Introduction

Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .

Publications

  1. ReMixT: clone-specific genomic structure estimation in cancer.
    Cite this
    McPherson AW, Roth A, Ha G, Chauve C, Steif A, de Souza CPE, Eirew P, Bouchard-Côté A, Aparicio S, Sahinalp SC, Shah SP, 2017-07-01 - Genome biology

Credits

  1. Andrew W McPherson
    Developer

    Department of Pathology and Laboratory Medicine, University of British Columbia, Canada

  2. Andrew Roth
    Developer

    Ludwig Institute for Cancer Research, Oxford University, United Kingdom of Great Britain and Northern Ireland

  3. Gavin Ha
    Developer

    Eli and Edythe L. Broad Institute of MIT and Harvard, 415 Main Street, United States of America

  4. Cedric Chauve
    Developer

    Department of Mathematics, Simon Fraser University, Canada

  5. Adi Steif
    Developer

    Department of Molecular Oncology, BC Cancer Agency, Canada

  6. Camila P E de Souza
    Developer

    Department of Pathology and Laboratory Medicine, University of British Columbia, Canada

  7. Peter Eirew
    Developer

    Department of Molecular Oncology, BC Cancer Agency, Canada

  8. Alexandre Bouchard-Côté
    Developer

    Department of Statistics, University of British Columbia, Canada

  9. Sam Aparicio
    Developer

    Department of Pathology and Laboratory Medicine, University of British Columbia, Canada

  10. S Cenk Sahinalp
    Developer

    Department of Computer Science, Indiana University Bloomington, United States of America

  11. Sohrab P Shah
    Investigator

    Department of Pathology and Laboratory Medicine, University of British Columbia, Canada

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Summary
AccessionBT003625
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionCanada
Submitted BySohrab P Shah