Abstract
Omics technologies have revolutionised fundamental and medical research. Oncology is perhaps the field where these technologies have been most rapidly adopted and where they have had their biggest impact, dramatically transforming clinical practice guidelines over a very short period of time. Along with this transformation has come an even larger array of technologies, tools and jargon, that make following the most recent developments in the field a truly daunting task for those not involved in it. This chapter is intended to provide a general overview of evolving topics in oncology research in the era of big data analysis and precision medicine, with a specific focus on the use of tumour biomarkers, tumour biomarker tests, targeted drugs and the changing landscape of clinical trial designs.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Schilsky RL (2009) Personalizing cancer care: American society of clinical oncology presidential address 2009. J Clin Oncol 27(23):3725–3730. https://doi.org/10.1200/JCO.2009.24.6827
Hayes DF (2013) OMICS-based personalized oncology: if it is worth doing, it is worth doing well! BMC Med 11:221. https://doi.org/10.1186/1741-7015-11-221
Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58(4):586–597. https://doi.org/10.1016/j.molcel.2015.05.004
Lopez J, Harris S, Roda D, Yap TA (2015) Precision medicine for molecularly targeted agents and immunotherapies in early-phase clinical trials. Transl Oncogenomics 7(Suppl 1):1–11. https://doi.org/10.4137/TOG.S30533
Chen R, Snyder M (2012) Systems biology: personalized medicine for the future? Curr Opin Pharmacol 12(5):623–628. https://doi.org/10.1016/j.coph.2012.07.011
Casamassimi A, Federico A, Rienzo M, Esposito S, Ciccodicola A (2017) Transcriptome profiling in human diseases: new advances and perspectives. Int J Mol Sci 18(8). https://doi.org/10.3390/ijms18081652
Hood LE, Omenn GS, Moritz RL, Aebersold R, Yamamoto KR, Amos M, Hunter-Cevera J, Locascio L, Workshop P (2012) New and improved proteomics technologies for understanding complex biological systems: addressing a grand challenge in the life sciences. Proteomics 12(18):2773–2783. https://doi.org/10.1002/pmic.201270086
Omenn GS, Menon R, Zhang Y (2013) Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. J Proteome 90:28–37. https://doi.org/10.1016/j.jprot.2013.04.007
Goossens N, Nakagawa S, Sun X, Hoshida Y (2015) Cancer biomarker discovery and validation. Transl Cancer Res 4(3):256–269. https://doi.org/10.3978/j.issn.2218-676X.2015.06.04
Wan JCM, Massie C, Garcia-Corbacho J, Mouliere F, Brenton JD, Caldas C, Pacey S, Baird R, Rosenfeld N (2017) Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer 17(4):223–238. https://doi.org/10.1038/nrc.2017.7
Hayes DF, Schott AF (2015) Personalized medicine: genomics trials in oncology. Trans Am Clin Climatol Assoc 126:133–143
Van Poznak C, Somerfield MR, Bast RC, Cristofanilli M, Goetz MP, Gonzalez-Angulo AM, Hicks DG, Hill EG, Liu MC, Lucas W, Mayer IA, Mennel RG, Symmans WF, Hayes DF, Harris LN (2015) Use of biomarkers to guide decisions on systemic therapy for women with metastatic breast cancer: American society of clinical oncology clinical practice guideline. J Clin Oncol 33(24):2695–2704. https://doi.org/10.1200/JCO.2015.61.1459
Cobleigh MA, Vogel CL, Tripathy D, Robert NJ, Scholl S, Fehrenbacher L, Wolter JM, Paton V, Shak S, Lieberman G, Slamon DJ (1999) 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 17(9):2639–2648. https://doi.org/10.1200/JCO.1999.17.9.2639
Slamon DJ, Leyland-Jones B, Shak S, Fuchs H, Paton V, Bajamonde A, Fleming T, Eiermann W, Wolter J, Pegram M, Baselga J, Norton L (2001) Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2. N Engl J Med 344(11):783–792. https://doi.org/10.1056/NEJM200103153441101
