Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

Application of Cancer Genomics to Solve Unmet Clinical Needs

  • Lee, Se-Hoon (Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine) ;
  • Sim, Sung Hoon (Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine) ;
  • Kim, Ji-Yeon (Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine) ;
  • Cha, SooJin (Cancer Research Institute, Seoul National University College of Medicine) ;
  • Song, Ahnah (Cancer Research Institute, Seoul National University College of Medicine)
  • Received : 2013.11.05
  • Accepted : 2013.11.15
  • Published : 2013.12.31
Download PDF
⟨ Previous Next ⟩

Abstract

The large amount of data on cancer genome research has contributed to our understanding of cancer biology. Indeed, the genomics approach has a strong advantage for analyzing multi-factorial and complicated problems, such as cancer. It is time to think about the actual usage of cancer genomics in the clinical field. The clinical cancer field has lots of unmet needs in the management of cancer patients, which has been defined in the pre-genomic era. Unmet clinical needs are not well known to bioinformaticians and even non-clinician cancer scientists. A personalized approach in the clinical field will bring potential additional challenges to cancer genomics, because most data to now have been population-based rather than individualbased. We can maximize the use of cancer genomics in the clinical field if cancer scientists, bioinformaticians, and clinicians think and work together in solving unmet clinical needs. In this review, we present one imaginary case of a cancer patient, with which we can think about unmet clinical needs to solve with cancer genomics in the diagnosis, prediction of prognosis, monitoring the status of cancer, and personalized treatment decision.

