eng
Schloss Dagstuhl – Leibniz-Zentrum für Informatik
Leibniz International Proceedings in Informatics
1868-8969
2018-08-02
22:1
22:19
10.4230/LIPIcs.WABI.2018.22
article
A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression
Karpov, Nikolai
1
Malikic, Salem
2
Rahman, Md. Khaledur
1
Sahinalp, S. Cenk
1
Department of Computer Science, Indiana University, Bloomington, IN, USA
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
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.
https://drops.dagstuhl.de/storage/00lipics/lipics-vol113-wabi2018/LIPIcs.WABI.2018.22/LIPIcs.WABI.2018.22.pdf
Intra-tumor heterogeneity
tumor evolution
multi-labeled tree
tree edit distance
dynamic programming