Joy Goffena from the University of Washington presented at London Calling 2025. The title of the session was “Variant phasing for antisense oligonucleotide design using adaptive sampling.” Goffena explained antisense oligonucleotide (ASO) technology as short DNA or RNA that can bind target RNA to block translation or even modulate splicing. The goal of their work is to provide complete allele-specific phasing to guide ASO development with the use of long-read sequencing. Once a sample arrives, Goffena explained, DNA is isolated and checked. Samples can be saliva, blood, cells, or even gDNA. Depending on the sample type, storage, and other conditions, DNA extraction and yield vary. Each sample is run on a Qubit, NanoDrop, and the FemtoPulse. The research team uses a custom bam file and adaptive sampling. After library prep using the LSK114 and 1-3 ug of DNA, the libraries are sequenced using PromethION24 instruments. Samples are sequenced for a limited time to allow reusing of flow cell. Goffena described the pipeline they use for analysis. Goffena shared a couple of examples of results. In one example, phasing and strong haplotype separation was visible. In another example, the phasing was more challenging. The level of coverage of the target genes was sufficient for phasing. Goffena emphasized the importance of good QC and how this approach can be very powerful for the development of ASO therapies.
