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Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples

Part of the Lecture Notes in Computer Science book series (LNBI,volume 9029)

Abstract

For a genomically unstable cancer, a single tumour biopsy will often contain a mixture of competing tumour clones. These tumour clones frequently differ with respect to their genomic content (copy number of each chromosome segment) and structure (order/adjacency of segments on tumour chromosomes). Whole genome sequencing mixes the signals of tumour clones and contaminating normal cells. The ability to unmix these signals and infer divergent genome structure and content is relevant to current avenues of cancer research. We propose a method to unmix tumour and contaminating normal signals and jointly predict genome structure and content of each tumour clone.

Keywords

  • Cancer
  • Heterogeneity
  • Copy number
  • Rearrangements

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  • DOI: 10.1007/978-3-319-16706-0_25
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References

  1. Oesper, L., et al.: Quantifying Tumor Heterogeneity in Whole-Genome and Whole-Exome Sequencing Data. Bioinformatics 30(24), 3532–3540 (2014)

    CrossRef  Google Scholar 

  2. Zerbino, D.R., et al.: An algebraic framework to sample the rearrangement histories of a cancer metagenome with double cut and join, duplication and deletion events. arXiv (2013)

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  3. Mahmoody, A., et al.: Reconstructing genome mixtures from partial adjacencies. BMC Bioinformatics 13(Suppl. 19), S9 (2012)

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  4. Fischer, A., et al.: High-definition reconstruction of clonal composition in cancer. Cell Reports 7, 17401752

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  5. Oesper, L., et al.: Reconstructing cancer genomes from paired-end sequencing data. BMC Bioinformatics 13(Suppl. 6), S10 (2012)

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Correspondence to Andrew McPherson .

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© 2015 Springer International Publishing Switzerland

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McPherson, A., Roth, A., Chauve, C., Sahinalp, S.C. (2015). Joint Inference of Genome Structure and Content in Heterogeneous Tumor Samples. In: Przytycka, T. (eds) Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science(), vol 9029. Springer, Cham. https://doi.org/10.1007/978-3-319-16706-0_25

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  • DOI: https://doi.org/10.1007/978-3-319-16706-0_25

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-16705-3

  • Online ISBN: 978-3-319-16706-0

  • eBook Packages: Computer ScienceComputer Science (R0)