Skip to main content
SpringerLink
Log in

Next-Generation Sequencing and Bioinformatics

  • Chapter
  • First Online:
Molecular Targeted Therapy of Lung Cancer

Abstract

Improvement of next-generation sequencing (NGS) has revealed novel driver genes and new therapeutic targets for cancer patients. We summarize here the history of NGS development, current situation of typical analysis pipeline utilizing NGS – especially whole exome sequencing (WES) – whole transcriptome sequencing (WTS/RNA-seq), and useful public databases and tools for NGS data analysis. Large-scale sequencing projects such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) have sequenced hundreds of tumor samples of different subtypes to provide catalogues of cancer genome. Chromothripsis, kataegis, and chromoplexy were discovered from those studies using second-generation technologies. Recent novel findings, such as RET gene fusion in lung cancer using these NGS following clinical translation, are also noted here. Clinical sequencing to find personalized treatment strategies for cancer patients has also been done for lung cancer. Mutations of EGFR and ALK are widely applied to screening for administration of EGFR-TKI and crizotinib, respectively. WES – targeting >100s mutation sequencing using NGS – has rapidly become a common way of clinical sequencing. Actionable mutations are used not only as targets of molecular therapy but also as markers for better stratifications in clinical trials.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    CAS  PubMed  PubMed Central  Google Scholar 

  2. Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  CAS  PubMed  Google Scholar 

  3. Buermans HP, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 842:1932–1941

    Article  Google Scholar 

  4. Mardis ER (2011) A decade’s perspective on DNA sequencing technology. Nature 470:198–203

    Article  CAS  PubMed  Google Scholar 

  5. Stephens PJ, Greenman CD, Fu B, Yang F, Bignell GR, Mudie LJ, Pleasance ED, Lau KW, Beare D, Stebbings LA et al (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27–40

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD, Raine K, Jones D, Hinton J, Marshall J, Stebbings LA, Menzies A, Martin S, Leung K, Chen L, Leroy C, Ramakrishna M, Rance R, Lau KW, Mudie LJ, Varela I, McBride DJ, Bignell GR, Cooke SL, Shlien A, Gamble J, Whitmore I, Maddison M, Tarpey PS, Davies HR, Papaemmanuil E, Stephens PJ, McLaren S, Butler AP, Teague JW, Jönsson G, Garber JE, Silver D, Miron P, Fatima A, Boyault S, Langerød A, Tutt A, Martens JW, Aparicio SA, Borg Å, Salomon AV, Thomas G, Børresen-Dale AL, Richardson AL, Neuberger MS, Futreal PA, Campbell PJ, Stratton MR, Breast Cancer Working Group of the International Cancer Genome Consortium (2012) Mutational processes molding the genomes of 21 breast cancers. Cell 149:979–993

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Baca SC, Prandi D, Lawrence MS, Mosquera JM, Romanel A, Drier Y, Park K, Kitabayashi N, MacDonald TY, Ghandi M, Van Allen E, Kryukov GV, Sboner A, Theurillat JP, Soong TD, Nickerson E, Auclair D, Tewari A, Beltran H, Onofrio RC, Boysen G, Guiducci C, Barbieri CE, Cibulskis K, Sivachenko A, Carter SL, Saksena G, Voet D, Ramos AH, Winckler W, Cipicchio M, Ardlie K, Kantoff PW, Berger MF, Gabriel SB, Golub TR, Meyerson M, Lander ES, Elemento O, Getz G, Demichelis F, Rubin MA, Garraway LA (2013) Punctuated evolution of prostate cancer genomes. Cell 153:666–677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Roberts RJ, Carneiro MO, Schatz MC (2013) The advantages of SMRT sequencing. Genome Biol 14:401–404

    Article  Google Scholar 

  9. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong X, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma C, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323:133–138

    Article  CAS  PubMed  Google Scholar 

  10. Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DE, Celniker SE, Phillippy AM, Bergman CM, Landolin JM (2014) Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data 1:140045. doi:10.1038/sdata.2014.45 eCollection 2014

