Single Duplex DNA Sequencing with CODEC Detects Mutations with High Sensitivity

Detecting mutations from single DNA molecules is crucial in many fields but challenging. Next generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules (single duplexes) to discern the true mutations on both strands. Here, we present Concatenating Original Duplex for Error Correction (CODEC) which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than Duplex Sequencing. CODEC revealed mutation frequencies of 2.72 x 10-8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability (MSI) with 10-fold greater sensitivity, and mutational signatures and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations which are commonly obscured by NGS errors. We applied CODEC to clinical colon and breast neoplasm samples and uncovered expected mutational signatures including homologous recombination deficiency (HRD) and MSI. ]]>
The breast cancer patients were selected based on patient's HRD status and ages. The colon cancer patient was selected based on MSI status. Both breast cancer and colon cancer samples were obtained by Dana-Farber Cancer Institute. The sperm sample was selected based on the availability and patient's age. The sperm sample was obtained as part of an IRB-approved human subjects protocol at New York University Grossman School of Medicine. The IRB of the Dana-Farber Cancer Institute and New York University Grossman School of Medicine approved these protocols. This research was conducted in accordance with the provisions of the Declaration of Helsinki and the US Common Rule. ]]>