Multigene assays in metastatic colorectal cancer

JNCCN Journal of the National Comprehensive Cancer Network

Volumn 11, Issue SUPPL.4, 2013, Pages

  Deeb, Kristin K ^a   Sram, Jakub P ^b   Gao, Hanlin ^c   Fakih, Marwan G ^b  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

^b CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^c Fulgent Therapeutics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; K RAS PROTEIN;

ALLELE; ARTICLE; ASSAY; CANCER GENETICS; CANCER TEST; CARCINOGENESIS; CLINICAL PRACTICE; DNA SEQUENCE; EXOME; GENE EXPRESSION; GENE MUTATION; HUMAN; METASTATIC COLORECTAL CANCER; MOLECULAR DIAGNOSIS; MULTIGENE ASSAY; PYROSEQUENCING; REAL TIME POLYMERASE CHAIN REACTION;

COLORECTAL NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASM METASTASIS; TUMOR MARKERS, BIOLOGICAL;

EID: 84887234728     PISSN: 15401405     EISSN: 15401413     Source Type: Journal    
DOI: 10.6004/jnccn.2013.0221     Document Type: Article

References (57)

1. Jemal A, Bray F, Center M.M., et al. Global cancer statistics. CA Cancer J Clin 2011; 61: 69-90.
2. Maughan TS, Adams RA, Smith C.G., et al. Addition of cetuximab to oxaliplatin-based first-line combination chemotherapy for treatment of advanced colorectal cancer: results of the randomised phase 3 MRC COIN trial. Lancet 2011; 377: 2103-2114.
3. Van Cutsem E., Kohne CH, Lang I, et al. Cetuximab plus irinotecan, fluorouracil, and leucovorin as first-line treatment for metastatic colorectal cancer: updated analysis of overall survival according to tumor KRAS and BRAF mutation status. J Clin Oncol 2011; 29: 2011-2019.
4. Hecht JR, Mitchell E, Chidiac T., et al. A randomized phase IIIB trial of chemotherapy, bevacizumab, and panitumumab compared with chemotherapy and bevacizumab alone for metastatic colorectal cancer. J Clin Oncol 2009; 27: 672-680.
5. Saltz LB, Clarke S, Diaz-Rubio E, et al. Bevacizumab in combination with oxaliplatin-based chemotherapy as first-line therapy in metastatic colorectal cancer: a randomized phase III study. J Clin Oncol 2008; 26: 2013-2019.
6. Kopetz S, Chang GJ, Overman M.J., et al. Improved survival in metastatic colorectal cancer is associated with adoption of hepatic resection and improved chemotherapy. J Clin Oncol 2009; 27: 3677-3683.
7. Shen L, Toyota M, Kondo Y., et al. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci U S A 2007; 104: 18654-18659.
8. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330-337.
9. Bokemeyer C, Bondarenko I, Makhson A., et al. Fluorouracil, leucovorin, and oxaliplatin with and without cetuximab in the first-line treatment of metastatic colorectal cancer. J Clin Oncol 2009; 27: 663-671.
10. Di Fiore F., Blanchard F, Charbonnier F., et al. Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by cetuximab plus chemotherapy. Br J Cancer 2007; 96: 1166-1169.
11. Fakih M. The role of targeted therapy in the treatment of advanced colorectal cancer. Curr Treat Options Oncol 2008; 9: 357-374.
12. Fakih MM. KRAS mutation screening in colorectal cancer: from paper to practice. Clin Colorectal Cancer 2010; 9: 22-30.
13. Karapetis CS, Khambata-Ford S, Jonker D.J., et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 2008; 359: 1757-1765.
14. Tejpar S, Celik I, Schlichting M., et al. Association of KRAS G13D tumor mutations with outcome in patients with metastatic colorectal cancer treated with first-line chemotherapy with or without cetuximab. J Clin Oncol 2012; 30: 3570-3577.
15. De Roock W., Jonker DJ, Di Nicolantonio F, et al. Association of KRAS p.G13D mutation with outcome in patients with chemotherapy-refractory metastatic colorectal cancer treated with cetuximab. JAMA 2010; 304: 1812-1820.
16. Peeters M, Douillard JY, Van Cutsem E, et al. Mutant KRAS codon 12 and 13 alleles in patients with metastatic colorectal cancer: assessment as prognostic and predictive biomarkers of response to panitumumab. J Clin Oncol 2013; 31: 759-765.
17. De Roock W., Claes B, Bernasconi D., et al. Effects of KRAS, BRAF, NRAS, and PIK3CA mutations on the efficacy of cetuximab plus chemotherapy in chemotherapy-refractory metastatic colorectal cancer: a retrospective consortium analysis. Lancet Oncol 2010; 11: 753-762.
18. Di Nicolantonio F., Martini M, Molinari F., et al. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol 2008; 26: 5705-5712.
19. De Roock W., De Vriendt V, Normanno N, et al. KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer. Lancet Oncol 2011; 12: 594-603.
20. Loupakis F, Pollina L, Stasi I., et al. PTEN expression and KRAS mutations on primary tumors and metastases in the prediction of benefit from cetuximab plus irinotecan for patients with metastatic colorectal cancer. J Clin Oncol 2009; 27: 2622-2629.
21. Prenen H, De Schutter J, Jacobs B, et al. PIK3CA mutations are not a major determinant of resistance to the epidermal growth factor receptor inhibitor cetuximab in metastatic colorectal cancer. Clin Cancer Res 2009; 15: 3184-3188.
22. Krumbach R, Schuler J, Hofmann M., et al. Primary resistance to cetuximab in a panel of patient-derived tumour xenograft models: activation of MET as one mechanism for drug resistance. Eur J Cancer 2011; 47: 1231-1243.
