Comprehensive analyses of cancer genomes promise to inform prognoses and precise cancer treatments. A major barrier, however, is inaccessibility of metastatic tissue. A potential solution is to characterize circulating tumor cells (CTCs), but this requires overcoming the challenges of isolating rare cells and sequencing low-input material. Here we report an integrated process to isolate, qualify and sequence whole exomes of CTCs with high fidelity using a census-based sequencing strategy. Power calculations suggest that mapping of >99.995% of the standard exome is possible in CTCs. We validated our process in two patients with prostate cancer, including one for whom we sequenced CTCs, a lymph node metastasis and nine cores of the primary tumor. Fifty-one of 73 CTC mutations (70%) were present in matched tissue. Moreover, we identified 10 early trunk and 56 metastatic trunk mutations in the non-CTC tumor samples and found 90% and 73% of these mutations, respectively, in CTC exomes. This study establishes a foundation for CTC genomics in the clinic.
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J.G.L. was supported by a Conquer Cancer Foundation Young Investigator Award, US National Institutes of Health grant 5P50CA100707-10 (DF/HCC SPORE) and the Wong Family Award. V.A.A. was supported in part by a graduate fellowship from the National Science Foundation. A.D.C. is supported by the Prostate Cancer Foundation Young Investigator Award and the Department of Defense Physician Scientist Training Award. J.C.L. is a Camille Dreyfus Teacher-Scholar. We acknowledge the Arthur and Linda Gelb Center for Translational Research for the acquisition and annotation of clinical samples and A. Abbott and A. Van Den Abbeele from the Dana-Farber Cancer Institute (DFCI) Department of Imaging for positron-emission tomography (PET) images. We also acknowledge P.K. Brastianos (Department of Medical Oncology, DFCI) and I. Dunn (Department of Neurosurgery, Brigham and Women's Hospital) for contributing samples for CTC analysis, D. Peck for help with technology development, O. Voznesensky and S. Balk for purification of DNA from the metastatic tumor for sequencing, C. Whittaker and S.S. Levine for advice on sequencing and analysis and the Broad Genomics Platform for the development of new sequencing approaches used here. This work was also supported in part by the Koch Institute Support (core) grant P30-CA14051 from the National Cancer Institute, and we thank the Koch Institute Swanson Biotechnology Center for technical support, specifically the BioMicroCenter. This work was also supported in part by Janssen Pharmaceuticals, Inc. and the Klarman Family Foundation. We would like to thank Illumina for providing the MagSweeper. The authors dedicate this paper to the memory of Officer Sean Collier, for his caring service to the MIT community and for his sacrifice.
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TrAC Trends in Analytical Chemistry (2019)