Routine clinical mutation profiling of non-small cell lung cancer using next-generation sequencing

Archives of Pathology and Laboratory Medicine

Volumn 139, Issue 7, 2015, Pages 913-921

  Deeb, Kristin K ^a,b   Hohman, Colleen M ^a   Risch, Nicholas F ^a,c   Metzger, Daniel J ^a   Starostik, Petr ^a,d  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

^b UNIVERSITY HOSPITALS OF CLEVELAND   (United States)

^c Life Technologies   (United States)

^d UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TUMOR MARKER;

DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; LUNG TUMOR; MUTATION; NON SMALL CELL LUNG CANCER; NUCLEOTIDE SEQUENCE; PATHOLOGY; PROCEDURES;

CARCINOMA, NON-SMALL-CELL LUNG; DNA MUTATIONAL ANALYSIS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; MUTATION; SEQUENCE ANALYSIS, DNA; TUMOR MARKERS, BIOLOGICAL;

EID: 84936854223     PISSN: 00039985     EISSN: 15432165     Source Type: Journal    
DOI: 10.5858/arpa.2014-0095-OA     Document Type: Article

References (32)

1. Shaw AT, Kim DW, Nakagawa K, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med. 2013;368(25):2385-2394.
2. Sequist LV, Yang JC, Yamamoto N, et al. Phase III study of afatinib or cisplatin plus pemetrexed in patients with metastatic lung adenocarcinoma with EGFR mutations. J Clin Oncol. 2013;31(27):3327-3334.
3. Gridelli C, de Marinis F, Cappuzzo F, et al. Treatment of advanced non-small-cell lung cancer with epidermal growth factor receptor (EGFR) mutation or ALK gene rearrangement: results of an international expert panel meeting of the Italian Association of Thoracic Oncology. Clin Lung Cancer. 2014;15(3):173-181.
4. American Cancer Society. Cancer facts and figures 2014. Atlanta, GA: American Cancer Society; 2014 http://www.cancer.org/acs/groups/content/@ research/documents/webcontent/acspc-042151.pdf. Accessed May 15, 2014.
5. Liu SV, Giaccone G. Lung cancer in 2013: refining standard practice and admitting uncertainty. Nat Rev Clin Oncol. 2014;11(2):69-70.
6. Lindeman NI, Cagle PT, Beasley MB, et al; College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. Molecular testing guideline for selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors: guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology. J Mol Diagn. 2013;15(4):415-453.
7. Kobayashi K, Hagiwara K. Epidermal growth factor receptor (EGFR) mutation and personalized therapy in advanced nonsmall cell lung cancer (NSCLC). Target Oncol. 2013;8(1):27-33.
8. Ettinger DS, Akerley W, Borghaei H, et al; NCCN (National Comprehensive Cancer Network). Non-small cell lung cancer. J Natl Compr Canc Netw. 2012; 10(10):1236-1271.
9. Pao W, Girard N. New driver mutations in non-small cell lung cancer. Lancet Oncol. 2011;12(2):175-180.
10. Kris MG, Johnson BE, Kwiatkowski DJ, et al. Identification of driver mutations in tumor specimens from 1000 patients with lung adenocarcinoma: the NCI's Lung Cancer Mutation Consortium (LCMC) [abstract]. J Clin Oncol. 2011; 29(18)(suppl):CRA7506.
11. Ali SM, Palma NA, Wang K, et al. Clinical next generation sequencing (NGS) to reveal high frequency of alterations to guide targeted therapy in lung cancer patients [abstract]. J Clin Oncol. 2013;31(suppl):8020.
12. 454 Life Sciences Corporation. 454 Sequencing System Software Manual v2.7. Branford, CT: Roche; 2012.
13. 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(1):82-93.
14. Duffy MJ, Crown J. Companion biomarkers: paving the pathway to personalized treatment for cancer. Clin Chem. 2013;59(10):1447-1456.
15. Buttitta F, Felicioni L, Del Grammastro M, et al. Effective assessment of EGFR mutation status in bronchoalveolar lavage and pleural fluids by next-generation sequencing. Clin Cancer Res. 2013;19(3):691-698.
16. Kohlmann A, Klein HU, Weissmann S, et al. The Interlaboratory Robustness of Next-Generation Sequencing (IRON) study: a deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories. Leukemia. 2011;25(12):1840-1848.
17. Moskalev EA, Stöhr R, Rieker R, et al. Increased detection rates of EGFR and KRAS mutations in NSCLC specimens with low tumour cell content by 454 deep sequencing. Virchows Arch. 2013;462(4):409-419.
18. Gullapalli RR, Lyons-Weiler M, Petrosko P, Dhir R, Becich MJ, LaFramboise WA. Clinical integration of next-generation sequencing technology. Clin Lab Med. 2012;32(4):585-599.
19. O'Brien CP, Taylor SE, O'Leary JJ, Finn SP. Molecular testing in oncology: problems, pitfalls and progress. Lung Cancer. 2014;83(3):309-315.
20. Chan M, Lee CW, Wu M. Integrating next-generation sequencing into clinical cancer diagnostics. Expert Rev Mol Diagn. 2013;13(7):647-650.
21. Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30(5): 434-439.
22. De Schrijver JM, De Leeneer K, Lefever S, et al. Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC Bioinformatics. 2010;11:269. doi:10.1186/1471-2105-11-269.
23. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics. 2011;12:245.
24. Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 2007;8(7): R143. doi:10.1186/gb-2007-8-7-r143.
25. Cheng L, Alexander RE, Maclennan GT, et al. Molecular pathology of lung cancer: key to personalized medicine. Mod Pathol. 2012;25(3):347-369.
26. Zhang L, Shi L, Zhao X, Wang Y, Yue W. PIK3CA gene mutation associated with poor prognosis of lung adenocarcinoma. Onco Targets Ther. 2013;6:497-502.
27. Janku F, Wheler JJ, Naing A, et al. PIK3CA mutation H1047R is associated with response to PI3K/AKT/mTOR signaling pathway inhibitors in early-phase clinical trials. Cancer Res. 2013;73(1):276-284.
28. Querings S, Altmüller J, Ansén S, et al. Benchmarking of mutation diagnostics in clinical lung cancer specimens. PLoS One. 2011;6(5):e19601. doi: 10.1371/journal.pone.0019601.
29. Tuononen K, Maki-Nevala S, Sarhadi VK, et al. Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS. Genes Chromosomes Cancer. 2013;52(5):503-511.
30. Chen G, Olson MT, O'Neill A, et al. A virtual pyrogram generator to resolve complex pyrosequencing results. J Mol Diagn. 2012;14(2):149-159.
31. Wadsworth Center New York State Department of Health. "Next generation" sequencing (NGS) guidelines for somatic genetic variant detection. Albany, NY: Wadsworth Center New York State Department of Health. http://www.wadsworth.org/labcert/TestApproval/forms/NextGenSeq-ONCO-Guidelines.pdf. Updated January 2014. Accessed June 8, 2014.
32. Schrijver I, Aziz N, Farkas DH, et al. Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. J Mol Diagn. 2012;14(6):525-540.