The next Nanopore Community Meeting 2022 session I watched was a longer: 27 min. “Finding the needle: haplotype-resolved discovery and annotation of clinically relevant genetic and epigenetic variants using whole-genome nanopore sequencing” was presented by Sissel Juul and Phillipp Rescheneder, both from Oxford Nanopore Technologies. Juul described the work of their team to sequence genomes for rare diseases and cancer research. They described why whole-genome sequencing may help precise diagnosis and better clinical management in these cases. The team used “true genome” sets and sequenced with depth and best chemistry to accurately determine genetic variation. They also used pore-C and long reads to determine phasing. Juul explained that the detection of clinically relevant variants is the challenge, and therefore improvements to the workflow were necessary. Juul shared data from a couple of examples in which they counted repeats and phased into haplotypes. Rescheneder then spoke about sequencing twelve matched tumor-healthy pairs. The samples were three replicates per tissue: kidney, lung, codon, breast. They found unique differentially methylated promoters in colorectal cancer tissues. Rescheneder noted that there is now a kit 14 compatible with 5hmC calling. I am hoping to start using some of these kits and basecalling models.
