Abstract
One of the well-known hallmarks of cancer is genomic instability. Although gradualism is a well-established process of cancer evolution, recent studies have shown that chromothripsis or chromoanasynthesis can result in complex genomic rearrangements by a single catastrophic event rather than several incremental steps. These two novel phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes or chromosome regions resulting in the random reassembling of shattered genetic material to form complex derivative chromosomes. Although sequencing methods are ideal for the detection of chromothripsis, single-nucleotide polymorphism (SNP)-based microarray methods are also useful in detecting chromothripsis in biopsy samples. Issues related to sample collection, storage, and transport, especially with tumor biopsies, may limit the options for sequencing studies, and in such cases, SNP-based microarray may be a viable alternative for detecting chromothripsis.
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References
Greaves M, Maley CC (2012) Clonal evolution in cancer. Nature 481:306–313
Nowell PC (1976) The clonal evolution of tumor cell populations. Science 194:23–28
Yates LR, Campbell PJ (2012) Evolution of the cancer genome. Nat Rev Genet 13:795–806
Mitelman F, Johansson B, Mertens F (2007) The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 7:233–245
Rabbits TH (2009) Commonality but diversity in cancer gene fusions. Cell 137:391–395
Stephens PJ, McBride DJ, Lin ML et al (2009) Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462:1005–1010
Stratton MR, Campbell PJ, Futreal PA (2009) The cancer genome. Nature 458:719–724
Baca SC, Prandi D, Lawrence MS et al (2013) Punctuated evolution of prostate cancer genomes. Cell 153:666–677
Liu P, Erez A, Nagamani SC et al (2011) Chromosome catastophes involve replication mechanisms generating complex genomic rearrangements. Cell 146:889–903
Rausch T, Jones DT, Zapatka M et al (2012) Genomic sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell 148:59–71
Stephens PJ, Greenman CD, Fu B et al (2011) Massive genomic rearrangements acquired in a single catastrophic event during cancer development. Cell 144:27–40
Foremont JV, Kaidi A, Jackson SP (2012) Chromothripsis and cancer: causes and consequences of chromosome shattering. Nat Rev Cancer 12:663–670
Jone MJ, Jallepalli PV (2012) Chromothripsis: chromosomes in crisis. Dev Cell 23:908–917
Maher CA, Wilson RK (2012) Chromothripsis and human disease: piecing together the shattering process. Cell 148:29–32
Meyerson M, Pellman D (2011) Cancer genomes evolve by pulverizing single chromosomes. Cell 144:9–10
Tubio JM, Estivill X (2011) Cancer: when catastrophe strikes a cell. Nature 470:476–477
Holland AJ, Cleveland DW (2012) Chromoanagenesis and cancer: mechanisms and consequences of localized, complex chromosomal rearrangements. Nat Med 18:1630–1638
Rode A, Maass KK, Willmund KV et al (2016) Chromothripsis in cancer cells: an update. Int J Cancer 138:2322–2333
Ortega V, Chaubey A, Mendiola C et al (2016) Complex chromosomal rearrangements in B-cell lymphoma: evidence of chromoanagenesis? A case report. Neoplasia 18:223–228
Kloosterman WP, Koster J, Molenaar JJ (2014) Prevalence and clinical implications of chromothripsis in cancer genomes. Curr Opin Oncol 26:64–72
Kinsella M, Patel A, Bafna V (2014) The elusive evidence for chromothripsis. Nucleic Acids Res 42:8231–8242
Acknowledgments
The authors express their sincere gratitude to Affymetrix (Thermo Fisher Scientific), especially to Dr. Clint VanValkenburgh, Alan Silverman, Dr. Xiaowen Rudner-Hobden, and Corina Nikolof for helpful suggestions, for assistance in validating and establishing the assay, and for continued technical support.
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Ortega, V., Mendiola, C., Velagaleti, G.V.N. (2018). Identification of Chromothripsis in Biopsy Using SNP-Based Microarray. In: Pellestor, F. (eds) Chromothripsis. Methods in Molecular Biology, vol 1769. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7780-2_7
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DOI: https://doi.org/10.1007/978-1-4939-7780-2_7
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