Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Benjamin J Raphael, Fabio Vandin

Abstract

Recent cancer sequencing studies provide a wealth of somatic mutation data from a large number of patients. One of the most intriguing and challenging questions arising from this data is to determine whether the temporal order of somatic mutations in a cancer follows any common progression. Since we usually obtain only one sample from a patient, such inferences are commonly made from cross-sectional data from different patients. This analysis is complicated by the extensive variation in the somatic mutations across different patients, variation that is reduced by examining combinations of mutations in various pathways. Thus far, methods to reconstruct tumor progression at the pathway level have restricted attention to known, a priori defined pathways. In this work we show how to simultaneously infer pathways and the temporal order of their mutations from cross-sectional data, leveraging on the exclusivity property of driver mutations within a pathway. We define the pathway linear progression model, and derive a combinatorial formulation for the problem of finding the optimal model from mutation data. We show that with enough samples the optimal solution to this problem uniquely identifies the correct model with high probability...Continue Reading

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Citations

Jan 27, 2016·BMC Systems Biology·Julia L FleckChristos G Cassandras
Jun 25, 2016·Seminars in Cell & Developmental Biology·Gajendra ShresthaAndrea H Bild
Feb 6, 2016·PLoS Computational Biology·Niko BeerenwinkelJens Lagergren
May 24, 2019·PLoS Computational Biology·Rebecca Sarto BassoFabio Vandin
Jun 30, 2019·Bioinformatics·Rudolf SchillRainer Spang
Oct 2, 2019·Molecular Omics·Julia L FleckChristos G Cassandras
Jul 1, 2017·Frontiers in Genetics·Fabio Vandin
Nov 12, 2019·PLoS Computational Biology·Sahand KhakabimamaghaniMartin Ester
Oct 10, 2020·PLoS Computational Biology·Mohammadreza Mohaghegh NeyshabouriJens Lagergren
Sep 17, 2021·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Wei ZhangYue Liu

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Software Mentioned

CPLEX
MutSigCV
mathop
MutSisCV
UPLPM
DeclareMathSizes

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