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Sequencing in Cancer

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Applications of Biotechnology in Oncology

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Abstract

The genome sequence is an organism’s blueprint: the set of instructions dictating its biological traits. The term DNA sequencing refers to methods for determining the exact order of the three billion nucleotide bases—adenine, guanine, cytosine, and thymine—that make up the DNA of the 23 pairs of human chromosomes. In de novo sequencing, short DNA fragments purified from individual bacterial colonies are individually sequenced and assembled electronically into one long, contiguous sequence. This method does not require any preexisting information about the sequence of the DNA. Whole-genome sequencing (WGS) is determination of the primary nucleotide sequence of the entire genome from a single individual. Resequencing using next-generation technologies means determination of variations of DNA sequence in an organism where the nominal sequence is already known. It is often performed using PCR to amplify the region of interest (preexisting DNA sequence is required to design the PCR primers). Resequencing is more relevant for translation into diagnostics and clinical applications.

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References

  • Ali MA, Sjöblom T. Molecular pathways in tumor progression: from discovery to functional understanding. Mol Biosyst 2009;5:902-8.

    Article  CAS  Google Scholar 

  • Balaj L, Lessard R, Dai L, et al. Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences. Nat Commun 2011;2:180.

    Article  Google Scholar 

  • Barbieri CE, Baca SC, Lawrence MS, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012;44(6):685-9. doi:10.1038/ng.2279

    Article  CAS  Google Scholar 

  • Bashir A, Volik S, Collins C, et al. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol 2008;4(4):e1000051.

    Article  Google Scholar 

  • Beck J, Urnovitz H, Mitchell WM, et al. Next Generation Sequencing of Serum Circulating Nucleic Acids from Patients with Invasive Ductal Breast Cancer Reveals Differences to Healthy and Nonmalignant Controls. Mol Cancer Research; 2010;8:335-42.

    Article  CAS  Google Scholar 

  • Bejar R, Stevenson K, Abdel-Wahab O, et al. Clinical Effect of Point Mutations in Myelodysplastic Syndromes. N Engl J Med 2011;364:2496-2506.

    Article  CAS  Google Scholar 

  • Berger MF, Lawrence MS, Demichelis F, et al. The genomic complexity of primary human prostate cancer. Nature 2011;470:214-20.

    Article  CAS  Google Scholar 

  • Campbell PJ, Stephens PJ, Pleasance ED, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008;40:722-9.

    Article  CAS  Google Scholar 

  • Chen W, Ullmann R, Langnick C, et al. Breakpoint analysis of balanced chromosome rearrangements by next-generation paired-end sequencing. Eur J Hum Genet 2010;18:539-43.

    Article  CAS  Google Scholar 

  • Clark MJ, Homer N, O’Connor BD, et al. U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line. PLoS Genet 2010;6(1): e1000832.

    Article  Google Scholar 

  • Conway C, Chalkley R, High A, et al. Next-Generation Sequencing for Simultaneous Determination of Human Papillomavirus Load, Subtype, and Associated Genomic Copy Number Changes in Tumors. J Mol Diagn 2012;14:104-11.

    Article  CAS  Google Scholar 

  • Craig DW, O’Shaughnessy JA, Kiefer JA, et al. Genome and transcriptome sequencing in prospective triple negative breast cancer uncovers therapeutic vulnerabilities. Mol Cancer Ther 2013;12:104-16.

    Article  CAS  Google Scholar 

  • Ding L, Ellis MJ, Li S, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature 2010;464:999-1005.

    Article  CAS  Google Scholar 

  • Farazi TA, Horlings HM, Ten Hoeve JJ, et al. MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res 2011;71:4443-53.

    Article  CAS  Google Scholar 

  • Gartner JJ, Parker SC, Prickett TD, et al. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. PNAS 2013;110(33):13481-6; doi: 10.1073/pnas.1304227110.

    Article  CAS  Google Scholar 

  • Grasso CS, Wu YM, Robinson DR, et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012;487:239-43.

    Article  CAS  Google Scholar 

  • Jan M, Snyder TM, Corces-ZimmermanMR, et al. Clonal evolution of preleukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci Transl Med 2012;4:149ra118.

    Google Scholar 

  • Jenkins RB, Xiao Y, Sicotte H, et al. A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nat Genet 2012;44:1122-5.

    Article  CAS  Google Scholar 

  • Jones DT, Jäger N, Kool M, et al. Dissecting the genomic complexity underlying medulloblastoma. Nature 2012;488:100-5.

    Article  CAS  Google Scholar 

  • Kohlmann A, Grossmann V, Klein HU, et al. Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1. J Clin Oncol 2010;28:3858-65.

    Article  CAS  Google Scholar 

  • Kumar V, Kato N, Urabe Y, et al. Genome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma. Nat Genet 2011;43:455-8.

    Article  CAS  Google Scholar 

  • Maher CA, Kumar-Sinha C, Cao X, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009;458:97-101.

    Article  CAS  Google Scholar 

  • Mardis ER, Ding L, Dooling DJ, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med 2009;361:1058-66.

