Institutional implementation of clinical tumor profiling on an unselected cancer population

JCI Insight

Volumn 1, Issue 19, 2016, Pages

  Sholl, Lynette M ^a   Do, Khanh ^a,b,c   Shivdasani, Priyanka ^a   Cerami, Ethan ^c   Dubuc, Adrian M ^a   Kuo, Frank C ^a   Garcia, Elizabeth P ^a   Jia, Yonghui ^a   Davineni, Phani ^a   Abo, Ryan P ^a,c   Pugh, Trevor J ^d,e   van Hummelen, Paul ^c   Thorner, Aaron R ^c   Ducar, Matthew ^a,c   Berger, Alice H ^a,b,f   Nishino, Mizuki ^a   Janeway, Katherine A ^b   Church, Alanna ^g   Harris, Marian ^g   Ritterhouse, Lauren L ^a   Campbell, Joshua D ^a,b   Rojas Rudilla, Vanesa ^a,b   Ligon, Azra H ^a   Ramkissoon, Shakti ^a   Cleary, James M ^a,b,c   Matulonis, Ursula ^a,b   Oxnard, Geoffrey R ^a,b   Chao, Richard ^h   Tassell, Vanessa ^h   Christensen, James ^h   Hahn, William C ^a,b,c,f,i   Kantoff, Philip W ^a,i   Kwiatkowski, David J ^a,b   Johnson, Bruce E ^a,b   Meyerson, Matthew ^a,b,c,f   Garraway, Levi A ^a,b,c,f   Shapiro, Geoffrey I ^a,b,c   Rollins, Barrett J ^a,b   Lindeman, Neal I ^a   MacConaill, Laura E ^a,c   more..

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c DFCI   (United States)

^d PRINCESS MARGARET HOSPITAL   (Canada)

^e UNIVERSITY OF TORONTO   (Canada)

^f BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^g BOSTON CHILDREN S HOSPITAL   (United States)

^h METHYLGENE INC   (Canada)

ⁱ Lank Center for Genitourinary Oncology

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85055595914     PISSN: None     EISSN: 23793708     Source Type: Journal    
DOI: 10.1172/jci.insight.87062     Document Type: Article

References (54)