23. Watkins D, Ayers M, Cunningham D., et al. Molecular analysis of the randomized phase II/III study of the anti-IGF-1R antibody dalotuzumab (MK-0646) in combination with cetuximab (Cx) and irinotecan (Ir) in the treatment of chemorefractory KRAS wildtype metastatic colorectal cancer (mCRC) [abstract]. J Clin Oncol 2012; 30(Suppl): Abstract 3531.
24. Shacham-Shmueli E., Beny A, Geva R., et al. Response to temozolomide in patients with metastatic colorectal cancer with loss of MGMT expression: a new approach in the era of personalized medicine? J Clin Oncol 2011; 29:e262-265.
25. Shirota Y, Stoehlmacher J, Brabender J., et al. ERCC1 and thymidylate synthase mRNA levels predict survival for colorectal cancer patients receiving combination oxaliplatin and fluorouracil chemotherapy. J Clin Oncol 2001; 19: 4298-4304.
26. Kelley RK, Van Bebber SL, Phillips KA, Venook A P. Personalized medicine and oncology practice guidelines: a case study of contemporary biomarkers in colorectal cancer. J Natl Compr Canc Netw 2011; 9: 13-25.
27. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11: 31-46.
28. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15: 733-747.
29. Majewski J, Schwartzentruber J, Lalonde E., et al. What can exome sequencing do for you? J Med Genet 2011; 48: 580-589.
30. Kerick M, Isau M, Timmermann B., et al. Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med Genomics 2011; 4: 68.
31. Schweiger MR, Kerick M, Timmermann B., et al. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One 2009; 4:e5548.
32. Wagle N, Berger M F, 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.
33. Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011; 11: 759-769.
34. Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 2011; 32: 177-195.
35. Mamanova L, Coffey AJ, Scott C.E., et al. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010; 7: 111-118.
36. Gnirke A, Melnikov A, Maguire J., et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009; 27: 182-189.
37. Hodges E, Rooks M, Xuan Z., et al. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 2009; 4: 960-974.
38. Fisher S, Barry A, Abreu J., et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 2011; 12:R1.
39. Grossmann V, Schnittger S, Schindela S., et al. Strategy for robust detection of insertions, deletions, and point mutations in CEBPA, a GC-rich content gene, using 454 next-generation deep-sequencing technology. J Mol Diagn 2011; 13: 129-136.
40. Oyola SO, Otto TD, Gu Y, et al. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 2012; 13: 1.
41. Quail MA, Smith M, Coupland P., et al. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012; 13: 341.
42. Querings S, Altmuller J, Ansen S., et al. Benchmarking of mutation diagnostics in clinical lung cancer specimens. PLoS One 2011; 6:e19601.
43. Toner B. At AACR, early providers of NGS-based cancer panel debate 'actionable' mutations, regulatory issues. Available at: www.genomeweb.com. Acccessed September 6, 2013.
44. Rehm HL, Bale SJ, Bayrak-Toydemir P, et al. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013; 15: 733-747.
45. Gargis AS, Kalman L, Berry M.W., et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012, 30: 1033-1036.
46. Fakih M. Targeting mechanisms of resistance to anti-EGF receptor therapy in KRAS wild-type colorectal cancer: the path to more personalized medicine. Future Oncol 2013; 9: 551-560.
47. Oliner K, Douillard J, Siena S., et al. Analysis of KRAS/NRAS and BRAF mutations in the phase III PRIME study of panitumumab (pmab) plus FOLFOX versus FOLFOX as first-line treatment (tx) for metastatic colorectal cancer (mCRC) [abstract]. J Clin Oncol 2013; 31(Suppl): Abstract 3511.
48. Kohlmann A, Grossmann V, Harbich S., et al. Next-generation deep-sequencing enables a quantitative monitoring of RUNX1 mutations in 534 patients with myelodysplastic/myeloproliferative neoplasms and myelodysplastic syndromes Blood 2011; 118: 2792.
49. Kohlmann A, Grossmann V, Fasan A., et al. Sensitive monitoring of mnimal residual disease status in CEBPA-mutated acute myeloid leukemia using amplicon deep-sequencing Blood 2011; 118: 2517.
50. Bentley DR, Balasubramanian S, Swerdlow H.P., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008; 456: 53-59.
51. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998; 281: 363.
52. Dressman D, Yan H, Traverso G., et al. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A 2003; 100: 8817-8822.
53. Margulies M, Egholm M, Altman W.E., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437: 376-380.
54. McKernan KJ, Peckham HE, Costa G.L., et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009; 19: 1527-1541.
55. Loman NJ, Misra RV, Dallman T.J., et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012; 30: 434-439.
56. Junemann S, Sedlazeck FJ, Prior K, et al. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013; 31: 294-296.
57. Rothberg JM, Hinz W, Rearick T.M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011; 475: 348-352.