Tonight I watched the session by Alyssa Barry from Deakin University in Australia. They presented on “Targeted nanopore sequencing using hybridisation probes reveals immune escape polymorphisms in malaria vaccine candidates.” Barry mentioned this work was done by a Ph.D. student in their lab. Barry spoke about malaria vaccines and the challenges with immune escape. The researchers wanted to study a longitudinal cohort. For the sequencing, they used a probe-based system with 239 probes to capture and sequence. The workflow included random whole genome amplification, hybridization, and sequencing. A custom pipeline called SNIPER was developed for single nucleotide variant calling. The workflow was benchmarked and used to define immune escape polymorphisms. The novel Nanopore sequencing assay sequences 38 malaria vaccine antigen genes in parallel, and the SNIPER workflow provides accurate variant calling. This approach is unique and powerful.