Viale G, Paterson J, Bloch M, Csathy G, Allen D, Dell’Orto P, Kjaersgaard G, Levy YY, Jorgensen JT (2016) Assessment of HER2 amplification status in breast cancer using a new automated HER2 IQFISH pharmDx (Dako Omnis) assay. Pathol Res Pract 212(8):735–742. https://doi.org/10.1016/j.prp.2016.06.002
Siegelin MD, Borczuk AC (2014) Epidermal growth factor receptor mutations in lung adenocarcinoma. Lab Invest 94(2):129–137. https://doi.org/10.1038/labinvest.2013.147
Sakurada A, Shepherd FA, Tsao MS (2006) Epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer: impact of primary or secondary mutations. Clin Lung Cancer 7(Suppl 4):S138–S144
Arrieta O, Cardona AF, Corrales L, Campos-Parra AD, Sanchez-Reyes R, Amieva-Rivera E, Rodriguez J, Vargas C, Carranza H, Otero J, Karachaliou N, Astudillo H, Rosell R, Clica P (2015) The impact of common and rare EGFR mutations in response to EGFR tyrosine kinase inhibitors and platinum-based chemotherapy in patients with non-small cell lung cancer. Lung Cancer 87(2):169–175. https://doi.org/10.1016/j.lungcan.2014.12.009
Arrieta O, Cardona AF, Martin C, Mas-Lopez L, Corrales-Rodriguez L, Bramuglia G, Castillo-Fernandez O, Meyerson M, Amieva-Rivera E, Campos-Parra AD, Carranza H, Gomez de la Torre JC, Powazniak Y, Aldaco-Sarvide F, Vargas C, Trigo M, Magallanes-Maciel M, Otero J, Sanchez-Reyes R, Cuello M (2015) Updated frequency of EGFR and KRAS mutations in nonsmall-cell lung cancer in Latin America: The Latin-American consortium for the investigation of lung cancer (CLICaP).. Journal of thoracic oncology : official publication of the International Association for the Study of. Lung Cancer 10(5):838–843. https://doi.org/10.1097/JTO.0000000000000481
Sheikine Y, Rangachari D, McDonald DC, Huberman MS, Folch ES, VanderLaan PA, Costa DB (2016) EGFR testing in advanced non-small-cell lung cancer, a mini-review. Clin Lung Cancer 17(6):483–492. https://doi.org/10.1016/j.cllc.2016.05.016
Cyriac G, Gandhi L (2018) Emerging biomarkers for immune checkpoint inhibition in lung cancer. Semin Cancer Biol 52:269–277. https://doi.org/10.1016/j.semcancer.2018.05.006
Li J, Witten DM, Johnstone IM, Tibshirani R (2012) Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3):523–538. https://doi.org/10.1093/biostatistics/kxr031
Witten DM, Tibshirani R (2013) Scientific research in the age of omics: the good, the bad, and the sloppy. JAMIA 20(1):125–127. https://doi.org/10.1136/amiajnl-2012-000972
Moore HM, Kelly A, Jewell SD, McShane LM, Clark DP, Greenspan R, Hainaut P, Hayes DF, Kim P, Mansfield E, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J (2011) Biospecimen reporting for improved study quality. Biopreserv Biobanking 9(1):57–70. https://doi.org/10.1089/bio.2010.0036
Moore HM, Kelly AB, Jewell SD, McShane LM, Clark DP, Greenspan R, Hayes DF, Hainaut P, Kim P, Mansfield E, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J (2011) Biospecimen reporting for improved study quality (BRISQ). J Proteome Res 10(8):3429–3438. https://doi.org/10.1021/pr200021n
Moore HM, Kelly AB, Jewell SD, McShane LM, Clark DP, Greenspan R, Hayes DF, Hainaut P, Kim P, Mansfield EA, Potapova O, Riegman P, Rubinstein Y, Seijo E, Somiari S, Watson P, Weier HU, Zhu C, Vaught J (2011) Biospecimen reporting for improved study quality (BRISQ). Cancer Cytopathol 119(2):92–101. https://doi.org/10.1002/cncy.20147
McShane LM, Hayes DF (2012) Publication of tumor marker research results: the necessity for complete and transparent reporting. J Clin Oncol 30(34):4223–4232. https://doi.org/10.1200/JCO.2012.42.6858
Ratain MJ, Glassman RH (2007) Biomarkers in phase I oncology trials: signal, noise, or expensive distraction? Clin Cancer Res 13(22):6545–6548
Goulart BH, Clark JW, Pien HH, Roberts TG, Finkelstein SN, Chabner BA (2007) Trends in the use and role of biomarkers in phase I oncology trials. Clin Cancer Res 13(22 Pt 1):6719–6726. https://doi.org/10.1158/1078-0432.CCR-06-2860
