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arXiv · 1412.8574

Fast and Scalable Inference of Multi-Sample Cancer Lineages

Victoria Popic·Raheleh Salari·Iman Hajirasouliha·Dorna Kashef-Haghighi·Robert B. West·Serafim Batzoglou
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Abstract

Somatic variants can be used as lineage markers for the phylogenetic reconstruction of cancer evolution. Since somatic phylogenetics is complicated by sample heterogeneity, novel specialized tree-building methods are required for cancer phylogeny reconstruction. We present LICHeE (Lineage Inference for Cancer Heterogeneity and Evolution), a novel method that automates the phylogenetic inference of cancer progression from multiple somatic samples. LICHeE uses variant allele frequencies of SSNVs obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open-sourced and available at http://viq854.github.io/lichee.

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Victoria Popic, Raheleh Salari, Iman Hajirasouliha, Dorna Kashef-Haghighi, Robert B. West, Serafim Batzoglou. 2014-12-30. Fast and Scalable Inference of Multi-Sample Cancer Lineages. https://arxiv.org/abs/1412.8574

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