Critical assessment of nanopore sequencing for the detection of multiple forms of DNA modifications.

ABSTRACT: While nanopore sequencing is increasingly used for mapping DNA modifications, it is important to recognize false positive calls as they can mislead biological interpretations. To assist biologists and methods developers, we describe a framework for rigorous evaluation that highlights the use of false discovery rate with rationally designed negative controls capturing both general background and confounding modifications. Our critical assessment across multiple forms of DNA modifications highlights that while nanopore sequencing performs reliably for high-abundance modifications, including 5-methylcytosine (5mC) at CpG sites in mammalian cells and 5-hydroxymethylcytosine (5hmC) in mammalian brain cells, it makes a significant proportion of false positive detections for low-abundance modific

SUBMITTER: Kong Y 

PROVIDER: S-EPMC11601653 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature