NCM 2022: Finding the needle — haplotype-resolved discovery and annotation of clinically relevant genetic and epigenetic variants using whole-genome nanopore sequencing

With the recent completion of the human genome from telomere to telomere, the possibility to leverage genetic information to aid in the understanding of the biology of disease is ever increasing. As whole-genome sequencing is becoming a commonplace method for interrogating the genetic component of disease, the ability to easily generate information-rich data encompassing a wide range of genetic and epigenetic variations is required. Here, we show how a single nanopore dataset enables the haplotype-specific identification of phased genetic and epigenetic variants and how they can be linked to disease phenotype in a disease-agnostic manner. Furthermore, we demonstrate how some of these methods may be utilised in the oncology research space through the sequencing and analysis of varied solid tumour/normal pairs as well as cell-free DNA.