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Rhoads A, Au KF. (2015) PacBio sequencing and its applications. Genomics Proteomics Bioinformatics: pii: S1672-0229(15)00134-5. doi:10.1016/j.gpb.2015.08.002

  12. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569

    Article  CAS  PubMed  Google Scholar 

  13. Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, BRIDGE Consortium, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HH, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A (2014) Transcriptional diversity during lineage commitment of human blood progenitors. Science 345:1251033

    Article  PubMed  PubMed Central  Google Scholar 

  14. Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy AM (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30:693–700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ (2014) Characterization of structural variants with single molecule and hybrid sequencing approaches. Bioinformatics 30:3458–3466

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Doi K, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, Ishiura H, Takahashi Y, Ichikawa Y, Goto J, Tsuji S, Morishita S (2014) Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. Bioinformatics 30:815–822

    Article  CAS  PubMed  Google Scholar 

  17. Tilgner H, Grubert F, Sharon D, Snyder MP (2014) Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A 111:9869–9874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF (2015) Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing. Nucleic Acids Res 43:e116

    Article  PubMed  PubMed Central  Google Scholar 

  19. Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG, Wong WH (2013) Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A 110:E4821–E4830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Pendleton M, Sebra R, Pang AW, Ummat A, Franzen O, Rausch T, Stütz AM, Stedman W, Anantharaman T, Hastie A, Dai H, Fritz MH, Cao H, Cohain A, Deikus G, Durrett RE, Blanchard SC, Altman R, Chin CS, Guo Y, Paxinos EE, Korbel JO, Darnell RB, McCombie WR, Kwok PY, Mason CE, Schadt EE, Bashir A (2015) Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat Methods 12:780–786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Fomenkov A, Lunnen KD, Zhu Z, Anton BP, Wilson GG, Vincze T, Roberts RJ (2015) Complete genome sequence and methylome analysis of bacillus strain x1. Genome Announc 3:e01593–e015914

    PubMed  PubMed Central  Google Scholar 

  22. Smith CC, Wang Q, Chin CS, Salerno S, Damon LE, Levis MJ, Perl AE, Travers KJ, Wang S, Hunt JP, Zarrinkar PP, Schadt EE, Kasarskis A, Kuriyan J, Shah NP (2012) Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature 485:260–263

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Smith CC, Zhang C, Lin KC, Lasater EA, Zhang Y, Massi E, Damon LE, Pendleton M, Bashir A, Sebra R, Perl A, Kasarskis A, Shellooe R, Tsang G, Carias H, Powell B, Burton EA, Matusow B, Zhang J, Spevak W, Ibrahim PN, Le MH, Hsu HH, Habets G, West BL, Bollag G, Shah NP (2015) Characterizing and overriding the structural mechanism of the Quizartinib-Resistant FLT3 “Gatekeeper” F691 L mutation with PLX3397. Cancer Discov 5:668–679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Cavelier L, Ameur A, Haggqvist S, Hoijer I, Cahill N, Olsson-Stromberg U, Hermanson M (2015) Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing. BMC Cancer 15:41–45

    Article  Google Scholar 

  25. Soverini S, De Benedittis C, Machova Polakova K, Brouckova A, Horner D, Iacono M, Castagnetti F, Gugliotta G, Palandri F, Papayannidis C, Iacobucci I, Venturi C, Bochicchio MT, Klamova H, Cattina F, Russo D, Bresciani P, Binotto G, Giannini B, Kohlmann A, Haferlach T, Roller A, Rosti G, Cavo M, Baccarani M, Martinelli G (2013) Unraveling the complexity of tyrosine kinase inhibitor-resistant populations by ultra-deep sequencing of the BCR-ABL kinase domain. Blood 122:1634–1648

    Article  CAS  PubMed  Google Scholar 

  26. Kastner R, Zopf A, Preuner S, Proll J, Niklas N, Foskett P, Valent P, Lion T, Gabriel C (2014) Rapid identification of compound mutations in patients with Philadelphia-positive leukaemias by long-range next generation sequencing. Eur J Cancer 50:793–800

    Article  CAS  PubMed  Google Scholar 

  27. Patel A, Schwab R, Liu YT, Bafna V (2014) Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Res 24:318–328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Mikheyev AS, Tin MM (2014) A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour 14:1097–1102

