Brynja Sigurpalsdottir, a Research Associate at deCODE genetics in Iceland, spoke as part of the Oxford Nanopore Technologies webinar. The title of the session was “Large-scale methylation studies using nanopore sequencing.” deCODE is a subsidiary of Amgen. Sigurpalsdottir spoke about 5-mCpG methylation calling for ONT data. Initially, Nanopolish was one of the first algorithms trained on the expanded alphabet. Now, Guppy and Dorado provide base calling algorithms that are trained using an expanded alphabet. The deCODE dataset includes 7,179 whole blood samples sequenced on 8,906 PromethION R9.4 flow cells. All methylation was called using Nanopolish. Additionally, 304 samples (325 flow cells) were methylation-called using Guppy. Twenty-two samples were sequenced with R10.4. The team compared methylation with ONT and bisulfite sequencing. The team observed bimodal methylation distribution, more CpGs detected than in short-read sequencing with ONT, and a lack of methylation within transcription start sites (TSS). The results indicate that CpG methylation calling of ONT data is “highly consistent with oxBS.” Next, Sigurpalsdottir spoke about a recently published study in Nature that used long-range phasing to identify “methylation-depleted sequences” (MDS). Using a high-quality dataset of SNPs, they found that 41% of MDS were associated with a sequence variant. The team then used 896 RNA-sequenced samples to study the association of variants and expression. Sigurpalsdottir concluded that “the correlation between CpG methylation and gene expression is largely driven by sequence variants.” Future studies include epigenetic aging and how diseases affect aging of different cell types and organs and the application of methylation to solve clinical cases and identify clinical biomarkers.
