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Quantification of Aneuploidy in Mammalian Systems

  • Hilda van den Bos
  • Bjorn Bakker
  • Aaron Taudt
  • Victor Guryev
  • Maria Colomé-Tatché
  • Peter M. Lansdorp
  • Floris Foijer
  • Diana C. J. Spierings
Part of the Methods in Molecular Biology book series (MIMB, volume 1896)

Abstract

High-throughput next generation sequencing karyotyping has emerged as a powerful tool for the detection of genomic heterogeneity in normal tissues and cancers. Here we describe a single-cell whole genome sequencing (scWGS) platform to assess whole-chromosome aneuploidy, structural aneuploidies involving only chromosome fragments and more local small copy number alterations in individual cells. We provide a detailed protocol for the isolation, library preparation, low coverage sequencing and data analysis of single cells. Since our approach does not involve a whole-genome preamplification step, our method allows for acquisition of reliable high-resolution single-cell copy number profiles. Moreover, the protocol allows multiplexing of 384 single-cell libraries in one sequencing run, thereby significantly reducing sequencing costs and can be completed in 3–4 days starting from single cell isolation to analysis of sequencing data.

Key words

Single-cell whole genome sequencing Aneuploidy Copy number alterations Library preparation 

Notes

Acknowledgments

This work was supported by a Dutch Cancer Society grant (KWF grant RUG-2012-5549) and a Groningen Foundation for Paediatric Oncology (SKOG) grant to FF and PML, an Advanced ERC grant to PML, and by an NWO (The Netherlands Organisation for Scientific Research) MEERVOUD grant and a University of Groningen Rosalind Franklin grant to MCT.

References

  1. 1.
    Bakker B, van den Bos H, Lansdorp PM, Foijer F (2015) How to count chromosomes in a cell: an overview of current and novel technologies. BioEssays 37:570–577.  https://doi.org/10.1002/bies.201400218CrossRefGoogle Scholar
  2. 2.
    van den Bos H, Spierings DCJ, Taudt AS et al (2016) Single-cell whole genome sequencing reveals no evidence for common aneuploidy in normal and Alzheimer’s disease neurons. Genome Biol 17:116.  https://doi.org/10.1186/s13059-016-0976-2CrossRefGoogle Scholar
  3. 3.
    Bakker B, Taudt A, Belderbos ME et al (2016) Single cell sequencing reveals karyotype heterogeneity in murine and human tumours. Genome Biol 17:1–15.  https://doi.org/10.1186/s13059-016-0971-7CrossRefGoogle Scholar
  4. 4.
    Levine MS, Bakker B, Boeckx B et al (2017) Centrosome amplification is sufficient to promote spontaneous tumorigenesis in mammals. Dev Cell 40:313–322.e5.  https://doi.org/10.1016/j.devcel.2016.12.022CrossRefGoogle Scholar
  5. 5.
    Foijer F, Albacker LA, Bakker B et al (2017) Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma. Elife 6:e20873.  https://doi.org/10.7554/eLife.20873CrossRefGoogle Scholar
  6. 6.
    Ferronika P, van den Bos H, Taudt A et al (2017) Copy number alterations assessed at the single-cell level revealed mono- and polyclonal seeding patterns of distant metastasis in a small cell lung cancer patient. Ann Oncol 28(7):1668–1670.  https://doi.org/10.1093/annonc/mdx182CrossRefGoogle Scholar
  7. 7.
    Soto M, Raaijmakers JA, Bakker B et al (2017) p53 prohibits propagation of chromosome segregation errors that produce structural aneuploidies. Cell Rep 19:2423–2431.  https://doi.org/10.1016/j.celrep.2017.05.055CrossRefGoogle Scholar
  8. 8.
    Hills M, O’Neill K, Falconer E et al (2013) BAIT: organizing genomes and mapping rearrangements in single cells. Genome Med 5:82.  https://doi.org/10.1186/gm486CrossRefGoogle Scholar
  9. 9.
    Szabó G, Kiss A, Damjanovich S (1981) Flow cytometric analysis of the uptake of hoechst 33342 dye by human lymphocytes. Cytometry 2:20–23.  https://doi.org/10.1002/cyto.990020104CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Hilda van den Bos
    • 1
  • Bjorn Bakker
    • 1
  • Aaron Taudt
    • 1
    • 2
  • Victor Guryev
    • 1
  • Maria Colomé-Tatché
    • 1
    • 2
  • Peter M. Lansdorp
    • 1
    • 3
    • 4
  • Floris Foijer
    • 1
  • Diana C. J. Spierings
    • 1
  1. 1.European Research Institute for the Biology of Ageing (ERIBA)University of Groningen, University Medical Center GroningenGroningenThe Netherlands
  2. 2.Institute for Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
  3. 3.Terry Fox LaboratoryBC Cancer AgencyVancouverCanada
  4. 4.Department of Medical GeneticsUniversity of British ColumbiaVancouverCanada

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