I am continuing to watch the London Calling 2023 on-demand lightning talks. Tonight, I watched the session “Discovering the missing variation: a long-read sequencing study into the structural variation in two dairy breeds” by Tuan Viet Nguyen, a research scientist from Agriculture Victoria in Australia. They spoke about structural variants, defined as genomic variants larger than 50 bps, such as deletions, duplications, and inversions. Structural variants are largely unexplored in most animal genomes and responsible for Mendelian disorders and complex traits, according to Nguyen. Together with the University of Queensland in Australia, they started the Bovine Long Read Consortium, working with other groups to improve the health and productivity of these important animals. The team is implementing the VALOR pipeline based deployed with Nexflow: Variant discovery pipeline using Long Read sequencing. Forty individuals (20 Holstein and 20 Jersey) were sequenced with PromethION flow cells 9.4 and 10.4 with various coverages. At the breed level, they found SVs that are unique. Long SVs also tend to be rare, likely due to their harmful consequences. The study has detected known variants and new ones. The data generated by this group, along with the workflow, will help other groups from the consortium.
