Journal Article

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

McPherson, John D., Ettayebi, Ilias, Chow, Signy, O’Brien, Catherine, Chen, Zhuo, Kis, Olena, Mansour, Mark, Zuzarte, Philip C., Pugh, Trevor J., Gallinger, Steven, Minden, Mark D., Roehrl, Michael H. A., Borgida, Ayelet, Murphy, Tracy, Bratman, Scott V., Zhao, Zhen, Wang, Ting Ting, De Carvalho, Daniel D., Spreafico, Anna, Fleshner, Neil, Li, Tiantian, Hung, Rayjean J., Hoffman, Michael M., Medina, Tiago da Silva, Wang, Yadon, Roulois, David, Shen, Shu Yi, Singhania, Rajat, Arruda, Andrea, Liu, Jessica, Bedard, Philippe L., Liu, Geoffrey, Fehringer, Gordon, Chakravarthy, Ankur, Leighl, Natasha, Chadwick, Dianne, O’Kane, Grainne M., Goldenberg, Anna

2018

Overview

The use of liquid biopsies for cancer detection and management is rapidly gaining prominence 1 . Current methods for the detection of circulating tumour DNA involve sequencing somatic mutations using cell-free DNA, but the sensitivity of these methods may be low among patients with early-stage cancer given the limited number of recurrent mutations 2 – 5 . By contrast, large-scale epigenetic alterations—which are tissue- and cancer-type specific—are not similarly constrained 6 and therefore potentially have greater ability to detect and classify cancers in patients with early-stage disease. Here we develop a sensitive, immunoprecipitation-based protocol to analyse the methylome of small quantities of circulating cell-free DNA, and demonstrate the ability to detect large-scale DNA methylation changes that are enriched for tumour-specific patterns. We also demonstrate robust performance in cancer detection and classification across an extensive collection of plasma samples from several tumour types. This work sets the stage to establish biomarkers for the minimally invasive detection, interception and classification of early-stage cancers based on plasma cell-free DNA methylation patterns. An immunoprecipitation-based protocol is developed to analyse DNA methylation in small quantities of circulating cell-free DNA, and can detect and classify cancers in plasma samples from several tumour types.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 45/23 / 631/1647/2210/2213 / 631/67/69 / Adenocarcinoma - blood / Adenocarcinoma - genetics / Animals / Biochemistry, Molecular Biology / Bioinformatics / Biological markers / Biomarkers / Biomarkers, Tumor - genetics / Cancer / Cancer diagnosis / Cell Line, Tumor / Cell-Free Nucleic Acids - blood / Cell-Free Nucleic Acids - metabolism / Change detection / Classification / Colorectal Neoplasms - blood / Colorectal Neoplasms - genetics / Deoxyribonucleic acid / DNA / DNA Methylation / DNA Mutational Analysis / DNA sequencing / DNA, Neoplasm - blood / DNA, Neoplasm - metabolism / Early Detection of Cancer - methods / Epigenesis, Genetic / Epigenetic inheritance / Epigenetics / Female / Generalized linear models / Genetic aspects / Genetic research / Genomes / Genomics / Heterografts / Humanities and Social Sciences / Humans / Identification and classification / Immunoprecipitation / Interception / Letter / Life Sciences / Liquid Biopsy / Male / Medical screening / Methods / Methylation / Mice / Mice, Inbred NOD / Mice, SCID / multidisciplinary / Multiple myeloma / Mutation / Neoplasm Transplantation / Neoplasms - blood / Neoplasms - classification / Neoplasms - genetics / Organ Specificity / Pancreatic cancer / Pancreatic Neoplasms - blood / Pancreatic Neoplasms - genetics / Patients / Science / Science (multidisciplinary) / Testing / Tumors