Io M (2012) Evolution of translational omics: lessons learned and the path forward. The National Academies Press, Washington, DC. https://doi.org/10.17226/13297
McShane LM, Cavenagh MM, Lively TG, Eberhard DA, Bigbee WL, Williams PM, Mesirov JP, Polley M-YC, Kim KY, Tricoli JV, Taylor JMG, Shuman DJ, Simon RM, Doroshow JH, Conley BA (2013) Criteria for the use of omics-based predictors in clinical trials. Nature 502(7471):317–320
Carden CP, Sarker D, Postel-Vinay S, Yap TA, Attard G, Banerji U, Garrett MD, Thomas GV, Workman P, Kaye SB, de Bono JS (2010) Can molecular biomarker-based patient selection in phase I trials accelerate anticancer drug development? Drug Discov Today 15(3–4):88–97. https://doi.org/10.1016/j.drudis.2009.11.006
Fukuoka M, Yano S, Giaccone G, Tamura T, Nakagawa K, Douillard JY, Nishiwaki Y, Vansteenkiste J, Kudoh S, Rischin D, Eek R, Horai T, Noda K, Takata I, Smit E, Averbuch S, Macleod A, Feyereislova A, Dong RP, Baselga J (2003) Multi-institutional randomized phase II trial of gefitinib for previously treated patients with advanced non-small-cell lung cancer (The IDEAL 1 Trial) [corrected]. J Clin Oncol 21(12):2237–2246. https://doi.org/10.1200/JCO.2003.10.038
Kris MG, Natale RB, Herbst RS, Lynch TJ Jr, Prager D, Belani CP, Schiller JH, Kelly K, Spiridonidis H, Sandler A, Albain KS, Cella D, Wolf MK, Averbuch SD, Ochs JJ, Kay AC (2003) Efficacy of gefitinib, an inhibitor of the epidermal growth factor receptor tyrosine kinase, in symptomatic patients with non-small cell lung cancer: a randomized trial. JAMA 290(16):2149–2158. https://doi.org/10.1001/jama.290.16.2149
Shepherd FA, Rodrigues Pereira J, Ciuleanu T, Tan EH, Hirsh V, Thongprasert S, Campos D, Maoleekoonpiroj S, Smylie M, Martins R, van Kooten M, Dediu M, Findlay B, Tu D, Johnston D, Bezjak A, Clark G, Santabarbara P, Seymour L, National Cancer Institute of Canada Clinical Trials G (2005) Erlotinib in previously treated non-small-cell lung cancer. N Engl J Med 353(2):123–132. https://doi.org/10.1056/NEJMoa050753
Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, Harris PL, Haserlat SM, Supko JG, Haluska FG, Louis DN, Christiani DC, Settleman J, Haber DA (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med 350(21):2129–2139. https://doi.org/10.1056/NEJMoa040938
Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, Singh B, Heelan R, Rusch V, Fulton L, Mardis E, Kupfer D, Wilson R, Kris M, Varmus H (2004) EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A 101(36):13306–13311. https://doi.org/10.1073/pnas.0405220101
Arrieta O, Anaya P, Morales-Oyarvide V, Ramirez-Tirado LA, Polanco AC (2016) Cost-effectiveness analysis of EGFR mutation testing in patients with non-small cell lung cancer (NSCLC) with gefitinib or carboplatin-paclitaxel. Eur J Health Econ 17(7):855–863. https://doi.org/10.1007/s10198-015-0726-5
(2018) Companies scaling back IDO1 inhibitor trials. Cancer Discov 8(7):OF5. https://doi.org/10.1158/2159-8290.CD-ND2018-007
Menis J, Hasan B, Besse B (2014) New clinical research strategies in thoracic oncology: clinical trial design, adaptive, basket and umbrella trials, new end-points and new evaluations of response. Eur Respir Rev 23(133):367–378. https://doi.org/10.1183/09059180.00004214
Catenacci DV (2015) Next-generation clinical trials: novel strategies to address the challenge of tumor molecular heterogeneity. Mol Oncol 9(5):967–996. https://doi.org/10.1016/j.molonc.2014.09.011
Herbst RS, Gandara DR, Hirsch FR, Redman MW, LeBlanc M, Mack PC, Schwartz LH, Vokes E, Ramalingam SS, Bradley JD, Sparks D, Zhou Y, Miwa C, Miller VA, Yelensky R, Li Y, Allen JD, Sigal EV, Wholley D, Sigman CC, Blumenthal GM, Malik S, Kelloff GJ, Abrams JS, Blanke CD, Papadimitrakopoulou VA (2015) Lung master protocol (Lung-MAP)-a biomarker-driven protocol for accelerating development of therapies for squamous cell lung cancer: SWOG S1400. Clin Cancer Res 21(7):1514–1524. https://doi.org/10.1158/1078-0432.CCR-13-3473
