Ensilication preserves high-molecular weight native DNA for clinical long-read sequencing

Abstract

Background: Native long-read DNA sequencing simultaneously captures genetic variants and epigenetic modifications from single molecules, but preserving molecular length and base modifications currently depends on cold-chain infrastructure that limits access to well-resourced settings.

Results: We demonstrate that ensilication, the encapsulation of DNA within silica matrices, preserves DNA at ambient temperature for 30 days with sequencing performance equivalent to conventional - 80 °C freezing. Across three Genome-in-a-Bottle reference genomes, ensilicated and frozen samples show no significant differences in read length (N50 ~ 8,000-11,000 bp), variant-calling accuracy, or genome-wide CpG methylation. Single-read methylation calls benchmarked against an independent bisulfite-sequencing reference confirm that ensilication introduces no detectable bias, with per-read accuracy differing by less than 0.4% between preservation conditions. Ensilicated DNA tolerates repeated handling better than frozen samples and maintains fragment integrity under accelerated weathering. In two patients with rare genetic disorders, ambient-preserved DNA resolves a de novo variant in the segmentally duplicated GTF2I locus and detects methylation patterns consistent with KDM2A-related disorder.

Conclusions: Ensilication enables diagnostic-quality native long-read sequencing without cold-chain infrastructure, supporting ambient storage and transport while preserving both sequence and methylation information.