    Article  CAS  Google Scholar 

  • Maxson JE, Gotlib J, Pollyea DA, et al. Oncogenic CSF3R Mutations in Chronic Neutrophilic Leukemia and Atypical CML. N Engl J Med 2013;368:1781-90.

    Article  CAS  Google Scholar 

  • Mehine M, Kaasinen E, Mäkinen N, et al. Characterization of uterine leiomyomas by whole-genome sequencing. NEJM 2013;369:43-53.

    Article  CAS  Google Scholar 

  • Mendes-Pereira AM, Sims D, Dexter T, et al. Genome-wide functional screen identifies a compendium of genes affecting sensitivity to tamoxifen. PNAS 2012;109:2730-5.

    Article  CAS  Google Scholar 

  • Navin N, Kendall J, Troge J, et al. Tumour evolution inferred by single-cell sequencing. Nature 2011;472:90-4.

    Article  CAS  Google Scholar 

  • Parsons DW, Li M, Zhang X, Jones S, et al. The genetic landscape of the childhood cancer medulloblastoma. Science 2011;331:435-9.

    Article  CAS  Google Scholar 

  • Patel JP, Gönen M, Figueroa ME, et al. Prognostic Relevance of Integrated Genetic Profiling in Acute Myeloid Leukemia. NEJM 2012;366:1079-89.

    Article  CAS  Google Scholar 

  • Pleasance ED, Stephens PJ, O’Meara S, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 2010;463:184-90.

    Article  CAS  Google Scholar 

  • Ramkissoon LA, Horowitz PG, Craig JM, et al. Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1. PNAS 2013;110(20):8188-93. doi: 10.1073/pnas.1300252110

    Article  CAS  Google Scholar 

  • Rampal RK, Levine RL. Finding a needle in a haystack: whole genome sequencing and mutation discovery in murine models. J Clin Invest 2011;121: 1255-58.

    Article  CAS  Google Scholar 

  • Santarius T, Shipley J, Brewer D, et al. A census of amplified and overexpressed human cancer genes. Nature Reviews Cancer 2010;10:59-64.

    Article  CAS  Google Scholar 

  • Slade I, Stephens P, Douglas J, et al. Constitutional translocation breakpoint mapping by genome-wide paired-end sequencing identifies HACE1 as a putative Wilms tumor susceptibility gene. J Med Genet 2010;47:342-7.

    Article  CAS  Google Scholar 

  • Spencer DH, Abel HJ, Lockwood CM, et al. Detection of FLT3 Internal Tandem Duplication in Targeted, Short-Read-Length, Next-Generation Sequencing Data. J Mol Diagn 2013;15:81-93.

    Article  CAS  Google Scholar 

  • Stephens PJ, Greenman CD, Fu B, et al. Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development. Cell 2011;144:27-40.

    Article  CAS  Google Scholar 

  • Stephens PJ, McBride DJ, Lin ML, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 2009;462:1005-10.

    Article  CAS  Google Scholar 

  • The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330-7.

    Article  Google Scholar 

  • The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 2011;474:609-15.

    Article  Google Scholar 

  • Tiacci E, Trifonov V, Schiavoni G, et al. BRAF mutations in hairy-cell leukemia. N Engl J Med 2011;364:2305-15.

    Article  CAS  Google Scholar 

  • Totoki Y, Tatsuno K, Arai Y, et al. High-resolution characterization of a hepatocellular carcinoma genome. Nat Genet 2011;43:464-9.

    Article  CAS  Google Scholar 

  • Tuch BB, Laborde RR, Xu X, et al. Tumor transcriptome sequencing reveals allelic expression imbalances associated with copy number alterations. PLoS One 2010;5(2):e9317.

    Article  Google Scholar 

  • Volinia S, Galasso M, Sana ME, et al. Breast cancer signatures for invasiveness and prognosis defined by deep sequencing of microRNA. PNAS 2012;109:3024-9.

    Article  CAS  Google Scholar 

  • Wagle N, Emery C, Berger MF, et al. Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling. J Clin Oncol 2011;29:3085-96.

    Article  CAS  Google Scholar 

  • Walsh T, Lee MK, Casadei S, et al. Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. PNAS 2010;107:12629-33.

    Article  CAS  Google Scholar 

  • Walter MJ, Shen D, Ding L, et al. Clonal Architecture of Secondary Acute Myeloid Leukemia. NEJM 2012;366:1090-8.

    Article  CAS  Google Scholar 

  • Wei X, Walia V, Lin JC, et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat Genet 2011;43:442-6.

    Article  CAS  Google Scholar 

  • Zhang J, Wu G, Miller CP, et al. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat Genet 2013;45(6):602-12. doi:10.1038/ng.2611.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Jain PharmaBiotech, Basel, Switzerland

    Kewal K. Jain MD, FRACS, FFPM

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  1. Kewal K. Jain MD, FRACS, FFPM
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© 2014 Springer Science+Business Media New York

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Jain, K.K. (2014). Sequencing in Cancer. In: Applications of Biotechnology in Oncology. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4614-9245-0_3

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