@article{b73e38dcfa6e496eb449cb71ca65c452,
title = "Fast and scalable inference of multi-sample cancer lineages.",
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 somatic single nucleotide variants obtained by deep sequencing to reconstruct multi-sample cell lineage trees and infer the subclonal composition of the samples. LICHeE is open source and available at http://viq854.github.io/lichee .",
author = "Victoria Popic and Raheleh Salari and Iman Hajirasouliha and Dorna Kashef-Haghighi and West, {Robert B} and Serafim Batzoglou",
note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: Authors would like to thank Arend Sidow for valuable discussions and Aaron C. Abajian for contributing to the simulation studies. VP was supported by the Stanford-KAUST grant. RS and IH were also supported by Natural Sciences and Engineering Research Council of Canada (NSERC) Postdoctoral Fellowships. DK was supported by an STMicroelectronics Stanford Graduate Fellowship. This work was funded by a grant from KAUST to SB. This publication acknowledges KAUST support, but has no KAUST affiliated authors.",
year = "2015",
month = may,
day = "6",
doi = "10.1186/s13059-015-0647-8",
language = "English (US)",
volume = "16",
journal = "Genome Biology",
issn = "1465-6906",
publisher = "Springer Verlag",
number = "1",
}
