Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era

Abstract

Summary: The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies. During and after the project, several sequencing technologies continue to dominate nucleic acid sequencing markets. Currently, Illumina (short-read), PacBio (long-read), and Oxford Nanopore (long-read) are the most popular sequencing technologies. Unlike PacBio or the popular short-read sequencers before it, which, as examples of the second or so-called Next-Generation Sequencing platforms, need to synthesize when sequencing, nanopore technology directly sequences native DNA and RNA molecules. Nanopore sequencing, therefore, avoids converting mRNA into cDNA molecules, which not only allows for the sequencing of extremely long native DNA and full-length RNA molecules but also document modifications that have been made to those native DNA or RNA bases. In this review on direct DNA sequencing and direct RNA sequencing using Oxford Nanopore technology, we focus on their development and application achievements, discussing their challenges and future perspective. We also address the problems researchers may encounter applying these approaches in their research topics, and how to resolve them. Public summary: • Nanopore-seq can dissect native DNA/RNA molecules from any organisms at unlimited length • A wide variety of algorithms greatly increase the accuracy of signal decoding in Nanopore-Seq • Nanopore-Seq significantly facilitates genome assembly and structural variant calling, and can simultaneously detect base modifications • These advantages ensure its great potentials in future medical and agricultural practices

Keywords

• nanopore sequencing
• direct DNA sequencing
• direct RNA sequencing
• base modification
• base-calling
• long-read sequencing