References

BRAF targets in melanoma. Biological mechanisms, resistance, and drug discovery. Cancer drug discovery and development. Volume 82. Ed. Ryan J. Sullivan. Springer (2015)


  1. Brose MS, Volpe P, Feldman M, et al. BRAF and RAS mutations in human lung cancer and melanoma. Cancer Res. 2002;62:6997–7000.
  2. Cappuzzo F. EGFR FISH versus mutation: different tests, different end-points. Lung Cancer. 2008;60:160–5.
  3. Chapman PB, Hauschild A, Robert C, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364:2507–16.
  4. Davies H, Bignell GR, Cox C, et al. Mutations of the BRAF gene in human cancer. Nature. 2002;417:949–54.
  5. Plesec TP, Hunt JL. KRAS mutation testing in colorectal cancer. Adv Anat Pathol. 2009;16:196–203.
  6. Howlader N NA, Krapcho M, Neyman N, Aminou R, Waldron W, Altekruse SF, Kosary CL, Ruhl J, Tatalovich Z, Cho H, Mariotto A, Eisner MP, Lewis DR, Chen HS, Feuer EJ, Cronin KA, editors. SEER Cancer Statistics Review, 1975–2009 (Vintage 2009 Populations), National Cancer Institute. Bethesda, MD, http.//seer.cancer.gov/ csr/1975_2009_pops09/, based on November 2011 SEER data submission, posted to the SEER web site, April 2012. 2012.
  7. Dhomen N, Marais R. BRAF signaling and targeted therapies in melanoma. Hematol Oncol Clin North Am. 2009;23:529–45, ix.
  8. Fecher LA, Amaravadi R, Schuchter LM. Effectively targeting BRAF in melanoma: a formidable challenge. Pigment Cell Melanoma Res. 2008;21:410–1.
  9. Fecher LA, Amaravadi RK, Flaherty KT. The MAPK pathway in melanoma. Curr Opin 2008;20:183–9.
  10. Ji Z, Flaherty KT, Tsao H. Molecular therapeutic approaches to melanoma. Mol Aspects Med. 2010;31:194–204.
  11. Hauschild A, Grob JJ, Demidov LV, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, open-label, phase 3 randomised controlled trial. Lancet. 2012;380:358–65.
  12. Sosman JA, Kim KB, Schuchter L, et al. Survival in BRAF V600-mutant advanced melanoma treated with vemurafenib. N Engl J Med. 2012;366:707–14.
  13. Carvajal RD, Antonescu CR, Wolchok JD, et al. KIT as a therapeutic target in metastatic melanoma. JAMA. 2011;305:2327–34.
  14. Guo J, Si L, Kong Y, et al. Phase II, open-label, single-arm trial of imatinib mesylate in patients with metastatic melanoma harboring c-Kit mutation or amplification. J Clin Oncol. 2011;29:2904–9.
  15. Hodi FS, Friedlander P, Corless CL, et al Major response to imatinib mesylate in KIT-mutated melanoma. J Clin Oncol. 2008;26:2046–51.
  16. Ivan D, Niveiro M, Diwan AH, et al. Analysis of protein tyrosine kinases expression in the melanoma metastases of patients treated with Imatinib Mesylate (STI571, Gleevec). J Cutan Pathol. 2006;33:280–5.
  17. Kim KB, Eton O, Davis DW, et al. Phase II trial of imatinib mesylate in patients with metastatic melanoma. Br J Cancer. 2008;99:734–40.
  18. Lutzky J, Bauer J, Bastian BC. Dose-dependent, complete response to imatinib of a metastatic mucosal melanoma with a K642E KIT mutation. Pigment Cell Melanoma Res. 2008;21:492–3.
  19. Woodman SE, Trent JC, Stemke-Hale K, et al. Activity of dasatinib against L576P KIT mutant melanoma: molecular, cellular, and clinical correlates. Mol Cancer Ther. 2009;8:2079–85.