Schwaederle M, Husain H, Fanta PT, Piccioni DE, Kesari S, Schwab RB, Patel SP, Harismendy O, Ikeda M, Parker BA, Kurzrock R (2016) Use of liquid biopsies in clinical oncology: pilot experience in 168 patients. Clin Cancer Res 22(22):5497–5505. https://doi.org/10.1158/1078-0432.CCR-16-0318
Schwaederle MC, Patel SP, Husain H, Ikeda M, Lanman RB, Banks KC, Talasaz A, Bazhenova L, Kurzrock R (2017) Utility of genomic assessment of blood-derived circulating tumor DNA (ctDNA) in patients with advanced lung adenocarcinoma. Clin Cancer Res 23(17):5101–5111. https://doi.org/10.1158/1078-0432.CCR-16-2497
Manem VSK, Salgado R, Aftimos P, Sotiriou C, Haibe-Kains B (2017) Network science in clinical trials: a patient-centered approach. Semin Cancer Biol 52:135–150. https://doi.org/10.1016/j.semcancer.2017.12.006
El-Osta H, Shahid K, Mills GM, Peddi P (2016) Immune checkpoint inhibitors: the new frontier in non-small-cell lung cancer treatment. OncoTargets Ther 9:5101–5116. https://doi.org/10.2147/OTT.S111209
Buder-Bakhaya K, Hassel JC (2018) Biomarkers for clinical benefit of immune checkpoint inhibitor treatment – a review from the melanoma perspective and beyond. Front Immunol 9:1474. https://doi.org/10.3389/fimmu.2018.01474
Reck M, Rodriguez-Abreu D, Robinson AG, Hui R, Csoszi T, Fulop A, Gottfried M, Peled N, Tafreshi A, Cuffe S, O’Brien M, Rao S, Hotta K, Leiby MA, Lubiniecki GM, Shentu Y, Rangwala R, Brahmer JR, Investigators K (2016) Pembrolizumab versus chemotherapy for PD-L1-positive non-small-cell lung cancer. N Engl J Med 375(19):1823–1833. https://doi.org/10.1056/NEJMoa1606774
Borghaei H, Paz-Ares L, Horn L, Spigel DR, Steins M, Ready NE, Chow LQ, Vokes EE, Felip E, Holgado E, Barlesi F, Kohlhaufl M, Arrieta O, Burgio MA, Fayette J, Lena H, Poddubskaya E, Gerber DE, Gettinger SN, Rudin CM, Rizvi N, Crino L, Blumenschein GR Jr, Antonia SJ, Dorange C, Harbison CT, Graf Finckenstein F, Brahmer JR (2015) Nivolumab versus docetaxel in advanced nonsquamous non-small-cell lung cancer. N Engl J Med 373(17):1627–1639. https://doi.org/10.1056/NEJMoa1507643
Brahmer J, Reckamp KL, Baas P, Crino L, Eberhardt WE, Poddubskaya E, Antonia S, Pluzanski A, Vokes EE, Holgado E, Waterhouse D, Ready N, Gainor J, Aren Frontera O, Havel L, Steins M, Garassino MC, Aerts JG, Domine M, Paz-Ares L, Reck M, Baudelet C, Harbison CT, Lestini B, Spigel DR (2015) Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer. N Engl J Med 373(2):123–135. https://doi.org/10.1056/NEJMoa1504627
Herbst RS, Baas P, Kim DW, Felip E, Perez-Gracia JL, Han JY, Molina J, Kim JH, Arvis CD, Ahn MJ, Majem M, Fidler MJ, de Castro G Jr, Garrido M, Lubiniecki GM, Shentu Y, Im E, Dolled-Filhart M, Garon EB (2016) Pembrolizumab versus docetaxel for previously treated, PD-L1-positive, advanced non-small-cell lung cancer (KEYNOTE-010): a randomised controlled trial. Lancet 387(10027):1540–1550. https://doi.org/10.1016/S0140-6736(15)01281-7
Lemery S, Keegan P, Pazdur R (2017) First FDA approval agnostic of cancer site – when a biomarker defines the indication. N Engl J Med 377(15):1409–1412. https://doi.org/10.1056/NEJMp1709968
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Hernandez-Martinez, JM., Sánchez-Reyes, R., De la Garza-Salazar, J.G., Arrieta, O. (2019). Onco-omics Approaches and Applications in Clinical Trials for Cancer Patients. In: Ruiz-Garcia, E., Astudillo-de la Vega, H. (eds) Translational Research and Onco-Omics Applications in the Era of Cancer Personal Genomics. Advances in Experimental Medicine and Biology, vol 1168. Springer, Cham. https://doi.org/10.1007/978-3-030-24100-1_5
Download citation
DOI: https://doi.org/10.1007/978-3-030-24100-1_5
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-24099-8
Online ISBN: 978-3-030-24100-1
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)