Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays
About Eilis Hannon
Eilis Hannon is a Senior Research Fellow in the Complex Disease Epigenetics Group at the University of Exeter Medical School. She studied Mathematics as an undergraduate and holds a Ph.D. in Bioinformatics. Her research focuses on integrating multiple layers of genomic data from a range of technologies to model the dynamic nature of gene expression and epigenetic variation, and explore how this mediates genetic risk for complex diseases.
Third-generation sequencing technologies, such as nanopore sequencing, have the potential to revolutionise the generation of epigenetic data by providing genuine genome-wide coverage. Here, we assess the viability of nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available. To attempt to rediscover genomic positions known to be differentially methylated in tobacco smokers, we implemented a CRISPR/Cas9 targeted sequencing approach, followed by nanopore sequencing. In summary, we detected smoking-associated hypomethylation at multiple sites, including within the AHRR gene, highlighting the viability of nanopore sequencing in epigenetic epidemiology.