Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing
Benchmarking ensilicated and frozen DNA preservation for Oxford Nanopore whole-genome sequencing using the Genome in a Bottle Ashkenazi trio (HG002, HG003, HG004). Matched genomic DNA from each sample was preserved by either conventional freezing at -80C or ensilication (silica-based anhydrous caching), then sequenced on PromethION 48 with R10.4.1 flow cells and SQK-LSK114 ligation library preparation. Two sequencing batches were performed, with additional replicate libraries for HG002 in batch 2. Data were used to compare read quality, small variant and structural variant calling accuracy against GIAB truth sets, Mendelian concordance across preservation conditions, and CpG methylation fidelity relative to EMseq.