Pyrosequencing data analysis software: a useful tool for EGFR, KRAS, and BRAF mutation analysis

Diagnostic Pathology

Volumn 7, Issue 1, 2012, Pages

  Shen, Shanxiang ^a   Qin, Dahui ^a  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

BRAF; EGFR; KRAS; Pyrosequencing; Software

Indexed keywords

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

ARTICLE; COMPUTER PROGRAM; GENETICS; HUMAN; METHODOLOGY; NUCLEOTIDE SEQUENCE;

DNA MUTATIONAL ANALYSIS; HUMANS; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; RECEPTOR, EPIDERMAL GROWTH FACTOR; SOFTWARE;

EID: 84861433613     PISSN: None     EISSN: 17461596     Source Type: Journal    
DOI: 10.1186/1746-1596-7-56     Document Type: Article

References (19)

1. Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, et al. 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 U S A 2004, 101(36):13306-13311. 10.1073/pnas.0405220101, 516528, 15329413.
2. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, et al. EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy. Science 2004, 304(5676):1497-1500. 10.1126/science.1099314, 15118125.
3. Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, et al. 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.
4. Lievre A, Bachet JB, Le Corre D, Boige V, Landi B, Emile JF, et al. KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res 2006, 66(8):3992-3995. 10.1158/0008-5472.CAN-06-0191, 16618717.
5. Amado RG, Wolf M, Peeters M, Van Cutsem E, Siena S, Freeman DJ, et al. 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.
6. Karapetis CS, Khambata-Ford S, Jonker DJ, O'Callaghan CJ, Tu D, Tebbutt NC, et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 2008, 359(17):1757-1765. 10.1056/NEJMoa0804385, 18946061.
7. Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, et al. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med 2010, 363(9):809-819. 10.1056/NEJMoa1002011, 20818844.
8. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, Larkin J, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 2011, 364(26):2507-2516. 10.1056/NEJMoa1103782, 21639808.
9. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Scienc 1998, 281(5375):363-365.
10. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P. Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996, 242(1):84-89. 10.1006/abio.1996.0432, 8923969.
11. Dufort S, Richard MJ, Lantuejoul S, de Fraipont F. Pyrosequencing, a method approved to detect the two major EGFR mutations for anti EGFR therapy in NSCLC. J Exp Clin Cancer Res 2011, 30:57. 10.1186/1756-9966-30-57, 3120717, 21575212.
12. Dufort S, Richard MJ, de Fraipont F. Pyrosequencing method to detect KRAS mutation in formalin-fixed and paraffin-embedded tumor tissues. Anal Biochem 2009, 391(2):166-168. 10.1016/j.ab.2009.05.027, 19464247.
13. Ibrahem S, Seth R, O'Sullivan B, Fadhil W, Taniere P, Ilyas M. Comparative analysis of pyrosequencing and QMC-PCR in conjunction with high resolution melting for KRAS/BRAF mutation detection. Int J Exp Pathol 2010, 91(6):500-505. 10.1111/j.1365-2613.2010.00733.x, 3010548, 21199003.
14. Packham D, Ward RL, Ap Lin V, Hawkins NJ, Hitchins MP. Implementation of novel pyrosequencing assays to screen for common mutations of BRAF and KRAS in a cohort of sporadic colorectal cancers. Diagn Mol Pathol 2009, 18(2):62-71. 10.1097/PDM.0b013e318182af52, 19430299.
15. Qiagen EGFR pyro handbook 2010, , Valencia, USA, Qiagen.
16. Qiagen PyroMark® KRAS v2.0 handbook 2010, , Valencia, USA, Qiagen.
17. Qiagen BRAF pyro® handbook 2010, , Valencia, USA, Qiagen.
18. Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyren P, Uhlen M, et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem 2000, 280(1):103-110. 10.1006/abio.2000.4493, 10805527.
19. Chen G, Olson MT, O'Neill A, Norris A, Beierl K, Harada S, et al. A virtual pyrogram generator to resolve complex pyrosequencing results. J Mol Diagn 2012, 14(2):149-159. 10.1016/j.jmoldx.2011.12.001, 22316529.