, (room 4105 unless otherwise noted).
Date |
Speaker |
Fac/
Postdoc/
Grad |
PI/Lab/Host |
Topic/Abstract |
Time (if other than 2pm) |
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Oct. 15, 2019 |
Dr. Mohammed El-Kebir |
Asst. Professor, CS Dept. |
University of Illinois Urbana-Champaign |
Implications of Non-uniqueness of Solutions in Cancer Phylogenetics
Abstract: In addition to enabling clinicians to devise patient-specific treatment plans, cancer phylogenies enable researchers to decipher the mechanisms of tumorigenesis and metastasis. However, the tumor phylogeny inference problem from DNA sequencing data exhibits many alternative solutions. Awareness of this non-uniqueness of solutions is key to drawing accurate conclusions in downstream analyses. Here, we discuss the theoretical and practical implications of non-uniqueness of solutions. Theoretically, we show that determining the exact number of solutions to the problem is #P-complete, and that sampling solutions uniformly at random is hard as well. Using simulated and real data, we identify factors that contribute to and counteract non-uniqueness of solutions. In addition, we study the sampling performance of current methods, identifying significant biases. Finally, we propose a method to accurately summarize a set of cancer phylogenies, overcoming limitations of current summary methods. Our work enables practitioners in cancer genomics to draw more informed conclusions from ambiguous sequencing data. |
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