  20. Hodis E, Watson IR, Kryukov GV, et al. A landscape of driver mutations in melanoma. Cell. 2012;150:251–63.
  21. Krauthammer M, Kong Y, Ha BH, et al. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat Genet. 2012;44:1006–14.
  22. Pleasance ED, Cheetham RK, Stephens PJ, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–6.
  23. Armstrong BK, Kricker A. The epidemiology of UV induced skin cancer. J Photochem Photobiol B. 2001;63:8–18.
  24. Leiter U, Garbe C. Epidemiology of melanoma and nonmelanoma skin cancer–the role of sunlight. Adv Exp Med Biol. 2008;624:89–103.
  25. Pfeifer GP, You YH, Besaratinia A. Mutations induced by ultraviolet light. Mutat Res. 2005;571:19–31.
  26. Daya-Grosjean L, Sarasin A. The role of UV induced lesions in skin carcinogenesis: an overview of oncogene and tumor suppressor gene modifications in xeroderma pigmentosum skin tumors. Mutat Res. 2005;571:43–56.
  27. de Gruijl FR, van Kranen HJ, Mullenders LH. UV-induced DNA damage, repair, mutations and oncogenic pathways in skin cancer. J Photochem Photobiol B. 2001;63:19–27.
  28. Nouspikel T. DNA repair in mammalian cells: Nucleotide excision repair: variations on versatility. Cell Mol Life Sci. 2009;66:994–1009.
  29. Shuck SC, Short EA, Turchi JJ. Eukaryotic nucleotide excision repair. from understanding mechanisms to influencing biology. Cell Res. 2008;18:64–72.
  30. Fousteri M, Mullenders LH. Transcription-coupled nucleotide excision repair in mammalian cells: molecular mechanisms and biological effects. Cell Res. 2008;18:73–84.
  31. Hanawalt PC, Spivak G. Transcription-coupled DNA repair: two decades of progress and surprises. Nat Rev Mol Cell Biol. 2008;9:958–70.
  32. Chin L, Garraway LA, Fisher DE. Malignant melanoma. genetics and therapeutics in the genomic era. Genes Dev. 2006;20:2149–82.
  33. Miller AJ, Mihm MC Jr. Melanoma. N Engl J Med. 2006;355:51–65.
  34. Omholt K, Platz A, Kanter L, et al. NRAS and BRAF mutations arise early during melanoma pathogenesis and are preserved throughout tumor progression. Clin Cancer Res. 2003;9:6483–8.
  35. Greshock J, Nathanson K, Medina A, et al. Distinct patterns of DNA copy number alterations associate with BRAF mutations in melanomas and melanoma-derived cell lines. Genes Chromosomes Cancer. 2009;48:419–28.
  36. Long GV, Menzies AM, Nagrial AM, et al. Prognostic and clinicopathologic associations of oncogenic BRAF in metastatic melanoma. J Clin Oncol. 2011;29:1239–46.
  37. Menzies AM, Haydu LE, Visintin L, et al. Distinguishing clinicopathologic features of patients with V600E and V600K BRAF-mutant metastatic melanoma. Clin Cancer Res. 2012;18:3242–9.
  38. Ellerhorst JA, Greene VR, Ekmekcioglu S, et al. Clinical correlates of NRAS and BRAF mutations in primary human melanoma. Clin Cancer Res. 2011;17:229–35.
  39. Falchook GS, Long GV, Kurzrock R, et al. Dabrafenib in patients with melanoma, untreated brain metastases, and other solid tumours: a phase 1 dose-escalation trial. Lancet. 2012;379:1893–901.
  40. Long GV, Trefzer U, Davies MA, et al. Dabrafenib in patients with Val600Glu or Val600Lys BRAF-mutant melanoma metastatic to the brain (BREAK-MB): a multicentre, open-label, phase 2 trial. Lancet Oncol. 2012;13:1087–95.
  41. Dahlman KB, Xia J, Hutchinson K, et al. BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer Discov. 2012;2:791–7.
  42. Edlundh-Rose E, Egyhazi S, Omholt K, et al. NRAS and BRAF mutations in melanoma tumours in relation to clinical characteristics: a study based on mutation screening by pyrosequencing. Melanoma Res. 2006;16:471–8.
  43. Goel VK, Lazar AJ, Warneke CL, et al. Examination of mutations in BRAF, NRAS, and PTEN in primary cutaneous melanoma. J Invest Dermatol. 2006;126:154–60.
