Translating Next-Generation Sequencing from Clinical Trials to Clinical Practice for the Treatment of Advanced Cancers

References

• Koboldt DC , SteinbergKM , LarsonDE , WilsonRK , MardisER . The next-generation sequencing revolution and its impact on genomics . Cell155 ( 1 ), 27 – 38 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Mardis ER , WilsonRK . Cancer genome sequencing: a review . Hum. Mol. Genet.18 ( R2 ), R163 – R168 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Mardis ER . Next-generation sequencing platforms . Annu. Rev. Anal. Chem.6 , 287 – 303 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hayden EC . Is the $1,000 genome for real?http://www.nature.com/news/is-the-1–000-genome-for-real-1.14530 .
   Google Scholar
• Weiss GJ , LiangWS , DemeureMJet al. A pilot study using next-generation sequencing in advanced cancers: feasibility and challenges . PLoS One8 ( 10 ), e76438 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Meldrum C , DoyleMA , TothillRW . Next-generation sequencing for cancer diagnostics: a practical perspective . Clin. Biochem. Rev.32 ( 4 ), 177 – 195 ( 2011 ).
   PubMedGoogle Scholar
• Gabor Miklos GL . The human cancer genome project-one more misstep in the war on cancer . Nat. Biotechnol.23 ( 5 ), 535 – 537 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Balak MN , GongY , RielyGJet al. Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors . Clin. Cancer Res.12 ( 21 ), 6494 – 6501 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Sequist LV , WaltmanBA , Dias-santagataDet al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors . Sci. Transl. Med.3 ( 75 ), 75ra26 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Spencer DH , SehnJK , AbelHJet al. Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens . J. Mol. Diagn.15 ( 5 ), 623 – 633 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Sweeney RT , ZhangB , ZhuSXet al. Desktop transcriptome sequencing from archival tissue to identify clnically relevant translocations . Am. J. Surg. Pathol.37 ( 6 ), 796 – 803 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Dawson S-J , TsuiDWY , MurtazaMet al. Analysis of circulating tumor DNA to monitor metastatic breast cancer . N. Engl. J. Med.368 ( 13 ), 1199 – 1209 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Newman AM , BratmanSV , WynneJFet al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage . Nat. Med.20 ( 5 ), 548 – 554 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Montassier E , BatardE , MassartSet al. 16S rRNA gene pyrosequencing reveals shift in patient faecal microbiota during high-dose chemotherapy as conditioning regimen for bone marrow transplantation . Microb. Ecol.67 ( 3 ), 690 – 699 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Yu T , FerberMJ , CheungTHet al. The role of viral integration in the development of cervical cancer . Cancer Genet. Cytogenet.158 ( 1 ), 27 – 34 ( 2005 ).
   PubMedGoogle Scholar
• Chen Y , YaoH , ThompsonEJet al. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue . Bioinformatics29 ( 2 ), 266 – 267 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Liao JB . Viruses and human cancer . Yale J. Biol. Med.79 ( 3–4 ), 115 – 122 ( 2006 ).
   PubMedGoogle Scholar
• Jones PA , BaylinSB . The epigenomics of cancer . Cell128 ( 4 ), 683 – 692 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Mensaert K , DenilS , TrooskensG , Van CriekingeW , ThasO , De MeyerT . Next-generation technologies and data analytical approaches for epigenomics . Environ. Mol. Mutagen.55 ( 3 ), 155 – 170 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Glass E , VialePH . Histone deacetylase inhibitors: novel agents in cancer treatment . Clin. J. Oncol. Nurs.17 ( 1 ), 34 – 40 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Huang Y , NayakS , JankowitzR , DavidsonNE , OesterreichS . Epigenetics in breast cancer: what’s new?Breast Cancer Res.13 ( 6 ), 225 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Chandramouli K , QianP-Y . Proteomics: challenges, techniques and possibilities to overcome biological sample complexity . Hum. Genomics Proteomic.2009 , 239204 ( 2009 ).
