Cancer and Metastasis Reviews

, Volume 30, Issue 2, pp 199–210 | Cite as

The power of NGS technologies to delineate the genome organization in cancer: from mutations to structural variations and epigenetic alterations

  • Michal R. Schweiger
  • Martin Kerick
  • Bernd Timmermann
  • Melanie Isau
NON-THEMATIC REVIEW

Abstract

The development of cancer is characterized by the joined occurrence of alterations on different levels—from single nucleotide changes via structural and copy number variations to epigenetic alterations. With the advent of advanced technologies such as next generation sequencing, we have now the tools in hands to put some light on complex processes and recognize systematic patterns that develop throughout cancer progression. The combination of single hypothesis-driven experiments with a system-wide genetic view enables us to prove so far not addressable questions such as the influence of DNA methylation on gene expression or the disruption of genome homeostasis by structural variations and miRNA expression patterns. Out of this enormous amount of information, specific biomarkers for cancer progression have been discovered, which pave the way for the development of new therapeutic strategies. Here, we will review the status quo of integrative cancer genomic approaches, give an overview over the power of next generation sequencing technologies in oncology, and outline future perspective. Both sides—clinical as well as basic research aspects—will be considered.

Keywords

Next generation sequencing NGS Cancer Personalized therapy 

References

  1. 1.
    Krawitz, P. M., Schweiger, M. R., Rodelsperger, C., Marcelis, C., Kolsch, U., et al. (2010). Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nature Genetics, 42, 827–829.PubMedCrossRefGoogle Scholar
  2. 2.
    Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., et al. (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272–276.PubMedCrossRefGoogle Scholar
  3. 3.
    Bagnyukova, T., Serebriiskii, I. G., Zhou, Y., Hopper-Borge, E. A., Golemis, E. A., et al. (2010). Chemotherapy and signaling: how can targeted therapies supercharge cytotoxic agents? Cancer Biol Ther, 10(9), 839–853.PubMedCrossRefGoogle Scholar
  4. 4.
    Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., et al. (2008). The potential and challenges of nanopore sequencing. Nature Biotechnology, 26, 1146–1153.PubMedCrossRefGoogle Scholar
  5. 5.
    Pleasance, E. D., Stephens, P. J., O’Meara, S., McBride, D. J., Meynert, A., et al. (2010). A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463, 184–190.PubMedCrossRefGoogle Scholar
  6. 6.
    Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., et al. (2010). A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191–196.PubMedCrossRefGoogle Scholar
  7. 7.
    Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., et al. (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66–72.PubMedCrossRefGoogle Scholar
  8. 8.
    Shah, S. P., Morin, R. D., Khattra, J., Prentice, L., Pugh, T., et al. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809–813.PubMedCrossRefGoogle Scholar
  9. 9.
    Gilbert, M. T., Haselkorn, T., Bunce, M., Sanchez, J. J., Lucas, S. B., et al. (2007). The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS ONE, 2, e537.PubMedCrossRefGoogle Scholar
  10. 10.
    Schweiger, M. R., Kerick, M., Timmermann, B., Albrecht, M. W., Borodina, T., et al. (2009). Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS ONE, 4, e5548.PubMedCrossRefGoogle Scholar
  11. 11.
    Bian, Y. S., Yan, P., Osterheld, M. C., Fontolliet, C., & Benhattar, J. (2001). Promoter methylation analysis on microdissected paraffin-embedded tissues using bisulfite treatment and PCR-SSCP. Biotechniques, 30, 66–72.PubMedGoogle Scholar
  12. 12.
    Chiu, R. W., Chan, K. C., Gao, Y., Lau, V. Y., Zheng, W., et al. (2008). Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proceedings of the National Academy of Sciences of the United States of America, 105, 20458–20463.PubMedCrossRefGoogle Scholar
  13. 13.
    Kerjean, A., Vieillefond, A., Thiounn, N., Sibony, M., Jeanpierre, M., et al. (2001). Bisulfite genomic sequencing of microdissected cells. Nucleic Acids Research, 29, E106–106.PubMedCrossRefGoogle Scholar
  14. 14.
    Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L., & Quake, S. R. (2008). Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proceedings of the National Academy of Sciences of the United States of America, 105, 16266–16271.PubMedCrossRefGoogle Scholar
  15. 15.