    Article  CAS  PubMed  Google Scholar 

  29. Quick J, Quinlan AR, Loman NJ (2014) A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer. Gigascience 3:22

    Article  PubMed  PubMed Central  Google Scholar 

  30. Kilianski A, Haas JL, Corriveau EJ, Liem AT, Willis KL, Kadavy DR, Rosenzweig CN, Minot SS (2015) Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer. Gigascience 4:11–18

    Article  Google Scholar 

  31. Rusk N (2015) MinION takes center stage. Nat Methods 12:12–13

    Article  CAS  PubMed  Google Scholar 

  32. H L, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  Google Scholar 

  33. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26:841–842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568–576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, Dahlman KB, Pao W, Zhao Z (2013) Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genitourin Med 5:91

    Google Scholar 

  37. Usuyama N, Shiraishi Y, Sato Y, Kume H, Homma Y, Ogawa S, Miyano S, Imoto S (2014) HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations. Bioinformatics 30:3302–3309

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499:214–218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Gonzalez-Perez A, Lopez-Bigas N (2012) Functional impact bias reveals cancer drivers. Nucleic Acids Res 40:e169

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Tamborero D, Gonzalez-Perez A, Lopez-Bigas N (2013) OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics 29:2238–2244

    Article  CAS  PubMed  Google Scholar 

  41. Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature 458:97–101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36

    Article  PubMed  PubMed Central  Google Scholar 

  43. Dobin A, Gingeras TR (2015) Mapping RNA-seq reads with STAR. Curr Protoc Bioinformatics 51:11.14.1–11.14.19

    Article  Google Scholar 

  44. Sun J, Nishiyama T, Shimizu K, Kadota K (2013) TCC: an R package for comparing tag count data with robust normalization strategies. BMC Bioinformatics 14:219

    Article  PubMed  PubMed Central  Google Scholar 

  45. Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ (2015) COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res 43:D805–D811

    Article  PubMed  Google Scholar 

  46. Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E, Cerami E, Sander C, Schultz N (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6:pl1

    Article  PubMed  PubMed Central  Google Scholar 

  47. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2:401–404

    Article  PubMed  Google Scholar 

  48. Huang da W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44–57

    Article  PubMed  Google Scholar 

  49. Griffith M, Griffith OL, Coffman AC, Weible JV, McMichael JF, Spies NC, Koval J, Das I, Callaway MB, Eldred JM, Miller CA, Subramanian J, Govindan R, Kumar RD, Bose R, Ding L, Walker JR, Larson DE, Dooling DJ, Smith SM, Ley TJ, Mardis ER, Wilson RK (2013) DGIdb: mining the druggable genome. Nat Methods 10:1209–1210

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Yang W, Soares J, Greninger P, Edelman EJ, Lightfoot H, Forbes S, Bindal N, Beare D, Smith JA, Thompson IR, Ramaswamy S, Futreal PA, Haber DA, Stratton MR, Benes C, McDermott U, Garnett MJ (2013) Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells. Nucleic Acids Res 41:D955–D961

    Article  CAS  PubMed  Google Scholar 

  51. Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, ‘t Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; FANTOM consortium. (2015) Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol 16:22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Mizuno H, Kitada K, Nakai K, Sarai A (2009) PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genet 2:18

    Google Scholar 

  53. Kohno T, Ichikawa H, Totoki Y, Yasuda K, Hiramoto M, Nammo T, Sakamoto H, Tsuta K, Furuta K, Shimada Y, Iwakawa R, Ogiwara H, Oike T, Enari M, Schetter AJ, Okayama H, Haugen A, Skaug V, Chiku S, Yamanaka I, Arai Y, Watanabe S, Sekine I, Ogawa S, Harris CC, Tsuda H, Yoshida T, Yokota J, Shibata T (2012) KIF5B-RET fusions in lung adenocarcinoma. Nat Med 18:375–377