  44. van ’t Veer LJ, Burgering, Versteeg R, et al. N-ras mutations in human cutaneous melanoma from sun-exposed body sites. Mol Cell Biol. 1989;9:3114–6.
  45. Russo AE, Torrisi E, Bevelacqua Y, et al. Melanoma. molecular pathogenesis and emerging target therapies (Review). Int J Oncol. 2009;34:1481–9.
  46. Saldanha G, Potter L, Daforno P, et al. Cutaneous melanoma subtypes show different BRAF and NRAS mutation frequencies. Clin Cancer Res. 2006;12:4499–505.
  47. Ball NJ, Yohn JJ, Morelli JG, et al. Ras mutations in human melanoma: a marker of malignant progression. J Invest Dermatol. 1994;102:285–90.
  48. Devitt B, Liu W, Salemi R, et al. Clinical outcome and pathological features associated with NRAS mutation in cutaneous melanoma. Pigment Cell Melanoma Res. 2011;24:666–72.
  49. Jakob JA, Bassett RL Jr., Ng CS, et al. NRAS mutation status is an independent prognostic factor in metastatic melanoma. Cancer. 2012;118:4014–23.
  50. Ascierto PA, Schadendorf D, Berking C, et al. MEK162 for patients with advanced melanoma harbouring NRAS or Val600 BRAF mutations: a non-randomised, open-label phase 2 study. Lancet Oncol. 2013;14:249–56.
  51. Britten CD. PI3K and MEK inhibitor combinations. examining the evidence in selected tumor types. Cancer Chemother Pharmacol. 2013;71:1395–409.
  52. Greger JG, Eastman SD, Zhang V, et al. Combinations of BRAF, MEK, and PI3K/mTOR inhibitors overcome acquired resistance to the BRAF inhibitor GSK2118436 dabrafenib, mediated by NRAS or MEK mutations. Mol Cancer Ther. 2012;11:909–20.
  53. Posch C, Moslehi H, Feeney L, et al. Combined targeting of MEK and PI3K/mTOR effector pathways is necessary to effectively inhibit NRAS mutant melanoma in vitro and in vivo. Proc Natl Acad Sci U S A. 2013;110:4015–20.
  54. Curtin JA, Busam K, Pinkel D, et al. Somatic activation of KIT in distinct subtypes of melanoma. J Clin Oncol. 2006;24:4340–6.
  55. Grichnik JM. Kit and melanocyte migration. J Invest Dermatol. 2006;126:945–7.
  56. Stefansson B, Brautigan DL. Protein phosphatase PP6 N terminal domain restricts G1 to S phase progression in human cancer cells. Cell Cycle. 2007;6:1386–92.
  57. Stefansson B, Ohama T, Daugherty AE, et al. Protein phosphatase 6 regulatory subunits composed of ankyrin repeat domains. Biochemistry. 2008;47:1442–51.
  58. Jaffe AB, Hall A. Rho GTPases: biochemistry and biology. Annu Rev Cell Dev Biol. 2005;21:247–69.
  59. Berger MF, Hodis E, Heffernan TP, et al. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature. 2012;485:502–6.
  60. Gartner JJ, Davis S, Wei X, et al. Comparative exome sequencing of metastatic lesions provides insights into the mutational progression of melanoma. BMC Genomics. 2012;13:505.
  61. Nikolaev SI, Rimoldi D, Iseli C, et al. Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet. 2011;44:133–9.
  62. Wei X, Walia V, Lin JC, et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet. 2011;43:442–6.
  63. Dufort S, Richard MJ, de Fraipont F. Pyrosequencing method to detect KRAS mutation in formalin-fixed and paraffin-embedded tumor tissues. Anal Biochem. 2009;391:166–8.
  64. Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol. 1975;94:441–8.
  65. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977;74:5463–7.
  66. Marsh S. Pyrosequencing applications. Methods Mol Biol. 2007;373:15–24.
  67. Thomas RK, Baker AC, Debiasi RM, et al. High-throughput oncogene mutation profiling in human cancer. Nat Genet. 2007;39:347–51.
  68. Vasudevan KM, Barbie DA, Davies MA, et al. AKT-independent signaling downstream of oncogenic PIK3CA mutations in human cancer. Cancer Cell. 2009;16:21–32.