    van der Vaart, M., Semenov, D. V., Kuligina, E. V., Richter, V. A., & Pretorius, P. J. (2009). Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform. Clinica Chimica Acta, 409, 21–27.CrossRefGoogle Scholar
  16. 16.
    Beck, J., Urnovitz, H. B., Mitchell, W. M., & Schutz, E. (2010). Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls. Molecular Cancer Research, 8, 335–342.PubMedCrossRefGoogle Scholar
  17. 17.
    McBride, D. J., Orpana, A. K., Sotiriou, C., Joensuu, H., Stephens, P. J., et al. (2010). Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes, Chromosomes & Cancer, 49, 1062–1069.CrossRefGoogle Scholar
  18. 18.
    Maxam, A. M., & Gilbert, W. (1977). A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America, 74, 560–564.PubMedCrossRefGoogle Scholar
  19. 19.
    Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74, 5463–5467.PubMedCrossRefGoogle Scholar
  20. 20.
    The International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945.CrossRefGoogle Scholar
  21. 21.
    Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921.PubMedCrossRefGoogle Scholar
  22. 22.
    Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9, 387–402.PubMedCrossRefGoogle Scholar
  23. 23.
    Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26, 1135–1145.PubMedCrossRefGoogle Scholar
  24. 24.
    Metzker, M. L. (2010). Sequencing technologies—the next generation. Nature Reviews. Genetics, 11, 31–46.PubMedCrossRefGoogle Scholar
  25. 25.
    Ding, L., Wendl, M. C., Koboldt, D. C., & Mardis, E. R. (2010). Analysis of next-generation genomic data in cancer: accomplishments and challenges. Human Molecular Genetics, 19, R188–R196.PubMedCrossRefGoogle Scholar
  26. 26.
    Meyerson, M., Gabriel, S., & Getz, G. (2010). Advances in understanding cancer genomes through second-generation sequencing. Nature Reviews. Genetics, 11, 685–696.PubMedCrossRefGoogle Scholar
  27. 27.
    Rothberg, J. M., & Leamon, J. H. (2008). The development and impact of 454 sequencing. Nature Biotechnology, 26, 1117–1124.PubMedCrossRefGoogle Scholar
  28. 28.
    Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–380.PubMedGoogle Scholar
  29. 29.
    Ronaghi, M. (2001). Pyrosequencing sheds light on DNA sequencing. Genome Research, 11, 3–11.PubMedCrossRefGoogle Scholar
  30. 30.
    Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53–59.PubMedCrossRefGoogle Scholar
  31. 31.
    Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728–1732.PubMedCrossRefGoogle Scholar
  32. 32.
    Blow, N. (2008). DNA sequencing: generation next-next. Nat Methods, 5(6), 267–274.CrossRefGoogle Scholar
  33. 33.
    Clarke, J., Wu, H. C., Jayasinghe, L., Patel, A., Reid, S., et al. (2009). Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnology, 4, 265–270.PubMedCrossRefGoogle Scholar
  34. 34.
    Greenleaf, W. J., & Block, S. M. (2006). Single-molecule, motion-based DNA sequencing using RNA polymerase. Science, 313, 801.PubMedCrossRefGoogle Scholar
  35. 35.
    Sugiyama, S. (2006). Application of scanning probe microscopy to genetic analysis. Japanese journal of applied physics, 45, 4.CrossRefGoogle Scholar
  36. 36.
    Pourmand, N., Karhanek, M., Persson, H. H., Webb, C. D., Lee, T. H., et al. (2006). Direct electrical detection of DNA synthesis. Proceedings of the National Academy of Sciences of the United States of America, 103, 6466–6470.PubMedCrossRefGoogle Scholar
  37. 37.
    Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., et al. (2007). Direct selection of human genomic loci by microarray hybridization. Nat Methods, 4, 903–905.PubMedCrossRefGoogle Scholar
  38. 38.
    Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., et al. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106, 19096–19101.PubMedCrossRefGoogle Scholar
  39. 39.
    Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology, 27, 182–189.PubMedCrossRefGoogle Scholar
  40. 40.
    Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M. N., et al. (2007). Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39, 1522–1527.PubMedCrossRefGoogle Scholar
  41. 41.
    Porreca, G. J., Zhang, K., Li, J. B., Xie, B., Austin, D., et al. (2007). Multiplex amplification of large sets of human exons. Nat Methods, 4, 931–936.PubMedCrossRefGoogle Scholar
  42. 42.
    The Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061–1068.CrossRefGoogle Scholar
  43. 43.
    Bardelli, A., Parsons, D. W., Silliman, N., Ptak, J., Szabo, S., et al. (2003). Mutational analysis of the tyrosine kinome in colorectal cancers. Science, 300, 949.PubMedCrossRefGoogle Scholar