    Article  CAS  PubMed  Google Scholar 

  54. Takeuchi K, Soda M, Togashi Y, Suzuki R, Sakata S, Hatano S, Asaka R, Hamanaka W, Ninomiya H, Uehara H, Lim Choi Y, Satoh Y, Okumura S, Nakagawa K, Mano H, Ishikawa Y (2012) RET, ROS1 and ALK fusions in lung cancer. Nat Med 18:378–381

    Article  CAS  PubMed  Google Scholar 

  55. Lipson D, Capelletti M, Yelensky R, Otto G, Parker A, Jarosz M, Curran JA, Balasubramanian S, Bloom T, Brennan KW, Donahue A, Downing SR, Frampton GM, Garcia L, Juhn F, Mitchell KC, White E, White J, Zwirko Z, Peretz T, Nechushtan H, Soussan-Gutman L, Kim J, Sasaki H, Kim HR, Park SI, Ercan D, Sheehan CE, Ross JS, Cronin MT, Jänne PA, Stephens PJ (2012) Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies. Nat Med 18:382–384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Ju YS, Lee WC, Shin JY, Lee S, Bleazard T, Won JK, Kim YT, Kim JI, Kang JH, Seo JS (2012) A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res 22:436–445

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Tsuta K, Kohno T, Yoshida A, Shimada Y, Asamura H, Furuta K, Kushima R (2014) RET-rearranged non-small-cell lung carcinoma: a clinicopathological and molecular analysis. Br J Cancer 110:1571–1578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, Cho J, Suh J, Capelletti M, Sivachenko A, Sougnez C, Auclair D, Lawrence MS, Stojanov P, Cibulskis K, Choi K, de Waal L, Sharifnia T, Brooks A, Greulich H, Banerji S, Zander T, Seidel D, Leenders F, Ansén S, Ludwig C, Engel-Riedel W, Stoelben E, Wolf J, Goparju C, Thompson K, Winckler W, Kwiatkowski D, Johnson BE, Jänne PA, Miller VA, Pao W, Travis WD, Pass HI, Gabriel SB, Lander ES, Thomas RK, Garraway LA, Getz G, Meyerson M (2012) Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150:1107–1120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Seo JS, Ju YS, Lee WC, Shin JY, Lee JK, Bleazard T, Lee J, Jung YJ, Kim JO, Shin JY, Yu SB, Kim J, Lee ER, Kang CH, Park IK, Rhee H, Lee SH, Kim JI, Kang JH, Kim YT (2012) The transcriptional landscape and mutational profile of lung adenocarcinoma. Genome Res 22:2109–2119

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Cancer Genome Atlas Research Network (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature 511:543–550

    Article  Google Scholar 

  61. Fernandez-Cuesta L, Plenker D, Osada H, Sun R, Menon R, Leenders F, Ortiz-Cuaran S, Peifer M, Bos M, Daßler J, Malchers F, Schöttle J, Vogel W, Dahmen I, Koker M, Ullrich RT, Wright GM, Russell PA, Wainer Z, Solomon B, Brambilla E, Nagy-Mignotte H, Moro-Sibilot D, Brambilla CG, Lantuejoul S, Altmüller J, Becker C, Nürnberg P, Heuckmann JM, Stoelben E, Petersen I, Clement JH, Sänger J, Muscarella LA, la Torre A, Fazio VM, Lahortiga I, Perera T, Ogata S, Parade M, Brehmer D, Vingron M, Heukamp LC, Buettner R, Zander T, Wolf J, Perner S, Ansén S, Haas SA, Yatabe Y, Thomas RK (2014) CD74-NRG1 fusions in lung adenocarcinoma. Cancer Discov 4:415–422

    Article  CAS  PubMed  Google Scholar 

  62. Jang JS, Lee A, Li J, Liyanage H, Yang Y, Guo L, Asmann YW, Li PW, Erickson-Johnson M, Sakai Y, Sun Z, Jeon HS, Hwang H, Bungum AO, Edell ES, Simon VA, Kopp KJ, Eckloff B, Oliveira AM, Wieben E, Aubry MC, Yi E, Wigle D, Diasio RB, Yang P, Jen J (2015) Common oncogene mutations and novel SND1-BRAF transcript fusion in lung adenocarcinoma from never smokers. Sci Rep 18(5):9755

