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Factor Models for Cancer Signatures

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  • Zura Kakushadze
  • Willie Yu

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

  • Zura Kakushadze & Willie Yu, 2016. "Factor Models for Cancer Signatures," Papers 1604.08743, arXiv.org, revised Jan 2017.
    • Handle: RePEc:arx:papers:1604.08743
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    References listed on IDEAS

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    1. Daniel D. Lee & H. Sebastian Seung, 1999. "Learning the parts of objects by non-negative matrix factorization," Nature, Nature, vol. 401(6755), pages 788-791, October.
    2. Harry Markowitz, 1952. "Portfolio Selection," Journal of Finance, American Finance Association, vol. 7(1), pages 77-91, March.
    3. Zura Kakushadze & Willie Yu, 2016. "Statistical Risk Models," Papers 1602.08070, arXiv.org, revised Jan 2017.
    4. Gunes Gundem & Peter Van Loo & Barbara Kremeyer & Ludmil B. Alexandrov & Jose M. C. Tubio & Elli Papaemmanuil & Daniel S. Brewer & Heini M. L. Kallio & Gunilla Högnäs & Matti Annala & Kati Kivinummi &, 2015. "The evolutionary history of lethal metastatic prostate cancer," Nature, Nature, vol. 520(7547), pages 353-357, April.
    5. Zura Kakushadze & Willie Yu, 2016. "Multifactor Risk Models and Heterotic CAPM," Papers 1602.04902, arXiv.org, revised Mar 2016.
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