Advertisement

A Platform for Comprehensive Genomic Profiling in Human Cancers and Pharmacogenomics Therapy Selection

Protocol
First Online:
  • 1k Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 1825)

Abstract

Recent innovations in next-generation sequencing (NGS) technologies have enabled comprehensive genomic profiling of human cancers in the clinical setting. The ability to profile has launched a worldwide trend known as precision medicine, and the fusion of genomic profiling and pharmacogenomics is paving the way for precision medicine for cancer. The profiling is coupled with information about chemical therapies available to patients with specific genotypes. As a result, the chemogenomic space in play is not only the standard chemical and genome space but also the mutational genome and chemical space. In this chapter, we introduce clinical genomic profiling using an NGS-based multiplex gene assay (OncoPrime™) at Kyoto University Hospital.

Key words

Multiplex gene assay Next-generation sequencing Precision medicine Pharmacogenomics Clinical execution 
This is a preview of subscription content, log in to check access.

References

  1. 1.
    Lawrence MS, Stojanov P, Polak P et al (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499:214–218.  https://doi.org/10.1038/nature12213CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Mok TS, Wu Y-L, Thongprasert S et al (2009) Gefitinib or carboplatin–paclitaxel in pulmonary adenocarcinoma. N Engl J Med 361:947–957.  https://doi.org/10.1056/NEJMoa0810699CrossRefPubMedGoogle Scholar
  3. 3.
    Garraway LA, Verweij J, Ballman KV (2013) Precision oncology: an overview. J Clin Oncol 31:1803–1805.  https://doi.org/10.1200/JCO.2013.49.4799CrossRefPubMedGoogle Scholar
  4. 4.
    Mendelsohn J (2013) Personalizing oncology: perspectives and prospects. J Clin Oncol 31:1904–1911.  https://doi.org/10.1200/JCO.2012.45.3605CrossRefPubMedGoogle Scholar
  5. 5.
    Werner HMJ, Mills GB, Ram PT (2014) Cancer systems biology: a peek into the future of patient care? Nat Rev Clin Oncol 11:167–176.  https://doi.org/10.1038/nrclinonc.2014.6CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Chapman PB, Hauschild A, Robert C et al (2011) Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 364:2507–2516.  https://doi.org/10.1056/NEJMoa1103782CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Lynch TJ, Bell DW, Sordella R et al (2004) Activating mutations in the epidermal growth factor receptor underlying responsiveness of non–small-cell lung cancer to gefitinib. N Engl J Med 350:2129–2139.  https://doi.org/10.1056/NEJMoa040938CrossRefPubMedGoogle Scholar
  8. 8.
    Douillard J-Y, Oliner KS, Siena S et al (2013) Panitumumab–FOLFOX4 treatment and RAS mutations in colorectal cancer. N Engl J Med 369:1023–1034.  https://doi.org/10.1056/NEJMoa1305275CrossRefPubMedGoogle Scholar
  9. 9.
    Kou T, Kanai M, Matsumoto S et al (2016) The possibility of clinical sequencing in the management of cancer. Jpn J Clin Oncol 46:399–406.  https://doi.org/10.1093/jjco/hyw018CrossRefPubMedGoogle Scholar
  10. 10.
    Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26:589–595.  https://doi.org/10.1093/bioinformatics/btp698CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359.  https://doi.org/10.1038/nmeth.1923CrossRefPubMedPubMedCentralGoogle Scholar
  12. 12.
    DePristo MA, Banks E, Poplin R et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498.  https://doi.org/10.1038/ng.806CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Li H, Handsaker B, Wysoker A et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079.  https://doi.org/10.1093/bioinformatics/btp352CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Koboldt DC, Zhang Q, Larson DE et al (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22:568–576.  https://doi.org/10.1101/gr.129684.111CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Cibulskis K, Lawrence MS, Carter SL et al (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31:213–219.  https://doi.org/10.1038/nbt.2514CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Kim S, Jeong K, Bhutani K et al (2013) Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol 14:R90.  https://doi.org/10.1186/gb-2013-14-8-r90CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164.  https://doi.org/10.1093/nar/gkq603CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Amberger JS, Bocchini CA, Schiettecatte F et al (2015) OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders. Nucleic Acids Res 43:D789–D798.  https://doi.org/10.1093/nar/gku1205CrossRefPubMedGoogle Scholar
  19. 19.
    Landrum MJ, Lee JM, Riley GR et al (2014) ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res 42:D980–D985.  https://doi.org/10.1093/nar/gkt1113CrossRefPubMedGoogle Scholar
  20. 20.
    Forbes SA, Beare D, Gunasekaran P et al (2015) COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res 43:D805–D811.  https://doi.org/10.1093/nar/gku1075CrossRefPubMedGoogle Scholar
  21. 21.
    Cancer Genome Atlas Research Network K, Weinstein JN, Collisson EA et al (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet 45:1113–1120.  https://doi.org/10.1038/ng.2764CrossRefPubMedCentralGoogle Scholar
  22. 22.
    Meric-Bernstam F, Johnson A, Holla V et al (2015) A decision support framework for genomically informed investigational cancer therapy. J Natl Cancer Inst.  https://doi.org/10.1093/jnci/djv098
  23. 23.
    Johnson DB, Dahlman KH, Knol J et al (2014) Enabling a genetically informed approach to cancer medicine: a retrospective evaluation of the impact of comprehensive tumor profiling using a targeted next-generation sequencing panel. Oncologist 19:616–622.  https://doi.org/10.1634/theoncologist.2014-0011CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Vidwans SJ, Turski ML, Janku F et al (2014) A framework for genomic biomarker actionability and its use in clinical decision making. Oncoscience 1:614–623CrossRefGoogle Scholar
  25. 25.
    Cornish A, Guda C (2015) A comparison of variant calling pipelines using genome in a bottle as a reference. Biomed Res Int 2015:1–11.  https://doi.org/10.1155/2015/456479CrossRefGoogle Scholar
  26. 26.
    O’Rawe J, Jiang T, Sun G et al (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med 5:28.  https://doi.org/10.1186/gm432CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Therapeutic Oncology, Graduate School of MedicineKyoto UniversityKyotoJapan
  2. 2.Department of Biomedical Data Intelligence, Graduate School of MedicineKyoto UniversityKyotoJapan

Personalised recommendations

Cite protocol

Buy options