1. Cobleigh MA, et al. Multinational study of the efficacy and safety of humanized anti-HER2 monoclonal antibody in women who have HER2-overexpressing metastatic breast cancer that has progressed after chemotherapy for metastatic disease. J Clin Oncol. 1999;17(9):2639–2648.
2. Demetri GD, et al. Efficacy and safety of imatinib mesylate in advanced gastrointestinal stromal tumors. N Engl J Med. 2002;347(7):472–480.
3. Druker BJ, et al. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med. 1996;2(5):561–566.
4. Kris MG, et al. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs. JAMA. 2014;311(19):1998–2006.
5. Lopez-Chavez A, et al. Molecular profiling and targeted therapy for advanced thoracic malignancies: a biomarker-derived, multiarm, multihistology phase II basket trial. J Clin Oncol. 2015;33(9):1000–1007.
6. Mok TS, et al. Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. N Engl J Med. 2009;361(10):947–957.
7. Chapman PB, et al. Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med. 2011;364(26):2507–2516.
8. Garraway LA. Genomics-driven oncology: framework for an emerging paradigm. J Clin Oncol. 2013;31(15):1806–1814.
9. Meric-Bernstam F, Farhangfar C, Mendelsohn J, Mills GB. Building a personalized medicine infrastructure at a major cancer center. J Clin Oncol. 2013;31(15):1849–1857.
10. Brannon AR, et al. Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions. Genome Biol. 2014;15(8):454.
11. Cheng DT, et al. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. J Mol Diagn. 2015;17(3):251–264.
12. Frampton GM, et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat Biotechnol. 2013;31(11):1023–1031.
13. Van Allen EM, et al. Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. Nat Med. 2014;20(6):682–688.
14. Wagle N, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2012;2(1):82–93.
15. Won HH, Scott SN, Brannon AR, Shah RH, Berger MF. Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J Vis Exp. 2013;(80):e50710.
16. Beltran H, et al. Whole-exome sequencing of metastatic cancer and biomarkers of treatment response. JAMA Oncol. 2015;1(4):466–474.
17. Boland GM, et al. Clinical next generation sequencing to identify actionable aberrations in a phase I program. Oncotarget. 2015;6(24):20099–20110.
18. Johnson DB, et al. Enabling a genetically informed approach to cancer medicine: a retrospective evaluation of the impact of comprehensive tumor profiling using a targeted next-generation sequencing panel. Oncologist. 2014;19(6):616–622.
19. Schwaederle M, et al. On the Road to Precision Cancer Medicine: Analysis of Genomic Biomarker Actionability in 439 Patients. Mol Cancer Ther. 2015;14(6):1488–1494.
20. Meric-Bernstam F, et al. Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials. J Clin Oncol. 2015;33(25):2753–2762.
21. Jameson GS, et al. A pilot study utilizing multi-omic molecular profiling to find potential targets and select individualized treatments for patients with previously treated metastatic breast cancer. Breast Cancer Res Treat. 2014;147(3):579–588.
22. Gray SW, Hicks-Courant K, Cronin A, Rollins BJ, Weeks JC. Physicians’ attitudes about multiplex tumor genomic testing. J Clin Oncol. 2014;32(13):1317–1323.
23. Von Hoff DD, et al. Pilot study using molecular profiling of patients’ tumors to find potential targets and select treatments for their refractory cancers. J Clin Oncol. 2010;28(33):4877–4883.
24. Tsimberidou AM, et al. Personalized medicine in a phase I clinical trials program: the MD Anderson Cancer Center initiative. Clin Cancer Res. 2012;18(22):6373–6383.
25. Le Tourneau C, et al. Molecularly targeted therapy based on tumour molecular profiling versus conventional therapy for advanced cancer (SHIVA): a multicentre, open-label, proof-of-concept, randomised, controlled phase 2 trial. Lancet Oncol. 2015;16(13):1324–1334.
26. MacConaill LE, et al. Prospective enterprise-level molecular genotyping of a cohort of cancer patients. J Mol Diagn. 2014;16(6):660–672.
27. Spencer DH, et al. Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data. J Mol Diagn. 2013;15(1):81–93.
28. Ramkissoon SH, et al. Clinical implementation of integrated whole-genome copy number and mutation profiling for glioblastoma. Neuro-oncology. 2015;17(10):1344–1355.
29. Mandelker D, Dal Cin P, Jacene HA, Armand P, Stone RM, Lindeman NI. Refractory myeloid sarcoma with a FIP1L1-PDGFRA rearrangement detected by clinical high throughput somatic sequencing. Exp Hematol Oncol. 2015;4:30.
30. Doyle LA, et al. Ewing sarcoma mimicking atypical carcinoid tumor: detection of unexpected genomic alterations demonstrates the use of next generation sequencing as a diagnostic tool. Cancer Genet. 2014;207(7-8):335–339.
31. Lawrence MS, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499(7457):214–218.
32. Gandhi L, et al. Phase I study of neratinib in combination with temsirolimus in patients with human epidermal growth factor receptor 2-dependent and other solid tumors. J Clin Oncol. 2014;32(2):68–75.
33. Yasuda H, et al. Structural, biochemical, and clinical characterization of epidermal growth factor receptor (EGFR) exon 20 insertion mutations in lung cancer. Sci Transl Med. 2013;5(216):216ra177.
34. Jackman D, et al. Clinical definition of acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors in non-small-cell lung cancer. J Clin Oncol. 2010;28(2):357–360.
35. Gao J, et al. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal. 2013;6(269):pl1.
36. Cerami E, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401–404.
37. Zhang Z, et al. Activation of the AXL kinase causes resistance to EGFR-targeted therapy in lung cancer. Nat Genet. 2012;44(8):852–860.
38. Rho JK, et al. MET and AXL inhibitor NPS-1034 exerts efficacy against lung cancer cells resistant to EGFR kinase inhibitors because of MET or AXL activation. Cancer Res. 2014;74(1):253–262.
39. Levin PA, Brekken RA, Byers LA, Heymach JV, Gerber DE. Axl Receptor Axis: A New Therapeutic Target in Lung Cancer. J Thorac Oncol. 2016;11(8):1357–1362.
40. Drilon A, et al. Broad, hybrid capture-based next-generation sequencing identifies actionable genomic alterations in lung adenocarcinomas otherwise negative for such alterations by other genomic testing approaches. Clin Cancer Res. 2015;21(16):3631–3639.
41. Iyer G, et al. Genome sequencing identifies a basis for everolimus sensitivity. Science. 2012;338(6104):221.
42. Wagle N, et al. Activating mTOR mutations in a patient with an extraordinary response on a phase I trial of everolimus and pazopanib. Cancer Discov. 2014;4(5):546–553.
43. Jones S, et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med. 2015;7(283):283ra53.
44. Garofalo A, et al. The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016;8(1):79.
45. Seifert BA, et al. Germline analysis from tumor-germline sequencing dyads to identify clinically actionable secondary findings. Clin Cancer Res. 2016;22(16):4087–4094.
46. Chau NG, et al. Incorporation of next-generation sequencing into routine clinical care to direct treatment of head and neck squamous cell carcinoma. Clin Cancer Res. 2016;22(12):2939–2949.
47. Harris MH, et al. Multicenter feasibility study of tumor molecular profiling to inform therapeutic decisions in advanced pediatric solid tumors: The Individualized Cancer Therapy (iCat) Study. JAMA Oncol. 2016;2(5):608–615.
48. Mason EF, et al. Detection of activating MAP2K1 mutations in atypical hairy cell leukemia and hairy cell leukemia variant. Leuk Lymphoma. 2017;58(1):233–236.
49. Redig AJ, et al. Clinical and molecular characteristics of NF1-mutant lung cancer. Clin Cancer Res. 2016;22(13):3148–3156.
50. Hwang DH, et al. KRAS and NKX2-1 mutations in invasive mucinous adenocarcinoma of the lung. J Thorac Oncol. 2016;11(4):496–503.
51. Awad MM, et al. MET exon 14 mutations in non-small-cell lung cancer are associated with advanced age and stage-dependent MET genomic amplification and c-Met overexpression. J Clin Oncol. 2016;34(7):721–730.
52. Gao X, Sholl LM, Nishino M, Heng JC, Jänne PA, Oxnard GR. Clinical Implications of Variant ALK FISH Rearrangement Patterns. J Thorac Oncol. 2015;10(11):1648–1652.
53. Lee JJ, et al. Targeted next-generation sequencing reveals high frequency of mutations in epigenetic regulators across treatment-naïve patient melanomas. Clin Epigenetics. 2015;7:59.
54. Tanizaki J, et al. Identification of oncogenic and drug-sensitizing mutations in the extracellular domain of FGFR2. Cancer Res. 2015;75(15):3139–3146.