Multigene Assays in Metastatic Colorectal Cancer

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  • a From the Center for Human Genetics Laboratory, Case Western Reserve University, Cleveland, Ohio; Clinical Molecular Diagnostic Laboratory, Department of Pathology, City of Hope Comprehensive Cancer Center, Duarte, California; Fulgent Therapeutics Inc, Temple City, California; and Medical Oncology and Experimental Therapeutics, City of Hope Comprehensive Cancer Center, Duarte, California.
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Specific genomic colorectal cancer alterations are increasingly linked to prognosis and/or response to specific anticancer agents. The identification of KRAS mutations as markers of resistance to epidermal growth factor receptor (EGFR) inhibitors has paved the way to the interrogation of numerous other markers of resistance to anti-EGFR therapy, such as NRAS, BRAF, and PI3KCA mutations. Other genomic and protein expression alterations have recently been identified as potential targets of treatment or as markers of chemotherapy or targeted-therapy resistance, including ERCC1 expression, c-Met expression, PTEN expression, HER2 amplification, HER3 expression, and rare KRAS mutations. As the number of distinct validated intratumor genomic assays increases, numerous molecular assays will need to be compiled into one multigene panel assay. Several companies and academic centers are now offering multigene assays to patients with metastatic colorectal cancer and other solid tumors. This article discusses the technology behind multigene assays, its limitations, its current advantages, and its potential in the clinical care of metastatic colorectal cancer.

Correspondence: Marwan G. Fakih, MD, Medical Oncology and Experimental Therapeutics, Gastrointestinal Medical Oncology, City of Hope Comprehensive Cancer Center, 1500 East Duarte Street, Duarte, CA 91010. E-mail: mfakih@coh.org
  • 1.

    Jemal A, Bray F, Center MM. Global cancer statistics. CA Cancer J Clin 2011;61:6990.

  • 2.

    Maughan TS, Adams RA, Smith CG. 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;377:21032114.

    • Search Google Scholar
    • Export Citation
  • 3.

    Van Cutsem E, Kohne CH, Lang I. 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;29:20112019.

    • Search Google Scholar
    • Export Citation
  • 4.

    Hecht JR, Mitchell E, Chidiac T. A randomized phase IIIB trial of chemotherapy, bevacizumab, and panitumumab compared with chemotherapy and bevacizumab alone for metastatic colorectal cancer. J Clin Oncol 2009;27:672680.

    • Search Google Scholar
    • Export Citation
  • 5.

    Saltz LB, Clarke S, Diaz-Rubio E. Bevacizumab in combination with oxaliplatin-based chemotherapy as first-line therapy in metastatic colorectal cancer: a randomized phase III study. J Clin Oncol 2008;26:20132019.

    • Search Google Scholar
    • Export Citation
  • 6.

    Kopetz S, Chang GJ, Overman MJ. Improved survival in metastatic colorectal cancer is associated with adoption of hepatic resection and improved chemotherapy. J Clin Oncol 2009;27:36773683.

    • Search Google Scholar
    • Export Citation
  • 7.

    Shen L, Toyota M, Kondo Y. Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci U S A 2007;104:1865418659.

    • Search Google Scholar
    • Export Citation
  • 8.

    Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330337.

  • 9.

    Bokemeyer C, Bondarenko I, Makhson A. Fluorouracil, leucovorin, and oxaliplatin with and without cetuximab in the first-line treatment of metastatic colorectal cancer. J Clin Oncol 2009;27:663671.

    • Search Google Scholar
    • Export Citation
  • 10.

    Di Fiore F, Blanchard F, Charbonnier F. Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by cetuximab plus chemotherapy. Br J Cancer 2007;96:11661169.

    • Search Google Scholar
    • Export Citation
  • 11.

    Fakih M. The role of targeted therapy in the treatment of advanced colorectal cancer. Curr Treat Options Oncol 2008;9:357374.

  • 12.

    Fakih MM. KRAS mutation screening in colorectal cancer: from paper to practice. Clin Colorectal Cancer 2010;9:2230.

  • 13.

    Karapetis CS, Khambata-Ford S, Jonker DJ. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 2008;359:17571765.

    • Search Google Scholar
    • Export Citation
  • 14.

    Tejpar S, Celik I, Schlichting M. 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;30:35703577.

    • Search Google Scholar
    • Export Citation
  • 15.

    De Roock W, Jonker DJ, Di Nicolantonio F. Association of KRAS p.G13D mutation with outcome in patients with chemotherapy-refractory metastatic colorectal cancer treated with cetuximab. JAMA 2010;304:18121820.

    • Search Google Scholar
    • Export Citation
  • 16.

    Peeters M, Douillard JY, Van Cutsem E. 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;31:759765.

    • Search Google Scholar
    • Export Citation
  • 17.

    De Roock W, Claes B, Bernasconi D. 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;11:753762.

    • Search Google Scholar
    • Export Citation
  • 18.

    Di Nicolantonio F, Martini M, Molinari F. Wild-type BRAF is required for response to panitumumab or cetuximab in metastatic colorectal cancer. J Clin Oncol 2008;26:57055712.

    • Search Google Scholar
    • Export Citation
  • 19.

    De Roock W, De Vriendt V, Normanno N. KRAS, BRAF, PIK3CA, and PTEN mutations: implications for targeted therapies in metastatic colorectal cancer. Lancet Oncol 2011;12:594603.

