Plasma DNA as a “liquid biopsy” incompletely complements tumor biopsy for identification of mutations in a case series of four patients with oligometastatic breast cancer

• Published in: Breast cancer research and treatment 2020-08, Vol.182 (3), p.665-677
• Main Authors: Chamberlin, Mary D., Wells, Jason D., Shee, Kevin, Bean, Jennifer R., Marotti, Jonathan D., Wells, Wendy A., Trask, Heidi W., Kolling, Fred W., Bhatt, Ananta, Kaufman, Peter A., Schwartz, Gary N., Gemery, John M., McNulty, Nancy J., Tsapakos, Michael J., Barth, Richard J., Arrick, Bradley A., Gui, Jiang, Miller, Todd W.
• Format: Article
• Language: English
• Subjects: Biomarkers, Tumor - blood; Biomarkers, Tumor - genetics; Biopsy; Breast cancer; Breast Neoplasms - blood; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Buffy coat; Cancer research; Circulating Tumor DNA - blood; Circulating Tumor DNA - genetics; Clinical Trial; Deoxyribonucleic acid; DNA; DNA fingerprinting; DNA sequencing; DNA, Neoplasm - blood; DNA, Neoplasm - genetics; Exons; Female; High-Throughput Nucleotide Sequencing; Humans; Liquid Biopsy - methods; Medicine; Medicine & Public Health; Metastasis; Mutation; Neoplasm Metastasis; Oncology; Patients; Plasma; Precision medicine; Prognosis; Tumors
• ISSN: 0167-6806; 1573-7217
• DOI: 10.1007/s10549-020-05714-2

Purpose Circulating tumor DNA in plasma may present a minimally invasive opportunity to identify tumor-derived mutations to inform selection of targeted therapies for individual patients, particularly in cases of oligometastatic disease where biopsy of multiple tumors is impractical. To assess the utility of plasma DNA as a “liquid biopsy” for precision oncology, we tested whether sequencing of plasma DNA is a reliable surrogate for sequencing of tumor DNA to identify targetable genetic alterations. Methods Blood and biopsies of 1–3 tumors were obtained from 4 evaluable patients with advanced breast cancer. One patient provided samples from an additional 7 tumors post-mortem. DNA extracted from plasma, tumor tissues, and buffy coat of blood were used for probe-directed capture of all exons in 149 cancer-related genes and massively parallel sequencing. Somatic mutations in DNA from plasma and tumors were identified by comparison to buffy coat DNA. Results Sequencing of plasma DNA identified 27.94 ± 11.81% (mean ± SD) of mutations detected in a tumor(s) from the same patient; such mutations tended to be present at high allelic frequency. The majority of mutations found in plasma DNA were not found in tumor samples. Mutations were also found in plasma that matched clinically undetectable tumors found post-mortem. Conclusions The incomplete overlap of genetic alteration profiles of plasma and tumors warrants caution in the sole reliance of plasma DNA to identify therapeutically targetable alterations in patients and indicates that analysis of plasma DNA complements, but does not replace, tumor DNA profiling. Trial Registration : Subjects were prospectively enrolled in trial NCT01836640 (registered April 22, 2013).