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Circulating mutant DNA to assess tumor dynamics

Abstract

The measurement of circulating nucleic acids has transformed the management of chronic viral infections such as HIV. The development of analogous markers for individuals with cancer could similarly enhance the management of their disease. DNA containing somatic mutations is highly tumor specific and thus, in theory, can provide optimum markers. However, the number of circulating mutant gene fragments is small compared to the number of normal circulating DNA fragments, making it difficult to detect and quantify them with the sensitivity required for meaningful clinical use. In this study, we applied a highly sensitive approach to quantify circulating tumor DNA (ctDNA) in 162 plasma samples from 18 subjects undergoing multimodality therapy for colorectal cancer. We found that ctDNA measurements could be used to reliably monitor tumor dynamics in subjects with cancer who were undergoing surgery or chemotherapy. We suggest that this personalized genetic approach could be generally applied to individuals with other types of cancer (pages 914–915).

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Figure 1: Measurement of ctDNA.
Figure 2: Representative flow cytometric data obtained from BEAMing.
Figure 3: Recurrence-free survival, as detected by ctDNA and CEA.
Figure 4: Comparison of ctDNA, CEA and imaging dynamics in individual study subjects.

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Acknowledgements

We thank G.Traverso for useful discussions; D. Heslop, C. Vaughn and D. Edelstein for their help with plasma collection; and L. Fayad for help with the interpretation of imaging studies. This work was supported by the Virginia and D.K. Ludwig Fund for Cancer Research, the Miracle Foundation, the US National Colorectal Cancer Research Alliance and US National Institutes of Health grants CA43460, CA57345, CA62924 and CA129825.

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F.D., K.S. and M.L. optimized the BEAMing assay and performed these experiments. F.D., K.S., N.A. and S.A.S. performed tissue and plasma DNA purification and quantification. S.G. was responsible for statistical analysis. L.S. performed CEA measurements. M.A.C., K.R., K.T. and L.A.D., Jr. developed the clinical protocol and collected clinical samples. F.D., K.S., K.K., B.V. and L.A.D., Jr. developed the experimental plan and wrote the manuscript.

Corresponding authors

Correspondence to Bert Vogelstein or Luis A Diaz Jr.

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Competing interests

Under agreements between the Johns Hopkins University and Exact Sciences, Genzyme Molecular Oncology and Beckman Instruments, K.W.K. and B.V. are entitled to a share of the royalties received by the University on sales of products related to certain of the genes described in this paper. The University and these authors also own stock in Exact Sciences and Genzyme, which is subject to certain restrictions under University policy. K.W.K., B.V., F.D., K.S., M.L. and L.A.D., Jr. are listed as inventors on patent applications filed by the University that are relevant to the results described in this paper. The terms of these arrangements are being managed by the University in accordance with its conflict of interest policies.

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Supplementary Figs. 1–5, Supplementary Tables 1 and 2 and Supplementary Methods (PDF 1678 kb)

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Diehl, F., Schmidt, K., Choti, M. et al. Circulating mutant DNA to assess tumor dynamics. Nat Med 14, 985–990 (2008). https://doi.org/10.1038/nm.1789

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