   PubMedGoogle Scholar
• Jensen ON . Modification-specific proteomics: characterization of post-translational modifications by mass spectrometry . Curr. Opin. Chem. Biol.8 ( 1 ), 33 – 41 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Weston AD , HoodL . Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine . J. Proteome. Res.3 ( 2 ), 179 – 196 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Cho WC . Proteomics in translational cancer research: biomarker discovery for clinical applications . Expert Rev. Proteomics11 ( 2 ), 131 – 133 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Albrethsen J , AngelettiRH , HorwitzSBet al. Proteomics of cancer cell lines resistant to microtubule-stabilizing agents . Mol. Cancer Ther.13 ( 1 ), 260 – 269 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Roychowdhury S , IyerMK , RobinsonDRet al. Personalized oncology through integrative high-throughput sequencing: a pilot study . Sci. Transl. Med.3 ( 111 ), 111 – 121 ( 2011 ).
   Web of Science ®Google Scholar
• Tran B , BrownAMK , BedardPLet al. Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial . Int. J. Cancer132 ( 7 ), 1547 – 1555 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Craig DW , O’ShaughnessyJA , KieferJAet al. Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities . Mol. Cancer Ter.12 ( 1 ), 104 – 116 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kris MG , JohnsonBE , BerryLDet al. Using multiplexed assays of oncogenic drivers in lung cancers to select targeted drugs . JAMA311 ( 19 ), 1998 – 2006 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• André F , BachelotT , CommoFet al. Comparative genomic hydridisation array and DNA sequencing to direct treatment of metastatic breast cancer: a multicenter, prospective trial (SAFIR01/UNICANCER) . Lancet Oncol.15 ( 3 ), 267 – 274 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Poutahidis T , KleinewietfeldM , ErdmanSE . Gut microbiota and the paradox of cancer immunotherapy . Front. Immunol.5 , 157 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Iida N , DzutsevA , StewartCAet al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment . Science342 ( 6161 ), 967 – 970 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Viaud S , SaccheriF , MignotGet al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide . Science342 ( 6161 ), 967 – 966 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Moossavi S , ZhangH , SunJet al. Host-microbiota interaction and intestinal. stem cells in chronic inflammation and colorectal cancer . Expert Rev. Clin. Immunol.9 ( 5 ), 409 – 422 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kyi C , PostowMA . Checkpoint blocking antibodies in cancer immunotherapy . FEBS Lett.588 ( 2 ), 368 – 376 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Chmielewski M , HombachAA , AbkenH . Antigen-specific T-cell activiation independently of the MHC: chimeric antigen receptor-redirected T cells . Front. Immunol.4 , 371 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Koboldt DC , DingL , MardisER , WilsonRK . Challenges of sequencing human genomes . Brief. Bioinform.11 ( 5 ), 484 – 498 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• U.S. Food & Drug Administration . FDA allows marketing of four “next generation” gene sequencing devices . http://www.fda.gov/newsevents/newsroom/pressannouncements/ucm375742.htm .
   Google Scholar
• Gargis AS , KalmanL , BerryMWet al. Assuring the quality of next-generation sequencing in clinical laboratory practice . Nat. Biotechnol.30 ( 11 ), 1033 – 1036 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Aziz N . Implementing next generation sequencing (NGS) as a clinical tool in the laboratory . http://www.cap.org/apps/docs/education/lapaudio/pdf/022013_presentation.pdf .
   Google Scholar
• Gray SW , Hicks-CourantK , CroninAet al. Physicians’ attitudes about multiplex tumor genomic testing . J. Clin. Oncol.32 ( 13 ), 1317 – 1323 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Liang WS , AldrichJ , TembeWet al. Long insert whole genome sequencing for copy number variant and translocation detection . Nucl. Acids Res.42 ( 2 ), e8 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Yang Y , LiuR , XieHet al. Advances in nanopore sequencing technology . J. Nanosci. Nanotechnol.13 ( 7 ), 4521 – 4538 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Ding L , LeyTJ , LarsonDEet al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing . Nature481 ( 7382 ), 506 – 510 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Mardis ER , WilsonRK . Cancer genome sequencing: a review . Hum. Mol. Genet.18 ( R2 ), R163 – R168 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Stadler ZK , SchraderKA , VijaiJet al. Cancer genomics and inherited risk . J. Clin. Oncol.32 ( 7 ), 687 – 698 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• National Cancer Institute . =www.visualsonline.cancer.gov/details.cfm?imageid=2306 .
   Google Scholar