  69. Hayden EC. Personalized cancer therapy gets closer. Nature. 2009;458:131–2.
  70. Hurst CD, Zuiverloon TC, Hafner C, et al. A SNaPshot assay for the rapid and simple detection of four common hotspot codon mutations in the PIK3CA gene. BMC Res Notes. 2009;2:66.
  71. Ragoussis J, Elvidge GP, Kaur K, et al. Matrix-assisted laser desorption/ionisation, time-offlight mass spectrometry in genomics research. PLoS Genet. 2006;2:e100.
  72. MacConaill LE, Campbell CD, Kehoe SM, et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009;4:e7887.
  73. Weber BL. Cancer genomics. Cancer Cell. 2002;1:37–47.
  74. Look AT, Hayes FA, Shuster JJ, et al. Clinical relevance of tumor cell ploidy and N-myc gene amplification in childhood neuroblastoma: a Pediatric Oncology Group study. J Clin Oncol. 1991;9:581–91.
  75. Henrichsen CN, Chaignat E, Reymond A. Copy number variants, diseases and gene expression. Hum Mol Genet. 2009;18:R1–8.
  76. Kuiper RP, Ligtenberg MJ, Hoogerbrugge N, et al. Germline copy number variation and cancer risk. Curr Opin Genet Dev. 2010;20:282–9.
  77. Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome. Nature. 2006;444:444–54.
  78. Sapkota Y, Ghosh S, Lai R, et al. Germline DNA copy number aberrations identified as potential prognostic factors for breast cancer recurrence. PLoS One. 2013;8:e53850.
  79. Gaiser T, Kutzner H, Palmedo G, et al. Classifying ambiguous melanocytic lesions with FISH and correlation with clinical long-term follow up. Mod Pathol. 2010;23:413–9.
  80. Lazar V, Ecsedi S, Vizkeleti L, et al. Marked genetic differences between BRAF and NRAS mutated primary melanomas as revealed by array comparative genomic hybridization. Melanoma Res. 2012;22:202–14.
  81. Gast A, Scherer D, Chen B, et al. Somatic alterations in the melanoma genome. a highresolution array-based comparative genomic hybridization study. Genes Chromosomes Cancer. 2010;49:733–45.
  82. Jonsson G, Dahl C, Staaf J, et al. Genomic profiling of malignant melanoma using tilingresolution arrayCGH. Oncogene. 2007;26:4738–48.
  83. Stark M, Hayward N. Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. Cancer Res. 2007;67:2632–42.
  84. Morrissette JJ, Bagg A. Acute myeloid leukemia: conventional cytogenetics, FISH, and moleculocentric methodologies. Clin Lab Med. 2011;31:659–86, x.
  85. Pepper C, Majid A, Lin TT, et al. Defining the prognosis of early stage chronic lymphocytic leukaemia patients. Br J Haematol. 2011.
  86. Just PA, Cazes A, Audebourg A, et al. Histologic subtypes, immunohistochemistry, FISH or molecular screening for the accurate diagnosis of ALK-rearrangement in lung cancer: a comprehensive study of Caucasian non-smokers. Lung Cancer. 2011.
  87. Senetta R, Paglierani M, Massi D. Fluorescence in-situ hybridization analysis for melanoma diagnosis. Histopathology. 2011.
  88. Hossain D, Qian J, Adupe J, et al. Differentiation of melanoma and benign nevi by fluorescence in-situ hybridization. Melanoma Res. 2011;21:426–30.
  89. Hogervorst FB, Nederlof PM, Gille JJ, et al. Large genomic deletions and duplications in the BRCA1 gene identified by a novel quantitative method. Cancer Res. 2003;63:1449–53.
  90. Schouten JP, McElgunn CJ, Waaijer R, et al. Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification. Nucleic Acids Res. 2002;30:e57.
  91. Bruno W, Ghiorzo P, Battistuzzi L, et al. Clinical genetic testing for familial melanoma in Italy: a cooperative study. J Am Acad Dermatol. 2009;61:775–82.
  92. Kozlowski P, Jasinska AJ, Kwiatkowski DJ. New applications and developments in the use of multiplex ligation-dependent probe amplification. Electrophoresis. 2008;29:4627–36.
