Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer

DNA Research

Volumn 24, Issue 6, 2017, Pages 585-596

  Suzuki, Ayako ^a   Suzuki, Mizuto ^b   Mizushima Sugano, Junko ^b,c   Frith, Martin C ^b,d   Makałowski, Wojciech ^e   Kohno, Takashi ^f   Sugano, Sumio ^b   Tsuchihara, Katsuya ^a   Suzuki, Yutaka ^b  

^a NATIONAL CANCER CENTER HOSPITAL EAST   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KOGAKUIN UNIVERSITY   (Japan)

^d NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^e UNIVERSITY OF MÜNSTER   (Germany)

^f NATIONAL CANCER CENTER RESEARCH INSTITUTE   (Japan)

Author keywords

Cancer mutations; Lung cancer cell lines; MinION; Phasing

Indexed keywords

COMPLEMENTARY DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; PROTEIN RET; EGFR PROTEIN, HUMAN; TUMOR MARKER;

ALLELE; AMPLICON; ARTICLE; CANCER GENETICS; CCDC6 RET GENE; CELL POPULATION; EML4 ALK GENE; GENE FUSION; GENE MUTATION; GENE SEQUENCE; GENETIC BACKGROUND; HUMAN; HUMAN CELL; LUNG CANCER; NCI-H1975 CELL LINE; NF1 GENE; ONCOGENE K RAS; ONCOGENE N RAS; SINGLE NUCLEOTIDE POLYMORPHISM; TUMOR-RELATED GENE; ADENOCARCINOMA; DEVICES; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; LUNG TUMOR; MUTATION; PROCEDURES;

ADENOCARCINOMA; BIOMARKERS, TUMOR; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; MUTATION; RECEPTOR, EPIDERMAL GROWTH FACTOR; SEQUENCE ANALYSIS, DNA;

EID: 85042540891     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsx027     Document Type: Article

References (39)

