Compound-specific DNA adduct profiling with nanopore sequencing and IonStats

Covalently bound DNA adducts are mutation precursors that contribute to aging and diseases such as cancer. Accurate detection of adducts in the genome will shed light on tumorigenesis. Commonly used adduct detection methods, such as liquid chromatography-mass spectrometry, are unable to pinpoint exact genomic locations of adducts. Long-read nanopore sequencing is an approach with the potential to accurately detect multiple types of DNA adducts at single-nucleotide precision. In this study, we developed a novel statistical toolkit, IonStats, to profile DNA adducts in nanopore sequencing data. Using IonStats, we investigated the effects of four adduct-inducing genotoxic compounds (aristolochic acid II, cisplatin, melphalan, and mitomycin C) using nanopore sequencing. Compared to untreated controls, adducted samples exhibited both shared and compound-specific perturbations in base quality scores, ionic current profiles, and read interruptions. Our study shows that nanopore sequencing can be effectively employed to detect and characterize DNA adducts, paving the way for high-resolution, high-throughput profiling of DNA damage and the exposome.