Targeted nanopore sequencing of myopathy gene panel in L158
Readfish59 (v0.0.10dev2) was used for live target selection or rejection utilising a custom panel of 331 loci associated with genetic myopathies (Supplementary Data 1 in the associated publication). These loci were chosen based on a literature review performed in January 2023, focusing on genetic myopathic disorders. This was supplemented by review of existing myopathy gene panels in PanelApp Australia60 ('green' and 'amber' genes) and external diagnostic genomic laboratories (Supplementary Data 2 in the associated publication) - genes and loci that were not thought to produce a predominant myopathy were excluded from our custom panel. The ABCD3 locus was added to the panel during the course of this study, such that it was sequenced in 26 out of the 53 proband samples. Gene targets were encoded relative to the T2T-chm13 (v2) reference genome and ReadFish was executed with the following configurations: config_name = 'dna_r10.4.1_e8.2_400bps_5khz_fast_prom'; min_chunks = 0; max_chunks = 16; single_on = 'stop_receiving'; multi_on = 'stop_receiving'; single_off = 'unblock'; multi_off = 'unblock'; no_seq = 'proceed'; no_map = 'proceed'. Libraries were run for 72 hours, with nuclease flushes and library reloading performed at approximately 24-hour and 48-hour time points.