  44. 44.
    Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., et al. (2007). Patterns of somatic mutation in human cancer genomes. Nature, 446, 153–158.PubMedCrossRefGoogle Scholar
  45. 45.
    Jones, S., Zhang, X., Parsons, D. W., Lin, J. C., Leary, R. J., et al. (2008). Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 321, 1801–1806.PubMedCrossRefGoogle Scholar
  46. 46.
    Parsons, D. W., Jones, S., Zhang, X., Lin, J. C., Leary, R. J., et al. (2008). An integrated genomic analysis of human glioblastoma multiforme. Science, 321, 1807–1812.PubMedCrossRefGoogle Scholar
  47. 47.
    Sjoblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., et al. (2006). The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268–274.PubMedCrossRefGoogle Scholar
  48. 48.
    Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjoblom, T., et al. (2007). The genomic landscapes of human breast and colorectal cancers. Science, 318, 1108–1113.PubMedCrossRefGoogle Scholar
  49. 49.
    Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., et al. (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England Journal of Medicine, 361, 1058–1066.PubMedCrossRefGoogle Scholar
  50. 50.
    Fredman, D., White, S. J., Potter, S., Eichler, E. E., Den Dunnen, J. T., et al. (2004). Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics, 36, 861–866.PubMedCrossRefGoogle Scholar
  51. 51.
    Druker, B. J. (2008). Translation of the Philadelphia chromosome into therapy for CML. Blood, 112, 4808–4817.PubMedCrossRefGoogle Scholar
  52. 52.
    Park, J. W., Neve, R. M., Szollosi, J., & Benz, C. C. (2008). Unraveling the biologic and clinical complexities of HER2. Clinical Breast Cancer, 8, 392–401.PubMedCrossRefGoogle Scholar
  53. 53.
    Campbell, P. J., Stephens, P. J., Pleasance, E. D., O’Meara, S., Li, H., et al. (2008). Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genetics, 40, 722–729.PubMedCrossRefGoogle Scholar
  54. 54.
    Stephens, P. J., McBride, D. J., Lin, M. L., Varela, I., Pleasance, E. D., et al. (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462, 1005–1010.PubMedCrossRefGoogle Scholar
  55. 55.
    Beck, S., & Rakyan, V. K. (2008). The methylome: approaches for global DNA methylation profiling. Trends in Genetics, 24, 231–237.PubMedCrossRefGoogle Scholar
  56. 56.
    Feinberg, A. P. (2007). Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433–440.PubMedCrossRefGoogle Scholar
  57. 57.
    Banerjee, H. N., & Verma, M. (2009). Epigenetic mechanisms in cancer. Biomarkers Medicine, 3, 14.Google Scholar
  58. 58.
    Lister, R., & Ecker, J. R. (2009). Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Research, 19, 959–966.PubMedCrossRefGoogle Scholar
  59. 59.
    Ball, M. P., Li, J. B., Gao, Y., Lee, J. H., LeProust, E. M., et al. (2009). Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnology, 27, 361–368.PubMedCrossRefGoogle Scholar
  60. 60.
    Rakyan, V. K., Down, T. A., Thorne, N. P., Flicek, P., Kulesha, E., et al. (2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research, 18, 1518–1529.PubMedCrossRefGoogle Scholar
  61. 61.
    Morozova, O., Hirst, M., & Marra, M. A. (2009). Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics, 10, 135–151.PubMedCrossRefGoogle Scholar
  62. 62.
    Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., et al. (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956–960.PubMedCrossRefGoogle Scholar
  63. 63.
    Friedel, C. C., & Dolken, L. (2009). Metabolic tagging and purification of nascent RNA: implications for transcriptomics. Molecular Biosystems, 5, 1271–1278.PubMedCrossRefGoogle Scholar
  64. 64.
    Klein, C. A. (2009). Parallel progression of primary tumours and metastases. Nature Reviews. Cancer, 9, 302–312.PubMedCrossRefGoogle Scholar
  65. 65.
    Campbell, P. J., Yachida, S., Mudie, L. J., Stephens, P. J., Pleasance, E. D., et al. (2010). The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature, 467, 1109–1113.PubMedCrossRefGoogle Scholar
  66. 66.
    Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., et al. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464, 999–1005.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Michal R. Schweiger
    • 1
  • Martin Kerick
    • 1
  • Bernd Timmermann
    • 1
  • Melanie Isau
    • 1
    • 2
  1. 1.Max Planck Institute for Molecular GeneticsBerlinGermany
  2. 2.Department of BiologyFree University Berlin, Chemistry and PharmacyBerlinGermany

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