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Factor models for cancer signatures

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  • Kakushadze, Zura
  • Yu, Willie

Abstract

We present a novel method for extracting cancer signatures by applying statistical risk models (http://ssrn.com/abstract=2732453) from quantitative finance to cancer genome data. Using 1389 whole genome sequenced samples from 14 cancers, we identify an “overall” mode of somatic mutational noise. We give a prescription for factoring out this noise and source code for fixing the number of signatures. We apply nonnegative matrix factorization (NMF) to genome data aggregated by cancer subtype and filtered using our method. The resultant signatures have substantially lower variability than those from unfiltered data. Also, the computational cost of signature extraction is cut by about a factor of 10. We find 3 novel cancer signatures, including a liver cancer dominant signature (96% contribution) and a renal cell carcinoma signature (70% contribution). Our method accelerates finding new cancer signatures and improves their overall stability. Reciprocally, the methods for extracting cancer signatures could have interesting applications in quantitative finance.

Suggested Citation

  • Kakushadze, Zura & Yu, Willie, 2016. "Factor models for cancer signatures," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 462(C), pages 527-559.
    • Handle: RePEc:eee:phsmap:v:462:y:2016:i:c:p:527-559
    DOI: 10.1016/j.physa.2016.06.089
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    References listed on IDEAS

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    Cited by:

    1. Zura Kakushadze & Willie Yu, 2017. "Mutation Clusters from Cancer Exome," Papers 1707.08504, arXiv.org.
    2. Chen, Shunjie & Yang, Sijia & Wang, Pei & Xue, Liugen, 2023. "Two-stage penalized algorithms via integrating prior information improve gene selection from omics data," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 628(C).
    3. Zura Kakushadze & Willie Yu, 2017. "*K-means and Cluster Models for Cancer Signatures," Papers 1703.00703, arXiv.org, revised Jul 2017.
    4. Zura Kakushadze & Willie Yu, 2020. "Machine Learning Treasury Yields," Bulletin of Applied Economics, Risk Market Journals, vol. 7(1), pages 1-65.
    5. Zura Kakushadze & Willie Yu, 2020. "Machine Learning Treasury Yields," Papers 2003.05095, arXiv.org.

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