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Identification of Chromothripsis in Biopsy Using SNP-Based Microarray

  • Veronica Ortega
  • Christina Mendiola
  • Gopalrao V. N. Velagaleti
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1769)

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.

Key words

Chromothripsis SNP microarray Copy number variants (CNVs) DNA Cancer Biopsy 

Notes

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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Copyright information

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

Authors and Affiliations

  • Veronica Ortega
    • 1
  • Christina Mendiola
    • 1
  • Gopalrao V. N. Velagaleti
    • 1
  1. 1.Department of Pathology and Laboratory MedicineUniversity of Texas Health Science CenterSan AntonioUSA

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