  93. Palma MD, Domchek SM, Stopfer J, et al. The relative contribution of point mutations and genomic rearrangements in BRCA1 and BRCA2 in high-risk breast cancer families. Cancer Res. 2008;68:7006–14.
  94. Stevens-Kroef M, Simons A, Gorissen H, et al. Identification of chromosomal abnormalities relevant to prognosis in chronic lymphocytic leukemia using multiplex ligation-dependent probe amplification. Cancer Genet Cytogenet. 2009;195:97–104.
  95. Dopierala J, Damato BE, Lake SL, et al. Genetic heterogeneity in uveal melanoma assessed by multiplex ligation-dependent probe amplification. Invest Ophthalmol Vis Sci. 2010;51:4898–905.
  96. Cesinaro AM, Schirosi L, Bettelli S, et al. Alterations of 9p21 analysed by FISH and MLPA distinguish atypical spitzoid melanocytic tumours from conventional Spitz’s nevi but do not predict their biological behaviour. Histopathology. 2010;57:515–27.
  97. Ross JS, Cronin M. Whole cancer genome sequencing by next-generation methods. Am J Clin Pathol. 2011;136:527–39.
  98. Wagle N, Berger MF, Davis MJ, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2012;2:82–93.
  99. Hadd AG, Houghton J, Choudhary A, et al. Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013;15:234–47.
  100. Holley T, Lenkiewicz E, Evers L, et al. Deep clonal profiling of formalin fixed paraffin embedded clinical samples. PLoS One. 2012;7:e50586.
  101. Menon R, Deng M, Boehm D, et al. Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue. Int J Mol Sci. 2012;13:8933–42.
  102. Asan, Xu Y, Jiang H, et al. Comprehensive comparison of three commercial human wholeexome capture platforms. Genome Biol. 2011;12:R95.
  103. Clark MJ, Chen R, Lam HY, et al. Performance comparison of exome DNA sequencing technologies. Nat Biotechnol. 2011;29:908–14.
  104. Parla JS, Iossifov I, Grabill I, et al. A comparative analysis of exome capture. Genome Biol. 2011;12:R97.
  105. Sulonen AM, Ellonen P, Almusa H, et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 2011;12:R94.
  106. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–60.
  107. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.
  108. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–303.
  109. Ye K, Schulz MH, Long Q, et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25:2865–71.
  110. Nord AS, Lee M, King MC, et al. Accurate and exact CNV identification from targeted high-throughput sequence data. BMC Genomics. 2011;12:184.
  111. Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2. somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568–76.
  112. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
  113. Chang X, Wang K. wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet. 2012;49:433–6.
  114. Adzhubei IA, Schmidt S, Peshkin L, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.
  115. Liu X, Jian X, Boerwinkle E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum Mutat. 2011;32:894–9.
  116. Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003;31:3812–4.
  117. Pollard KS, Hubisz MJ, Rosenbloom KR, et al. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res, 2010;20:110–21.
  118. Schwarz JM, Rodelsperger C, Schuelke M, et al. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7:575–6.
  119. Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–9.
  120. Karlsson R, Pedersen ED, Wang Z, et al. Rho GTPase function in tumorigenesis. Biochim Biophys Acta. 2009;1796:91–8.
  121. Ghai R, Mobli M, Norwood SJ, et al. Phox homology band 4.1/ezrin/radixin/moesin-like proteins function as molecular scaffolds that interact with cargo receptors and Ras GTPases. Proc Natl Acad Sci U S A. 2011;108:7763–8.
  122. Cully M, Shiu J, Piekorz RP, et al. Transforming acidic coiled coil 1 promotes transformation and mammary tumorigenesis. Cancer Res. 2005;65;10363–70.
  123. Li M, Zhao H, Zhang X, et al. Inactivating mutations of the chromatin remodeling gene ARID2 in hepatocellular carcinoma. Nat Genet. 2011;43:828–9.
  124. Sivaram MV, Wadzinski TL, Redick SD, et al. Dynein light intermediate chain 1 is required for progress through the spindle assembly checkpoint. EMBO J. 2009;28:902–14.

[contact-form-7 id=»5168″ title=»Контактная форма 1″]

0

Добавить комментарий

Войти с помощью: 

Ваш e-mail не будет опубликован. Обязательные поля помечены *