Introduction

MOTIVATION: Cancer cell genomes acquire several genetic alterations during somatic evolution from a normal cell type. The relative order in which these mutations accumulate and contribute to cell fitness is affected by epistatic interactions. Inferring their evolutionary history is challenging because of the large number of mutations acquired by cancer cells as well as the presence of unknown epistatic interactions. RESULTS: We developed Bayesian Mutation Landscape (BML), a probabilistic approach for reconstructing ancestral genotypes from tumor samples for much larger sets of genes than previously feasible. BML infers the likely sequence of mutation accumulation for any set of genes that is recurrently mutated in tumor samples. When applied to tumor samples from colorectal, glioblastoma, lung and ovarian cancer patients, BML identifies the diverse evolutionary scenarios involved in tumor initiation and progression in greater detail, but broadly in agreement with prior results. AVAILABILITY AND IMPLEMENTATION: Source code and all datasets are freely available at bml.molgen.mpg.de. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Publications

  1. Inferring the paths of somatic evolution in cancer.
    Cite this
    Misra N, Szczurek E, Vingron M, 2014-09-01 - Bioinformatics (Oxford, England)

Credits

  1. Navodit Misra
    Developer

    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Germany

  2. Ewa Szczurek
    Developer

    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Germany

  3. Martin Vingron
    Investigator

    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Germany

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000070
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionSwitzerland
Submitted ByMartin Vingron