Abstract

Variant affecting more than 50 nucleotides, or structural variants, can have important functional impacts. They are unfortunately understudied because of technical challenges hindering their detection. I will present two approaches to integrate those variants in genomic studies. The first uses pangenomes as augmented reference genome containing common variants (including structural variants). With this more complete reference, like the one produced by the Human Pangenome Reference Consortium, short sequencing reads are better analyzed, resulting in a larger number of structural variants that can finally be genotyped accurately and could be considered in large association studies. The second approach uses cost-efficient long read sequencing technology, such as Oxford Nanopore, to infer phased variants at unprecedented resolution. This protocol is currently being tested to help diagnose rare disease patients in diagnostic impasse.