Calling disease variants in human samples using automated EPI2ME end-to-end workflows

Abstract
Comprehensive genomic analysis requires methods that can fully resolve complex genetic variation, especially in challenging regions of the genome. This means calling all variant types (single nucleotide polymorphisms, small indels, structural variants/copy number variants, and repeat expansions) while also calling DNA modifications (5mC/5hmC) for fully phased, haplotype-resolved genetic and epigenetic changes. Here, in collaboration with Boston Children’s Hospital, we applied the automated EPI2ME wf-human-variation analysis workflow across 756 undiagnosed rare disease samples, using its full end-to-end capabilities for comprehensive variant detection. This integrated approach streamlined analysis and enabled resolution of previously unsolved complex disease-associated variants.

Biography
Rebecca Stubbs is a bioinformatician in Commercial Applications at Oxford Nanopore Technologies, where she applies computational approaches to complex genomic questions. Her work spans multiomic data analysis, complex variant resolution, and projects involving de novo assembly, methylation analysis, and transcriptomics. She completed a post doctorate at the University of Zurich and earned her PhD from the University of Florida, where she studied the evolutionary genomics of plants. After beginning her career in polyploid plants, she now finds working with diploid human genomes a delight.