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

Abstract

Long-read DNA sequencing detects genetic variants and epigenetic modifications simultaneously, but optimal preservation of molecular length and base modifications typically requires cold-chain infrastructure. This infrastructure dependence restricts genomics to well-resourced laboratories and limits field research. We show that ensilication, the encapsulation of DNA within silica matrices, preserves DNA integrity at ambient temperature equivalent to -80 {degrees}C freezing. Using Genome-in-a-Bottle (GIAB) reference samples, we show that ensilicated DNA maintains sequencing performance comparable to frozen samples, while exhibiting resistance to degradation during repeated handling and accelerated weathering conditions simulating decades of ambient storage.. In real world samples from patients, native long-read sequencing of ensilicated samples resolved a de novo variant in the segmentally duplicated GTF2I locus in one case and detected methylation episignatures diagnostic of KDM2A-related disorder in another. Ensilication removes cold-chain dependence for diagnostic-quality long-read sequencing, expanding access to molecular diagnostics in resource-limited settings.