Subclonal reconstruction from bulk tumor DNA sequencing has become a pillar of cancer evolution studies, providing insight into the clonality and relative ordering of mutations and mutational processes. We provide an outline of the complex computational approaches used for subclonal reconstruction from single and multiple tumor samples. We identify the underlying assumptions and uncertainties in each step and suggest best practices for analysis and quality assessment. This guide provides a pragmatic resource for the growing user community of subclonal reconstruction methods.
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A.S. was supported by an NSERC CGS. M.T. and P.V.L. are supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001202), the UK Medical Research Council (FC001202) and the Wellcome Trust (FC001202). M.T. is a postdoctoral fellow supported by the European Union’s Horizon 2020 research and innovation program (Marie Skłodowska-Curie grant agreement no. 747852-SIOMICS). P.V.L. is a Winton Group Leader in recognition of the Winton Charitable Foundation’s support towards the establishment of the Francis Crick Institute. M.N.L. was supported by a Junior Research Fellowship (Trinity College, University of Oxford). P.C.B. was supported by a Terry Fox Research Institute New Investigator Award and a CIHR New Investigator Award. Q.M. is supported by an Associate Investigator Award from the Ontario Institute of Cancer Research and holds a Canada CIFAR AI chair. This work was supported by the NIH/NCI under award numbers P30CA016042 (P.C.B.) and P30-CA008748 (Q.M.), and through support from the ITCR (1U24CA248265-01) to P.C.B.
P.C.B is a member of the Scientific Advisory Boards of BioSymetrics Inc. and Intersect Diagnostics Inc. M.T., A.S., A.G.D., M.N.L., J.W., D.C.W., Q.D.M., and P.V.L. declare no competing interests.
Peer review information Nature Methods thanks the anonymous reviewers for their contribution to the peer review of this work. Lin Tang was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
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Tarabichi, M., Salcedo, A., Deshwar, A.G. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat Methods 18, 144–155 (2021). https://doi.org/10.1038/s41592-020-01013-2
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