutations predict resistance to cetuximab plus irinotecan in KRAS codon 12 and 13 wild-type metastatic colorectal cancer. Br J Cancer 2009, 101(4):715-721. 10.1038/sj.bjc.6605177, 2736831, 19603018.
16. Bokemeyer C, Kohne C, Rougier P, Stroh C, Schlichting M, Van Cutsem E. Cetuximab with chemotherapy (CT) as first-line treatment for metastatic colorectal cancer (mCRC): analysis of the CRYSTAL and OPUS studies according to KRAS and BRAF mutation status. J Clin Oncol 2010, 28:15s. Abstract 3506.
17. Wilson PM, Labonte MJ, Lenz HJ. Molecular markers in the treatment of metastatic colorectal cancer. Cancer J 2010, 16(3):262-272. 10.1097/PPO.0b013e3181e07738, 20526105.
18. National Comprehensive Cancer Network. Guidelines for Colon and Rectal Cancer. v.1.2010.
19. National Comprehensive Cancer Network. Non-Small Cell Lung Cancer Clinical Practice Guidelines. January 2011 update..
20. Keedy VL, Temin S, Somerfield MR, Beasley MB, Johnson DH, McShane LM, Milton DT, Strawn JR, Wakelee HA, Giaccone G. American Society of Clinical Oncology provisional clinical opinion: epidermal growth factor receptor (EGFR) Mutation testing for patients with advanced non-small-cell lung cancer considering first-line EGFR tyrosine kinase inhibitor therapy. J Clin Oncol 2011, 29(15):2121-2127. 10.1200/JCO.2010.31.8923, 21482992.
21. van Krieken JH, Jung A, Kirchner T, Carneiro F, Seruca R, Bosman FT, Quirke P, Fléjou JF, Plato Hansen T, de Hertogh G, Jares P, Langner C, Hoefler G, Ligtenberg M, Tiniakos D, Tejpar S, Bevilacqua G, Ensari A. KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program. Virchows Arch 2008, 453(5):417-431. 10.1007/s00428-008-0665-y, 18802721.
22. Taylor CF. Mutation scanning using high-resolution melting. Biochem Soc Trans 2009, 37(Pt 2):433-437.
23. NCBI/Primer - BLAST. , http://www.ncbi.nlm.nih.gov/tools/primer-blast
24. DNA Melting - Stitch Profile. , http://stitchprofiles.uio.no
25. The DINAMelt Web Server. , http://mfold.rna.albany.edu/?q = DINAMelt
26. Ma ES, Wong CL, Law FB, Chan WK, Siu D. Detection of KRAS mutations in colorectal cancer by high-resolution melting analysis. J Clin Pathol 2009, 62(10):886-891. 10.1136/jcp.2008.063677, 19783717.
27. Do H, Krypuy M, Mitchell PL, Fox SB, Dobrovic A. High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies. BMC Cancer 2008, 8:142. 10.1186/1471-2407-8-142, 2408599, 18495026.
28. de Gunst MM, Gallegos-Ruiz MI, Giaccone G, Rodriguez JA. Functional analysis of cancer-associated EGFR mutants using a cellular assay with YFP-tagged EGFR intracellular domain. Mol Cancer 2007, 6:56. 10.1186/1476-4598-6-56, 2064929, 17877814.
29. Gonzalez-Bosquet J, Calcei J, Wei JS, Garcia-Closas M, Sherman ME, Hewitt S, Vockley J, Lissowska J, Yang HP, Khan J, Chanock S. Detection of somatic mutations by high-resolution DNA melting (HRM) analysis in multiple cancers. PLoS One 2011, 6(1):e14522. 10.1371/journal.pone.0014522, 3022009, 21264207.
30. Simi L, Pratesi N, Vignoli M, Sestini R, Cianchi F, Valanzano R, Nobili S, Mini E, Pazzagli M, Orlando C. High-resolution melting analysis for rapid detection of KRAS, BRAF, and PIK3CA gene mutations in colorectal cancer. Am J Clin Pathol 2008, 130(2):247-253. 10.1309/LWDY1AXHXUULNVHQ, 18628094.
31. Amado RG, Wolf M, Peeters M, Van Cutsem E, Siena S, Freeman DJ, Juan T, Sikorski R, Suggs S, Radinsky R, Patterson SD, Chang DD. Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J Clin Oncol 2008, 26(10):1626-1634. 10.1200/JCO.2007.14.7116, 18316791.
32. Krypuy M, Newnham GM, Thomas DM, Conron M, Dobrovic A. 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 2006, 6:295. 10.1186/1471-2407-6-295, 1769510, 17184525.
33. Kramer D, Thunnissen FB, Gallegos-Ruiz MI, Smit EF, Postmus PE, Meijer CJ, Snijders PJ, Heideman DA. A fast, sensitive and accurate high resolution melting (HRM) technology-based assay to screen for common K-ras mutations. Cell Oncol 2009, 31(3):161-167.
34. Ogino S, Kawasaki T, Brahmandam M, Yan L, Cantor M, Namgyal C, Mino-Kenudson M, Lauwers GY, Loda M, Fuchs CS. Sensitive sequencing method for KRAS mutation detection by Pyrosequencing. J Mol Diagn 2005, 7(3):413-421. 10.1016/S1525-1578(10)60571-5, 1867544, 16049314.
35. Genome Sequencer System - Application Note No. 5/February 2007, Amplicon Sequencing. , http://www.roche-applied-science.com