    Article  Google Scholar 

  63. Cancer Genome Atlas Research Network (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature 489:519–525

    Article  Google Scholar 

  64. Kim Y, Hammerman PS, Kim J, Yoon JA, Lee Y, Sun JM, Wilkerson MD, Pedamallu CS, Cibulskis K, Yoo YK, Lawrence MS, Stojanov P, Carter SL, McKenna A, Stewart C, Sivachenko AY, Oh IJ, Kim HK, Choi YS, Kim K, Shim YM, Kim KS, Song SY, Na KJ, Choi YL, Hayes DN, Kim J, Cho S, Kim YC, Ahn JS, Ahn MJ, Getz G, Meyerson M, Park K (2014) Integrative and comparative genomic analysis of lung squamous cell carcinomas in East Asian patients. J Clin Oncol 32:121–128

    Article  CAS  PubMed  Google Scholar 

  65. Roth GJ, Binder R, Colbatzky F, Dallinger C, Schlenker-Herceg R, Hilberg F, Wollin SL, Kaiser R (2015) Nintedanib: from discovery to the clinic. J Med Chem 58:1053–1063

    Article  CAS  PubMed  Google Scholar 

  66. Durm G, Hanna N (2014) Targeting multiple angiogenic pathways simultaneously: experience with nintedanib in non-small-cell lung cancer. Future Oncol 10:1167–1173

    Article  CAS  PubMed  Google Scholar 

  67. Peifer M, Fernández-Cuesta L, Sos ML, George J, Seidel D, Kasper LH, Plenker D, Leenders F, Sun R, Zander T, Menon R, Koker M, Dahmen I, Müller C, Di Cerbo V, Schildhaus HU, Altmüller J, Baessmann I, Becker C, de Wilde B, Vandesompele J, Böhm D, Ansén S, Gabler F, Wilkening I, Heynck S, Heuckmann JM, Lu X, Carter SL, Cibulskis K, Banerji S, Getz G, Park KS, Rauh D, Grütter C, Fischer M, Pasqualucci L, Wright G, Wainer Z, Russell P, Petersen I, Chen Y, Stoelben E, Ludwig C, Schnabel P, Hoffmann H, Muley T, Brockmann M, Engel-Riedel W, Muscarella LA, Fazio VM, Groen H, Timens W, Sietsma H, Thunnissen E, Smit E, Heideman DA, Snijders PJ, Cappuzzo F, Ligorio C, Damiani S, Field J, Solberg S, Brustugun OT, Lund-Iversen M, Sänger J, Clement JH, Soltermann A, Moch H, Weder W, Solomon B, Soria JC, Validire P, Besse B, Brambilla E, Brambilla C, Lantuejoul S, Lorimier P, Schneider PM, Hallek M, Pao W, Meyerson M, Sage J, Shendure J, Schneider R, Büttner R, Wolf J, Nürnberg P, Perner S, Heukamp LC, Brindle PK, Haas S, Thomas RK (2012) Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nat Genet 44:1104–1110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Rudin CM, Durinck S, Stawiski EW, Poirier JT, Modrusan Z, Shames DS, Bergbower EA, Guan Y, Shin J, Guillory J, Rivers CS, Foo CK, Bhatt D, Stinson J, Gnad F, Haverty PM, Gentleman R, Chaudhuri S, Janakiraman V, Jaiswal BS, Parikh C, Yuan W, Zhang Z, Koeppen H, Wu TD, Stern HM, Yauch RL, Huffman KE, Paskulin DD, Illei PB, Varella-Garcia M, Gazdar AF, de Sauvage FJ, Bourgon R, Minna JD, Brock MV, Seshagiri S (2012) Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer. Nat Genet 44:1111–1116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. George J, Lim JS, Jang SJ, Cun Y, Ozretić L, Kong G, Leenders F, Lu X, Fernández-Cuesta L, Bosco G, Müller C, Dahmen I, Jahchan NS, Park KS, Yang D, Karnezis AN, Vaka D, Torres A, Wang MS, Korbel JO, Menon R, Chun SM, Kim D, Wilkerson M, Hayes N, Engelmann D, Pützer B, Bos M, Michels S, Vlasic I, Seidel D, Pinther B, Schaub P, Becker C, Altmüller J, Yokota J, Kohno T, Iwakawa R, Tsuta K, Noguchi M, Muley T, Hoffmann H, Schnabel PA, Petersen I, Chen Y, Soltermann A, Tischler V, Choi CM, Kim YH, Massion PP, Zou Y, Jovanovic D, Kontic M, Wright GM, Russell PA, Solomon B, Koch I, Lindner M, Muscarella LA, la Torre A, Field JK, Jakopovic M, Knezevic J, Castaños-Vélez E, Roz L, Pastorino U, Brustugun OT, Lund-Iversen M, Thunnissen E, Köhler J, Schuler M, Botling J, Sandelin M, Sanchez-Cespedes M, Salvesen HB, Achter V, Lang U, Bogus M, Schneider PM, Zander T, Ansén S, Hallek M, Wolf J, Vingron M, Yatabe Y, Travis WD, Nürnberg P, Reinhardt C, Perner S, Heukamp L, Büttner R, Haas SA, Brambilla E, Peifer M, Sage J, Thomas RK (2015) Comprehensive genomic profiles of small cell lung cancer. Nature 524:47–53

