I started watching a core webinar from Oxford Nanopore Technologies (ONT) tonight. Nick Sisneros from ONT facilitated the presentation. The topic was scalable human genomic characterization with nanopore. The first presentation was by Philipp Rescheneder, Senior Director of Applications Bioinformatics at ONT. They described three end-to-end workflows using EPI2ME: the human variation, cancer genomics, and single-cell transcriptomics workflows. Rescheneder described the importance of understanding haplotypes and epigenetic variation. Nanopore sequencing enables de novo identification of SNPs and indels potentially affecting disease. Rescheneder shared an example of variants that were phased. They noted that “long reads enable precise detection of structural variation.” Also, the detection of methylated and hydroxymethylated cytosines helps determine epigenetic variation. Once you have sequence data, Rescheneder explained, you can perform secondary analysis using EPI2ME workflows that are “open-source analysis pipelines packaged for ease of use.” The BAM files are used for the secondary analysis and then visualized in the Integrated Genome Browser (IGB). Rescheneder mentioned that telomere-to-telomere assembly with nanopore-only data can be achieved. The last part of this presentation was on cancer genomics. The examples included the use of cancer genomic workflows. For single-cell genomics, Rescheneder said you can obtain long-read full length transcript reads at the single-cell level. In the single-cell example, isoform-level expression in memory B cells was analyzed. Isoform switching was then determined between two clusters of cells. I learned some of the options available in these workflows that I had not considered.