    • Search Google Scholar
    • Export Citation
  • 20.

    Loupakis F, Pollina L, Stasi I. 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;27:26222629.

    • Search Google Scholar
    • Export Citation
  • 21.

    Prenen H, De Schutter J, Jacobs B. 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;15:31843188.

    • Search Google Scholar
    • Export Citation
  • 22.

    Krumbach R, Schuler J, Hofmann M. 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;47:12311243.

    • Search Google Scholar
    • Export Citation
  • 23.

    Watkins D, Ayers M, Cunningham D. 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 wild-type metastatic colorectal cancer (mCRC) [abstract]. J Clin Oncol 2012;30(Suppl):Abstract 3531.

    • Search Google Scholar
    • Export Citation
  • 24.

    Shacham-Shmueli E, Beny A, Geva R. 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:e262265.

    • Search Google Scholar
    • Export Citation
  • 25.

    Shirota Y, Stoehlmacher J, Brabender J. ERCC1 and thymidylate synthase mRNA levels predict survival for colorectal cancer patients receiving combination oxaliplatin and fluorouracil chemotherapy. J Clin Oncol 2001;19:42984304.

    • Search Google Scholar
    • Export Citation
  • 26.

    Kelley RK, Van Bebber SL, Phillips KA, Venook AP. Personalized medicine and oncology practice guidelines: a case study of contemporary biomarkers in colorectal cancer. J Natl Compr Canc Netw 2011;9:1325.

    • Search Google Scholar
    • Export Citation
  • 27.

    Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010;11:3146.

  • 28.

    Rehm HL, Bale SJ, Bayrak-Toydemir P. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013;15:733747.

  • 29.

    Majewski J, Schwartzentruber J, Lalonde E. What can exome sequencing do for you? J Med Genet 2011;48:580589.

  • 30.

    Kerick M, Isau M, Timmermann B. 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.

    • Search Google Scholar
    • Export Citation
  • 31.

    Schweiger MR, Kerick M, Timmermann B. Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS One 2009;4:e5548.

    • Search Google Scholar
    • Export Citation
  • 32.

    Wagle N, Berger MF, Davis MJ. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2012;2:8293.

    • Search Google Scholar
    • Export Citation
  • 33.

    Glenn TC. Field guide to next-generation DNA sequencers. Mol Ecol Resour 2011;11:759769.

  • 34.

    Meldrum C, Doyle MA, Tothill RW. Next-generation sequencing for cancer diagnostics: a practical perspective. Clin Biochem Rev 2011;32:177195.

    • Search Google Scholar
    • Export Citation
  • 35.

    Mamanova L, Coffey AJ, Scott CE. Target-enrichment strategies for next-generation sequencing. Nat Methods 2010;7:111118.

  • 36.

    Gnirke A, Melnikov A, Maguire J. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009;27:182189.

    • Search Google Scholar
    • Export Citation
  • 37.

    Hodges E, Rooks M, Xuan Z. Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing. Nat Protoc 2009;4:960974.

    • Search Google Scholar
    • Export Citation
  • 38.

    Fisher S, Barry A, Abreu J. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 2011;12:R1.

    • Search Google Scholar
    • Export Citation
  • 39.

    Grossmann V, Schnittger S, Schindela S. 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;13:129136.

    • Search Google Scholar
    • Export Citation
  • 40.

    Oyola SO, Otto TD, Gu Y. Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics 2012;13:1.

    • Search Google Scholar
    • Export Citation
  • 41.

    Quail MA, Smith M, Coupland P. A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 2012;13:341.

    • Search Google Scholar
    • Export Citation
  • 42.

    Querings S, Altmuller J, Ansen S. 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.

    • Search Google Scholar
    • Export Citation
  • 44.

    Rehm HL, Bale SJ, Bayrak-Toydemir P. ACMG clinical laboratory standards for next-generation sequencing. Genet Med 2013;15:733747.

  • 45.

    Gargis AS, Kalman L, Berry MW. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nat Biotechnol 2012,30:10331036.

    • Search Google Scholar
    • Export Citation
  • 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;9:551560.

    • Search Google Scholar
    • Export Citation
  • 47.

    Oliner K, Douillard J, Siena S. 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.

    • Search Google Scholar
    • Export Citation
  • 48.

    Kohlmann A, Grossmann V, Harbich S. 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.

    • Search Google Scholar
    • Export Citation
  • 49.

    Kohlmann A, Grossmann V, Fasan A. Sensitive monitoring of mnimal residual disease status in CEBPA-mutated acute myeloid leukemia using amplicon deep-sequencing Blood 2011;118:2517.

    • Search Google Scholar
    • Export Citation
  • 50.

    Bentley DR, Balasubramanian S, Swerdlow HP. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008;456:5359.

    • Search Google Scholar
    • Export Citation
  • 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. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations. Proc Natl Acad Sci U S A 2003;100:88178822.

    • Search Google Scholar
    • Export Citation
  • 53.

    Margulies M, Egholm M, Altman WE. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005;437:376380.

  • 54.

    McKernan KJ, Peckham HE, Costa GL. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 2009;19:15271541.

    • Search Google Scholar
    • Export Citation
  • 55.

    Loman NJ, Misra RV, Dallman TJ. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 2012;30:434439.

  • 56.

    Junemann S, Sedlazeck FJ, Prior K. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013;31:294296.

  • 57.

    Rothberg JM, Hinz W, Rearick TM. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475: 348352.

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