High-intensity sequencing reveals the sources of plasma circulating cell-free DNA variants

• Published in: Nature medicine Vol. 25; no. 12; pp. 1928 - 1937
• Main Authors: Razavi, Pedram, Li, Bob T., Brown, David N., Jung, Byoungsok, Hubbell, Earl, Shen, Ronglai, Abida, Wassim, Juluru, Krishna, De Bruijn, Ino, Hou, Chenlu, Venn, Oliver, Lim, Raymond, Anand, Aseem, Maddala, Tara, Gnerre, Sante, Vijaya Satya, Ravi, Liu, Qinwen, Shen, Ling, Eattock, Nicholas, Yue, Jeanne, Blocker, Alexander W., Lee, Mark, Sehnert, Amy, Xu, Hui, Hall, Megan P., Santiago-Zayas, Angie, Novotny, William F., Isbell, James M., Rusch, Valerie W., Plitas, George, Heerdt, Alexandra S., Ladanyi, Marc, Hyman, David M., Jones, David R., Morrow, Monica, Riely, Gregory J., Scher, Howard I., Rudin, Charles M., Robson, Mark E., Diaz, Luis A., Solit, David B., Aravanis, Alexander M., Reis-Filho, Jorge S.
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.12.2019; Nature Publishing Group
• Subjects: 631/114/2785; 631/1647/514; 631/61/514/2254; 631/67/69; 692/699/67/1857; Adult; Biomarkers, Tumor - blood; Biomedical and Life Sciences; Biomedicine; Blood plasma; Cancer; Cancer Research; Cell-Free Nucleic Acids - blood; Circulating Tumor DNA - blood; Circulating Tumor DNA - genetics; Deoxyribonucleic acid; DNA; DNA Mutational Analysis; DNA sequencing; DNA, Neoplasm - blood; Female; Gene Expression Regulation, Neoplastic; Genetic aspects; Genetic research; Genetic variation; Genomics; Hematopoiesis; High-Throughput Nucleotide Sequencing; Humans; Infectious Diseases; Leukocytes; Male; Metabolic Diseases; Metastases; Methods; Microsatellite Instability; Middle Aged; Molecular Medicine; Mutation; Neoplasms - blood; Neoplasms - genetics; Neoplasms - pathology; Neurosciences; Nucleotide sequencing; Observations; Physiological aspects; Somatic cells; Tumors; United States
• ISSN: 1078-8956; 1546-170X
• DOI: 10.1038/s41591-019-0652-7

Accurate identification of tumor-derived somatic variants in plasma circulating cell-free DNA (cfDNA) requires understanding of the various biological compartments contributing to the cfDNA pool. We sought to define the technical feasibility of a high-intensity sequencing assay of cfDNA and matched white blood cell DNA covering a large genomic region (508 genes; 2 megabases; >60,000× raw depth) in a prospective study of 124 patients with metastatic cancer, with contemporaneous matched tumor tissue biopsies, and 47 controls without cancer. The assay displayed high sensitivity and specificity, allowing for de novo detection of tumor-derived mutations and inference of tumor mutational burden, microsatellite instability, mutational signatures and sources of somatic mutations identified in cfDNA. The vast majority of cfDNA mutations (81.6% in controls and 53.2% in patients with cancer) had features consistent with clonal hematopoiesis. This cfDNA sequencing approach revealed that clonal hematopoiesis constitutes a pervasive biological phenomenon, emphasizing the importance of matched cfDNA–white blood cell sequencing for accurate variant interpretation. Ultra-sensitive cell-free DNA (cfDNA) sequencing uncovers clonal hematopoiesis as a major source of somatic cfDNA variants in healthy individuals and patients with cancer, and underscores the importance of matched white blood cell DNA sequencing in liquid biopsy procedures.