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A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression

Authors Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, S. Cenk Sahinalp

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Author Details

Nikolai Karpov
  • Department of Computer Science, Indiana University, Bloomington, IN, USA
Salem Malikic
  • School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
Md. Khaledur Rahman
  • Department of Computer Science, Indiana University, Bloomington, IN, USA
S. Cenk Sahinalp
  • Department of Computer Science, Indiana University, Bloomington, IN, USA

Funding

NK is supported by NSF CCF-1525024 and IIS-1633215. SM is supported by a Vanier Canada Graduate Scholarship.

Cite AsGet BibTex

Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, and S. Cenk Sahinalp. A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 22:1-22:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
https://doi.org/10.4230/LIPIcs.WABI.2018.22

Abstract

We introduce a new edit distance measure between a pair of "clonal trees", each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk high throughput sequencing data. In a clonal tree, each vertex represents a specific tumor clone, and is labeled with one or more mutations in a way that each mutation is assigned to the oldest clone that harbors it. Given two clonal trees, our multi-labeled tree edit distance (MLTED) measure is defined as the minimum number of mutation/label deletions, (empty) leaf deletions, and vertex (clonal) expansions, applied in any order, to convert each of the two trees to the maximal common tree. We show that the MLTED measure can be computed efficiently in polynomial time and it captures the similarity between trees of different clonal granularity well. We have implemented our algorithm to compute MLTED exactly and applied it to a variety of data sets successfully. The source code of our method can be found in: https://github.com/khaled-rahman/leafDelTED.

Subject Classification

ACM Subject Classification
  • Applied computing → Computational genomics
  • Computing methodologies → Combinatorial algorithms
Keywords
  • Intra-tumor heterogeneity
  • tumor evolution
  • multi-labeled tree
  • tree edit distance
  • dynamic programming

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