The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data.

BMC Bioinformatics
Giulio CaravagnaAndrea Sottoriva

Abstract

The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories. In a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution. We present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly...Continue Reading

References

May 23, 2012·Cell·Serena Nik-ZainalUNKNOWN Breast Cancer Working Group of the International Cancer Genome Consortium
Jul 3, 2013·Proceedings of the National Academy of Sciences of the United States of America·David A Kessler, Herbert Levine
Feb 11, 2015·Nature Genetics·Andrea SottorivaChristina Curtis
Jan 19, 2016·Nature Genetics·Marc J WilliamsAndrea Sottoriva
Jul 1, 2016·Proceedings of the National Academy of Sciences of the United States of America·Giulio CaravagnaBud Mishra
Apr 27, 2017·The New England Journal of Medicine·Mariam Jamal-HanjaniUNKNOWN TRACERx Consortium
Oct 24, 2017·Cell·Iñigo MartincorenaPeter J Campbell
Apr 17, 2018·Cell·Samra TurajlicUNKNOWN TRACERx Renal Consortium
Apr 17, 2018·Cell·Samra TurajlicUNKNOWN TRACERx Renal Consortium
May 29, 2018·Nature Genetics·Marc J WilliamsTrevor A Graham
Sep 2, 2018·Nature Methods·Giulio CaravagnaAndrea Sottoriva
Nov 20, 2018·Annals of Oncology : Official Journal of the European Society for Medical Oncology·I SpiteriA Sottoriva
Mar 29, 2019·Nature Reviews. Genetics·Samra TurajlicCharles Swanton
Sep 4, 2020·Nature Genetics·Giulio CaravagnaAndrea Sottoriva

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Citations

Jul 10, 2021·Signal Transduction and Targeted Therapy·Ruixue Huang, Ping-Kun Zhou
Sep 10, 2021·Frontiers in Physiology·Thomas Stiehl, Anna Marciniak-Czochra

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Methods Mentioned

BETA
biopsies
biopsy

Software Mentioned

fit
dndscv
mobster
R package
R
TEMULATOR
ctree R

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