PT  - JOURNAL ARTICLE
AU  - Marcus Stoiber
AU  - Joshua Quick
AU  - Rob Egan
AU  - Ji Eun Lee
AU  - Susan Celniker
AU  - Robert K. Neely
AU  - Nicholas Loman
AU  - Len A Pennacchio
AU  - James Brown
TI  - <em>De novo</em> Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing
AID  - 10.1101/094672
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 094672
4099  - http://biorxiv.org/content/early/2016/12/15/094672.short
4100  - http://biorxiv.org/content/early/2016/12/15/094672.full
AB  - Advances in single molecule sequencing technology have enabled the investigation of the full catalogue of covalent DNA modifications. We present an assay, Modified DNA sequencing (MoD-seq), that leverages raw nanopore data processing, visualization and statistical testing to directly survey DNA modifications without the need for a large prior training dataset. We present case studies applying MoD-seq to identify three distinct marks, 4mC, 5mC, and 6mA, and demonstrate quantitative reproducibility across biological replicates processed in different labs. In a ground-truth dataset created via in vitro treatment of synthetic DNA with selected methylases, we show that modifications can be detected in a variety of distinct sequence contexts. We recapitulated known methylation patterns and frequencies in E. coli, and propose a pipeline for the comprehensive discovery of DNA modifications in a genome without a priori knowledge of their chemical identities.