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Tumor subclonal progression model for cancer hallmark acquisition

View ORCID ProfileYusuke Matsui, Satoru Miyano, Teppei Shimamura
doi: https://doi.org/10.1101/149252
Yusuke Matsui
1 Nagoya University Graduate School of Medicine, Division of Systems Biology, 65 Tsurumai-cho Showa-ku, Nagoya, 466-8550, Japan,
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  • For correspondence: ymatsui@med.nagoya-u.ac.jp
Satoru Miyano
2 Institute of Medical Science, The University of Tokyo, Laboratory of DNA Information Analysis, Human Genome Center, 4-6-1 Shirokanedai, Minatoku, Tokyo 108-8639, Japan
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Teppei Shimamura
1 Nagoya University Graduate School of Medicine, Division of Systems Biology, 65 Tsurumai-cho Showa-ku, Nagoya, 466-8550, Japan,
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  • For correspondence: ymatsui@med.nagoya-u.ac.jp
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Abstract

Recent advances in the methodologies of reconstructing cancer evolutionary trajectories opened the horizon for deciphering the subclonal populations and their evolutionary architectures under the cancer ecosystems. An important challenge of the cancer evolution studies is connecting genetic aberrations in subclones to clinically interpretable and actionable target of subclones for individual patients. In this paper, we present a novel method for constructing tumor subclonal progression model for cancer hallmark acquisition using multi-regional sequencing data. We parepare a subclonal evolutionary tree inferred from variant allele frequencies and estimate the pathway alternation probabilities from large scale cohort genomic data. We then construct an evolutionary tree of pathway alternation that takes account of selectivity of pathway alternations by the notion of probabilistic causality. We show the effectiveness of our method using a dataset of clear cell renal cell carcinomas.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 12, 2017.
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Tumor subclonal progression model for cancer hallmark acquisition
Yusuke Matsui, Satoru Miyano, Teppei Shimamura
bioRxiv 149252; doi: https://doi.org/10.1101/149252
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Tumor subclonal progression model for cancer hallmark acquisition
Yusuke Matsui, Satoru Miyano, Teppei Shimamura
bioRxiv 149252; doi: https://doi.org/10.1101/149252

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