1. The Cancer Genome Atlas Research Network, Weinstein, J.N., Collisson, E.A., et al. 2013, The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet., 45, 1113-20.
2. International Cancer Genome Consortium 2010, International network of cancer genome projects. Nature, 464, 993-8.
3. Sharma, S.V., Bell, D.W., Settleman, J. and Haber, D.A. 2007, Epidermal growth factor receptor mutations in lung cancer. Nat. Rev. Cancer, 7, 169-81.
4. Soda, M., Choi, Y.L., Enomoto, M., et al. 2007, Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature, 448, 561-6.
5. Kwak, E.L., Bang, Y.J., Camidge, D.R., et al. 2010, Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N. Engl J. Med., 363, 1693-1703.
6. Jain, M., Fiddes, I.T., Miga, K.H., Olsen, H.E., Paten, B. and Akeson, M. 2015, Improved data analysis for the MinION nanopore sequencer. Nat. Methods, 12, 351-6.
7. Ashton, P.M., Nair, S., Dallman, T., et al. 2015, MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol., 33, 296-300.
8. Quick, J., Ashton, P., Calus, S., et al. 2015, Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol., 16, 114.
9. Quick, J., Loman, N.J., Duraffour, S., et al. 2016, Real-time, portable genome sequencing for Ebola surveillance. Nature, 530, 228-32.
10. Norris, A.L., Workman, R.E., Fan, Y., Eshleman, J.R. and Timp, W. 2016, Nanopore sequencing detects structural variants in cancer. Cancer Biol. Ther., 17, 246-53.
11. Minervini, C.F., Cumbo, C., Orsini, P., et al. 2016, TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing. Diagn. Pathol., 11, 96.
12. Suzuki, A., Makinoshima, H., Wakaguri, H., et al. 2014, Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines. Nucleic Acids Res., 42, 13557-72.
13. Kohno, T., Ichikawa, H., Totoki, Y., et al. 2012, KIF5B-RET fusions in lung adenocarcinoma. Nat. Med., 18, 375-7.
14. Untergasser, A., Nijveen, H., Rao, X., Bisseling, T., Geurts, R. and Leunissen, J.A. 2007, Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res., 35, W71-4.
15. Loman, N.J. and Quinlan, A.R. 2014, Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics, 30, 3399-401.
16. Kiełbasa, S.M., Wan, R., Sato, K., Horton, P. and Frith, M.C. 2011, Adaptive seeds tame genomic sequence comparison. Genome Res., 21, 487-93.
17. Li, H. and Durbin, R. 2009, Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-60.
18. Hamada, M., Ono, Y., Asai, K. and Frith, M.C. 2016, Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinformatics, 33, 926-8.
19. Frith, M.C., Wan, R. and Horton, P. 2010, Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res, 38, e100.
20. Speir, M.L., Zweig, A.S., Rosenbloom, K.R., et al. 2016, The UCSC Genome Browser database: 2016 update. Nucleic Acids Res, 44, D717-25.
21. Wu, T.D. and Nacu, S. 2010, Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics, 26, 873-81.
22. Frith, M.C. and Kawaguchi, R. 2015, Split-alignment of genomes finds orthologies more accurately. Genome Biol., 16, 106.
23. Matsubara, D., Kanai, Y., Ishikawa, S., et al. 2012, Identification of CCDC6-RET fusion in the human lung adenocarcinoma cell line, LC-2/ ad. J. Thorac. Oncol., 7, 1872-6.
24. Suzuki, M., Makinoshima, H., Matsumoto, S., et al. 2013, Identification of a lung adenocarcinoma cell line with CCDC6-RET fusion gene and the effect of RET inhibitors in vitro and in vivo. Cancer Sci., 104, 896-903.
25. Jung, Y., Kim, P., Keum, J., et al. 2012, Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing. Genes Chromosomes Cancer, 51, 590-7.
26. Ding, L., Getz, G., Wheeler, D.A., et al. 2008, Somatic mutations affect key pathways in lung adenocarcinoma. Nature, 455, 1069-75.
27. Imielinski, M., Berger, A.H., Hammerman, P.S., et al. 2012, Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell, 150, 1107-20.
28. Seo, J.S., Ju, Y.S., Lee, W.C., et al. 2012, The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res., 22, 2109-19.
29. Suzuki, A., Mimaki, S., Yamane, Y., et al. 2013, Identification and characterization of cancer mutations in Japanese lung adenocarcinoma without sequencing of normal tissue counterparts. PLoS One, 8, e73484.
30. The Cancer Genome Atlas Research Network 2014, Comprehensive molecular profiling of lung adenocarcinoma. Nature, 511, 543-50.
31. Pao, W., Miller, V.A., Politi, K.A., et al. 2005, Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain. PLoS Med., 2, e73.
32. Thress, K.S., Paweletz, C.P., Felip, E., et al. 2015, Acquired EGFR C797S mutation mediates resistance to AZD9291 in non-small cell lung cancer harboring EGFR T790M. Nat. Med., 21, 560-2.
33. Soda, M., Isobe, K., Inoue, A., et al. 2012, A prospective PCR-based screening for the EML4-ALK oncogene in non-small cell lung cancer. Clin. Cancer Res., 18, 5682-9.
34. Yang, Z., Hackshaw, A., Feng, Q., et al. 2017, Comparison of gefitinib, erlotinib and afatinib in non-small cell lung cancer: A meta-analysis. Int. J. Cancer, 140, 2805-19.
35. Katayama, R., Friboulet, L., Koike, S., et al. 2014, Two novel ALK mutations mediate acquired resistance to the next-generation ALK inhibitor alectinib. Clin Cancer Res., 20, 5686-96.
36. Kohno, T., Tsuta, K., Tsuchihara, K., Nakaoku, T., Yoh, K. and Goto, K. 2013, RET fusion gene: translation to personalized lung cancer therapy. Cancer Sci., 104, 1396-1400.
37. Camidge, D.R., Pao, W. and Sequist, L.V. 2014, Acquired resistance to TKIs in solid tumours: learning from lung cancer. Nat. Rev. Clin. Oncol., 11, 473-81.
38. Niederst, M.J., Hu, H., Mulvey, H.E., et al. 2015, The allelic context of the C797S mutation acquired upon treatment with third-generation EGFR inhibitors impacts sensitivity to subsequent treatment strategies. Clin. Cancer Res., 21, 3924-33.
39. Shaw, A.T., Friboulet, L., Leshchiner, I., et al. 2016, Resensitization to crizotinib by the lorlatinib ALK resistance mutation L1198F. N. Engl J. Med., 374, 54-61.