Mutation Clusters from Cancer Exome

Genes 8(8) (2017) 201

84 Pages Posted: 4 Apr 2017 Last revised: 16 Aug 2017

See all articles by Zura Kakushadze

Zura Kakushadze

Quantigic Solutions LLC; Free University of Tbilisi

Willie Yu

Duke-NUS Medical School - Centre for Computational Biology

Date Written: March 31, 2017

Abstract

We apply our statistically deterministic machine learning/clustering algorithm *K-means (recently developed in http://ssrn.com/abstract=2908286) to 10,656 published exome samples for 32 cancer types. A majority of cancer types exhibit mutation clustering structure. Our results are in-sample stable. They are also out-of-sample stable when applied to 1,389 published genome samples across 14 cancer types. In contrast, we find in- and out-of-sample instabilities in cancer signatures extracted from exome samples via nonnegative matrix factorization (NMF), a computationally costly and non-deterministic method. Extracting stable mutation structures from exome data could have important implications for speed and cost, which are critical for early-stage cancer diagnostics such as novel blood-test methods currently in development.

Keywords: Clustering, K-Means, Nonnegative Matrix Factorization, Somatic Mutation, Cancer Signatures, Genome, Exome, DNA, eRank, Correlation, Covariance, Machine Learning, Sample, Matrix, Source Code, Quantitative Finance, Statistical Risk Model, Industry Classification

JEL Classification: G00

Suggested Citation

Kakushadze, Zura and Yu, Willie, Mutation Clusters from Cancer Exome (March 31, 2017). Genes 8(8) (2017) 201. Available at SSRN: https://ssrn.com/abstract=2945010 or http://dx.doi.org/10.2139/ssrn.2945010

Zura Kakushadze (Contact Author)

Quantigic Solutions LLC ( email )

1127 High Ridge Road #135
Stamford, CT 06905
United States
6462210440 (Phone)
6467923264 (Fax)

HOME PAGE: http://www.linkedin.com/in/zurakakushadze

Free University of Tbilisi ( email )

Business School and School of Physics
240, David Agmashenebeli Alley
Tbilisi, 0159
Georgia

Willie Yu

Duke-NUS Medical School - Centre for Computational Biology ( email )

8 College Road
Singapore, 169857
Singapore

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