Abstract
The sequencing of cancer genomes may enable tailoring of therapeutics to the underlying biological abnormalities driving a particular patient's tumor. However, sequencing-based strategies rely heavily on representative sampling of tumors. To understand the subclonal structure of primary breast cancer, we applied whole-genome and targeted sequencing to multiple samples from each of 50 patients' tumors (303 samples in total). The extent of subclonal diversification varied among cases and followed spatial patterns. No strict temporal order was evident, with point mutations and rearrangements affecting the most common breast cancer genes, including PIK3CA, TP53, PTEN, BRCA2 and MYC, occurring early in some tumors and late in others. In 13 out of 50 cancers, potentially targetable mutations were subclonal. Landmarks of disease progression, such as resistance to chemotherapy and the acquisition of invasive or metastatic potential, arose within detectable subclones of antecedent lesions. These findings highlight the importance of including analyses of subclonal structure and tumor evolution in clinical trials of primary breast cancer.
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Acknowledgements
This work is supported by the Wellcome Trust. P.J.C. is a Wellcome Trust Senior Clinical Fellow (103858/Z/14/Z). L.R.Y., Y.L. and L.B.A. are funded by Wellcome Trust PhD fellowships. S.N.-Z. is funded by a Wellcome Trust Intermediate Clinical Research Fellowship (WT100183MA). P.V.L. is a postdoctoral researcher at the Research Foundation Flanders (FWO). Work within the project is supported by the Belgian Cancer Plan–Ministry of Health, the Breast Cancer Research Foundation, the Brussels Region, the Norwegian Cancer Society, the Norwegian Health Region West and the Bergen Research Foundation. Some samples referenced in this publication will be included in the Breast Cancer Genome Analyses for the International Cancer Genome Consortium (ICGC) Working Group led by the Wellcome Trust Sanger Institute. BASIS is a part of the ICGC working group and is funded by the European Community's Seventh Framework Programme (FP7/2010-2014) under grant agreement number 242006. This working group also encompasses a triple-negative breast cancer project funded by the Wellcome Trust (grant 077012/Z/05/Z) and a HER2+ breast cancer project funded by Institut National du Cancer (INCa). We thank B. Leirvaag, D. Ekse, N.K. Duong and C. Eriksen for technical assistance. Research performed at Los Alamos National Laboratory was carried out under the auspices of the National Nuclear Security Administration of the US Department of Energy.
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Contributions
L.R.Y. and P.J.C. designed and directed the study and prepared the manuscript. L.R.Y. and M.G. performed analyses and prepared figures. S.K., T.A. and P.E.L. contributed to the study design and sample preparation for cohort 1. C.D., C.S., M.I. and M.M. contributed to the study design and sample preparation for cohort 2. D.C.W., P.V.L., G.G., H.D., Y.S.J., S. McLaren, M.R., S.N.-Z., A.B., D.G., A.M., K.R., J.H., D.J., M.R.S., Y.L. and L.B.A. contributed to analysis. S. Martin managed samples. A.L.R., D.L., H.K.H. and P.K.L. conducted histopathological assessment. P.-Y.A., D.V., B.J., A.G.-C. and A.F. performed DNA extraction. L.J.M. contributed to library preparation, PCR and gel electrophoresis.
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P.J.C. and M.R.S. are founders, stock holders and consultants for 14M Genomics Ltd, a genomics diagnostic company.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–6, Supplementary Note (PDF 7718 kb)
Supplementary Source Code
R code for mutation clustering (ZIP 3 kb)
Supplementary Table 1
Patient and sample characteristics (XLS 144 kb)
Supplementary Table 2
Sequencing coverage (XLS 91 kb)
Supplementary Table 3
Annotation of potential driver genes (XLS 59 kb)
Supplementary Table 4
Validation data (XLS 201 kb)
Supplementary Table 5
Mutation clusters. (XLS 145 kb)
Supplementary Table 6
Heterogeneity scores. (XLS 72 kb)
Supplementary Table 7
Mutation and copy number calls from capture data. (XLS 131 kb)
Supplementary Table 8
Coding mutations and oncogenic copy number events from whole genome data (XLS 199 kb)
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Yates, L., Gerstung, M., Knappskog, S. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat Med 21, 751–759 (2015). https://doi.org/10.1038/nm.3886
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DOI: https://doi.org/10.1038/nm.3886
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