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK (2012) Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 150:1121–1134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Gou LY, Niu FY, Wu YL, Zhong WZ (2015) Differences in driver genes between smoking-related and non-smoking-related lung cancer in the Chinese population. Cancer 121:3069–3079

    Article  CAS  PubMed  Google Scholar 

  72. Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, Lee W, Yuan J, Wong P, Ho TS, Miller ML, Rekhtman N, Moreira AL, Ibrahim F, Bruggeman C, Gasmi B, Zappasodi R, Maeda Y, Sander C, Garon EB, Merghoub T, Wolchok JD, Schumacher TN, Chan TA (2015) Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348:124–128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Fox JL (2014) Master protocol for squamous cell lung cancer readies for launch. Nat Biotechnol 32:116–118

    Article  CAS  PubMed  Google Scholar 

  74. Song M, Kim SH, Yoon SK (2015) Cabozantinib for the treatment of non-small cell lung cancer with KIF5B-RET fusion. An example of swift repositioning. Arch Pharm Res. doi:10.1007/s12272-015-0660-1 [Epub ahead of print]

    Google Scholar 

Download references

Acknowledgments

We are grateful to Drs. S. Yoshiyama (Gunma University Initiative for Advanced Research), T. Kohno, M. Saito, M. Kato (National Cancer Center Research Institute), and A. Fujimoto (Kyoto University) for their insightful comments and suggestions.

Author information

Authors and Affiliations

  1. Department of Molecular Pharmacology and Oncology, Gunma University Graduate School of Medicine, 3-39-22 Showa-Machi, Maebashi, Gunma, 371-8511, Japan

    Reika Kawabata-Iwakawa & Masahiko Nishiyama

  2. Database Center for Life Science (DBCLS), National Institute of Genetics, Research Organization of Information and Systems, Mishima, Shizuoka, Japan

    Hidemasa Bono

  3. Research Program for Omics-Based Medical Science, Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research, Maebashi, Gunma, Japan

    Masahiko Nishiyama

Authors
  1. Reika Kawabata-Iwakawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hidemasa Bono
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Masahiko Nishiyama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Masahiko Nishiyama .

Editor information

Editors and Affiliations

  1. Department of Medical Oncology Graduate School of Medicine, Chiba University, Chiba, Japan

    Yuichi Takiguchi

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media Singapore

About this chapter

Cite this chapter

Kawabata-Iwakawa, R., Bono, H., Nishiyama, M. (2017). Next-Generation Sequencing and Bioinformatics. In: Takiguchi, Y. (eds) Molecular Targeted Therapy of Lung Cancer. Springer, Singapore. https://doi.org/10.1007/978-981-10-2002-5_6

Download citation

  • DOI: https://doi.org/10.1007/978-981-10-2002-5_6

  • Published:

  • Publisher Name: Springer, Singapore

  • Print ISBN: 978-981-10-2000-1

  • Online ISBN: 978-981-10-2002-5

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation