It takes two — haplotype-specific identification of genetic and epigenetic variation using nanopore sequencing

Event overview

Knowledge Exchanges provide the perfect opportunity to hear some of the very latest developments in nanopore sequencing from members of the Oxford Nanopore team.

In this Knowledge Exchange, Philipp Rescheneder shares how the long-read capabilities of nanopore sequencing can be used to accurately identify genetic and epigenetic variation in a single dataset and illustrate the importance of assigning variants to the correct haplotype through phasing. He also shows how Oxford Nanopore’s adaptive sampling enables genome-wide characterisation of methylation patterns across samples of interest in a cost-effective way as well as how to use data from Oxford Nanopore’s chromosome conformation capture protocol (Pore-C) to achieve parent-of-origin inference without the need for trio-sequencing. Finally, Philipp shows how nanopore sequencing can improve the understanding of tumour development by enabling haplotype-specific copy number variation and DNA methylation profiling in heterogeneous tumours.

Meet the speaker

Philipp Rescheneder works as a bioinformatician in the Applications team at Oxford Nanopore. In his current role he identifies, benchmarks and adapts the most appropriate tools and workflows for analysing Oxford Nanopore data in the context of a wide range of applications, including variant calling, assembly, and methylation calling. Before joining Oxford Nanopore, his research focused on developing computational tools for efficiently aligning noisy long and short next-generation sequencing reads.

Authors: Philipp Rescheneder