Keywords

References

  1. Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R. Next-generation sequencing in the clinic: are we ready? Nat Rev Genet 2012;13:818-824. https://doi.org/10.1038/nrg3357
  2. Shyr D, Liu Q. Next generation sequencing in cancer research and clinical application. Biol Proced Online 2013;15:4. https://doi.org/10.1186/1480-9222-15-4
  3. Rehm HL. Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet 2013;14:295-300. https://doi.org/10.1038/nrg3463
  4. NCCN Guidelines(R) Updates. J Natl Compr Canc Netw 2013;11:xxxii-xxxvi.
  5. Roychowdhury S, Iyer MK, Robinson DR, Lonigro RJ, Wu YM, Cao X, et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med 2011;3:111ra121.
  6. Buettner R, Wolf J, Thomas RK. Lessons learned from lung cancer genomics: the emerging concept of individualized diagnostics and treatment. J Clin Oncol 2013;31:1858-1865. https://doi.org/10.1200/JCO.2012.45.9867
  7. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, et al. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 2013;369:1502-1511. https://doi.org/10.1056/NEJMoa1306555
  8. National Lung Screening Trial Research Team, Aberle DR, Adams AM, Berg CD, Black WC, Clapp JD, et al. Reduced lung-cancer mortality with low-dose computed tomographic screening. N Engl J Med 2011;365:395-409. https://doi.org/10.1056/NEJMoa1102873
  9. Goldstraw P, Crowley J, Chansky K, Giroux DJ, Groome PA, Rami-Porta R, et al. The IASLC Lung Cancer Staging Project: proposals for the revision of the TNM stage groupings in the forthcoming (seventh) edition of the TNM Classification of malignant tumours. J Thorac Oncol 2007;2:706-714. https://doi.org/10.1097/JTO.0b013e31812f3c1a
  10. Marcus PM, Bergstralh EJ, Fagerstrom RM, Williams DE, Fontana R, Taylor WF, et al. Lung cancer mortality in the Mayo Lung Project: impact of extended follow-up. J Natl Cancer Inst 2000;92:1308-1316. https://doi.org/10.1093/jnci/92.16.1308
  11. Oken MM, Hocking WG, Kvale PA, Andriole GL, Buys SS, Church TR, et al. Screening by chest radiograph and lung cancer mortality: the Prostate, Lung, Colorectal, and Ovarian (PLCO) randomized trial. JAMA 2011;306:1865-1873. https://doi.org/10.1001/jama.2011.1591
  12. Kovalchik SA, Tammemagi M, Berg CD, Caporaso NE, Riley TL, Korch M, et al. Targeting of low-dose CT screening according to the risk of lung-cancer death. N Engl J Med 2013; 369:245-254. https://doi.org/10.1056/NEJMoa1301851
  13. Bremnes RM, Sirera R, Camps C. Circulating tumour-derived DNA and RNA markers in blood: a tool for early detection, diagnostics, and follow-up? Lung Cancer 2005;49:1-12. https://doi.org/10.1016/j.lungcan.2004.12.008
  14. Hung RJ, McKay JD, Gaborieau V, Boffetta P, Hashibe M, Zaridze D, et al. A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature 2008;452:633-637. https://doi.org/10.1038/nature06885
  15. McKay JD, Hung RJ, Gaborieau V, Boffetta P, Chabrier A, Byrnes G, et al. Lung cancer susceptibility locus at 5p15.33. Nat Genet 2008;40:1404-1406. https://doi.org/10.1038/ng.254
  16. Lan Q, Hsiung CA, Matsuo K, Hong YC, Seow A, Wang Z, et al. Genome-wide association analysis identifies new lung cancer susceptibility loci in never-smoking women in Asia. Nat Genet 2012;44:1330-1335. https://doi.org/10.1038/ng.2456
  17. Brookman-Amissah N. Next-generation sequencing in the clinic. New Rochelle: Genetic Engineering and Biotechnology News, 2013. Accessed 2013 Nov 1. Available from: http:// www.genengnews.com/gen-articles/next-generation-sequencing- in-the-clinic/4737/.
  18. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 2013;368:1199-1209. https://doi.org/10.1056/NEJMoa1213261
  19. Winton T, Livingston R, Johnson D, Rigas J, Johnston M, Butts C, et al. Vinorelbine plus cisplatin vs. observation in resected non-small-cell lung cancer. N Engl J Med 2005;352:2589-2597. https://doi.org/10.1056/NEJMoa043623
  20. Douillard JY, Rosell R, De Lena M, Carpagnano F, Ramlau R, Gonzáles-Larriba JL, et al. Adjuvant vinorelbine plus cisplatin versus observation in patients with completely resected stage IB-IIIA non-small-cell lung cancer (Adjuvant Navelbine International Trialist Association [ANITA]): a randomised controlled trial. Lancet Oncol 2006;7:719-727. https://doi.org/10.1016/S1470-2045(06)70804-X
  21. Albain KS, Swann RS, Rusch VW, Turrisi AT 3rd, Shepherd FA, Smith C, et al. Radiotherapy plus chemotherapy with or without surgical resection for stage III non-small-cell lung cancer: a phase III randomised controlled trial. Lancet 2009; 374:379-386. https://doi.org/10.1016/S0140-6736(09)60737-6
  22. van Meerbeeck JP, Kramer GW, Van Schil PE, Legrand C, Smit EF, Schramel F, et al. Randomized controlled trial of resection versus radiotherapy after induction chemotherapy in stage IIIA-N2 non-small-cell lung cancer. J Natl Cancer Inst 2007;99: 442-450. https://doi.org/10.1093/jnci/djk093
  23. Bae HM, Lee SH, Kim TM, Kim DW, Yang SC, Wu HG, et al. Prognostic factors for non-small cell lung cancer with bone metastasis at the time of diagnosis. Lung Cancer 2012;77: 572-577. https://doi.org/10.1016/j.lungcan.2012.05.094
  24. Henschke CI, McCauley DI, Yankelevitz DF, Naidich DP, McGuinness G, Miettinen OS, et al. Early Lung Cancer Action Project: overall design and findings from baseline screening. Lancet 1999;354:99-105. https://doi.org/10.1016/S0140-6736(99)06093-6
  25. Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, et al. Detection of mutations in EGFR in circulating lung-cancer cells. N Engl J Med 2008;359:366-377. https://doi.org/10.1056/NEJMoa0800668
  26. Ju YS, Lee WC, Shin JY, Lee S, Bleazard T, Won JK, et al. A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res 2012;22:436-445. https://doi.org/10.1101/gr.133645.111
  27. Bergethon K, Shaw AT, Ou SH, Katayama R, Lovly CM, McDonald NT, et al. ROS1 rearrangements define a unique molecular class of lung cancers. J Clin Oncol 2012;30:863-870. https://doi.org/10.1200/JCO.2011.35.6345
  28. Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature 2013;500:415-421. https://doi.org/10.1038/nature12477
  29. Zack TI, Schumacher SE, Carter SL, Cherniack AD, Saksena G, Tabak B, et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013;45:1134-1140. https://doi.org/10.1038/ng.2760
  30. Scagliotti GV, Parikh P, von Pawel J, Biesma B, Vansteenkiste J, Manegold C, et al. Phase III study comparing cisplatin plus gemcitabine with cisplatin plus pemetrexed in chemotherapy- naive patients with advanced-stage non-small-cell lung cancer. J Clin Oncol 2008;26:3543-3551. https://doi.org/10.1200/JCO.2007.15.0375
  31. Sleijfer S, Bogaerts J, Siu LL. Designing transformative clinical trials in the cancer genome era. J Clin Oncol 2013;31: 1834-1841. https://doi.org/10.1200/JCO.2012.45.3639
  32. Wartman L. Doctor survives cancer he studies. St. Louis: Genome Institue, c1993-2013. Accessed 2013 Nov 1. Available from: http://genome.wustl.edu/articles/detail/ doctor-survives-cancer-he-studies/.
  33. O'Hanlon LH. How next-generation sequencing could change cancer care. J Natl Cancer Inst 2013;105:836-838. https://doi.org/10.1093/jnci/djt162
  34. Schiller JH, Harrington D, Belani CP, Langer C, Sandler A, Krook J, et al. Comparison of four chemotherapy regimens for advanced non-small-cell lung cancer. N Engl J Med 2002;346: 92-98. https://doi.org/10.1056/NEJMoa011954
  35. Mok TS, Wu YL, Thongprasert S, Yang CH, Chu DT, Saijo N, et al. Gefitinib or carboplatin-paclitaxel in pulmonary adenocarcinoma. N Engl J Med 2009;361:947-957. https://doi.org/10.1056/NEJMoa0810699
  36. Shaw AT, Kim DW, Nakagawa K, Seto T, Crino L, Ahn MJ, et al. Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med 2013;368:2385-2394. https://doi.org/10.1056/NEJMoa1214886
  37. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012;366:883-892. https://doi.org/10.1056/NEJMoa1113205
  38. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B, et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010;467:1114-1117. https://doi.org/10.1038/nature09515
  39. Sequist LV, Waltman BA, Dias-Santagata D, Digumarthy S, Turke AB, Fidias P, et al. Genotypic and histological evolution of lung cancers acquiring resistance to EGFR inhibitors. Sci Transl Med 2011;3:75ra26.

Cited by

  1. Clinical application of genomic profiling to find druggable targets for adolescent and young adult (AYA) cancer patients with metastasis vol.16, pp.1, 2016, https://doi.org/10.1186/s12885-016-2209-1
  2. Killing Me Softly—Future Challenges in Apoptosis Research vol.15, pp.3, 2014, https://doi.org/10.3390/ijms15033746