Analysis of Chromothripsis by Combined FISH and Microarray Analysis

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1769)

Abstract

Fluorescence in situ hybridization (FISH) to metaphase chromosomes, in conjunction with SNP array, array CGH, or whole genome sequencing, can help determine the organization of abnormal genomes after chromothripsis and other types of complex genome rearrangement. DNA microarrays can identify the changes in copy number, but they do not give information on the organization of the abnormal chromosomes, balanced rearrangements, or abnormalities of the centromeres and other regions comprised of highly repetitive DNA. Many of these details can be determined by the strategic use of metaphase FISH. FISH is a single-cell technique, so it can identify low-frequency chromosome abnormalities, and it can determine which chromosome abnormalities occur in the same or different clonal populations. These are important considerations in cancer. Metaphase chromosomes are intact, so information about abnormalities of the chromosome homologues is preserved. Here we describe strategies for working out the organization of highly rearranged genomes by combining SNP array data with various metaphase FISH methods. This approach can also be used to address some of the uncertainties arising from whole genome or mate-pair sequencing data.

Key words

Chromothripsis Metaphase FISH Chromosome Cytogenetics M-FISH M-BAND Microarray SNP array Cytogenomics 

Notes

Acknowledgments

Many thanks to Meaghan Wall for critical reading of the manuscript.

References

  1. 1.
    Palumbo E, Russo A (2016) Chromosome imbalances in cancer: molecular cytogenetics meets genomics. Cytogenet Genome Res 150:176–184CrossRefPubMedGoogle Scholar
  2. 2.
    Garsed DW, Marshall OJ, Corbin VDA et al (2014) The architecture and evolution of cancer neochromosomes. Cancer Cell 26:653–667CrossRefPubMedGoogle Scholar
  3. 3.
    Li Y, Schwab C, Ryan SL et al (2014) Constitutional and somatic rearrangement of chromosome 21 in acute lymphoblastic leukaemia. Nature 508:98–102CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Stephens PJ, Greenman CD, Fu B et al (2011) Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 144:27–40CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Landry JJ, Pyl PT, Rausch T et al (2013) The genomic and transcriptomic landscape of a HeLa cell line. G3 (Bethesda) 3:1213–1224CrossRefGoogle Scholar
  6. 6.
    MacKinnon RN, Wall M, Zordan A et al (2013) Genome organization and the role of centromeres in evolution of the erythroleukaemia cell line HEL. Evol Med Publ Health 2013:225–240CrossRefGoogle Scholar
  7. 7.
    MacKinnon RN, Campbell LJ (2013) Chromothripsis under the microscope: a cytogenetic perspective of two cases of AML with catastrophic chromosome rearrangement. Cancer Genet 206:238–251Google Scholar
  8. 8.
    Floutsakou I, Agrawal S, Nguyen TT et al (2013) The shared genomic architecture of human nucleolar organizer regions. Genome Res 23:2003–2012CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Korbel JO, Campbell PJ (2013) Criteria for inference of chromothripsis in cancer genomes. Cell 152:1226–1236CrossRefPubMedGoogle Scholar
  10. 10.
    Donlon TA, Litt M, Newcom SR et al (1983) Localization of the restriction fragment length polymorphism D14S1 (pAW-101) to chromosome 14q32.1 -> 32.2 by in situ hybridization. Am J Hum Genet 35:1097–1106Google Scholar
  11. 11.
    Moorhead PS, Nowell PC, Mellman WJ et al (1960) Chromosome preparations of leukocytes cultured from human peripheral blood. Exp Cell Res 20:613–616CrossRefPubMedGoogle Scholar
  12. 12.
    MacKinnon RN, Chudoba I (2011) The use of M-FISH and M-BAND to define chromosome abnormalities. In: Campbell LJ (ed) Cancer cytogenetics methods and protocols. Humana Press, New York, pp 203–218CrossRefGoogle Scholar
  13. 13.
    MacKinnon RN, Campbell LJ (2007) Dicentric chromosomes and 20q11.2 amplification in MDS/AML with apparent monosomy 20. Cytogenet Genome Res 119:211–220CrossRefPubMedGoogle Scholar
  14. 14.
    MacKinnon RN, Campbell LJ (2010) Monosomy 20 in the karyotypes of myeloid malignancies is usually the result of misclassification of unbalanced chromosome 20 abnormalities. In: Urbano KV (ed) Advances in genetic research. Nova Science Publishers, pp 57–72Google Scholar
  15. 15.
    MacKinnon RN, Campbell LJ (2011) The role of dicentric chromosome formation and secondary centromere deletion in the evolution of myeloid malignancy. Genet Res Int 2011:643628PubMedPubMedCentralGoogle Scholar
  16. 16.
    MacKinnon RN, Patsouris C, Chudoba I et al (2007) A FISH comparison of variant derivatives of the recurrent dic(17;20) of myelodysplastic syndromes and acute myeloid leukemia: obligatory retention of genes on 17p and 20q may explain the formation of dicentric chromosomes. Genes Chromosom Cancer 46:27–36Google Scholar
  17. 17.
    Camps J, Mrasek K, Prat E et al (2004) Molecular cytogenetic characterisation of the colorectal cancer cell line SW480. Oncol Rep 11:1215–1218PubMedGoogle Scholar
  18. 18.
    Liehr T, Weise A, Kosyakova N (2016) cenM-FISH approaches. In: Liehr T (ed) Fluorescence in situ hybridization (FISH) application guide. Springer, Berlin, Heidelberg, pp 249–255Google Scholar
  19. 19.
    MacKinnon RN, Duivenvoorden HM, Campbell LJ et al (2016) The dicentric chromosome dic(20;22) is a recurrent abnormality in myelodysplastic syndromes and is a product of telomere fusion. Cytogenet Genome Res 150:262–272Google Scholar
  20. 20.
    MacKinnon RN, Selan C, Wall M et al (2010) The paradox of 20q11.21 amplification in a subset of cases of myeloid malignancy with chromosome 20 deletion. Genes Chromosom Cancer 48:998–1013CrossRefGoogle Scholar
  21. 21.
    Choo KH (1997) Centromere DNA dynamics: latent centromeres and neocentromere formation. Am J Hum Genet 61:1225–1233CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Sullivan BA, Schwartz S (1995) Identification of centromeric antigens in dicentric Robertsonian translocations: CENP-C and CENP-E are necessary components of functional centromeres. Hum Mol Genet 4:2189–2197CrossRefPubMedGoogle Scholar

Copyright information

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

Authors and Affiliations

  1. 1.Department of Medicine (St. Vincent’s)University of MelbourneMelbourneAustralia
  2. 2.Victorian Cancer Cytogenetics ServiceSt Vincent’s HospitalMelbourneAustralia

Personalised recommendations