Alexis Ferrasse, Rodrigo Mendez, John E. Gorzynski, Chloe M. Reuter, Jennefer N. Carter, Michael Blas, Undiagnosed Diseases Network, Alyssa A. Tran, Arjun Tarakad, Ashok Balasubramanyam, Brendan H. Lee, Carlos A. Bacino, Daryl A. Scott, Elaine Seto, Gary D. Clark, Hongzheng Dai, Hsiao-Tuan Chao, Ivan Chinn, James P. Orengo, Jill A. Rosenfeld, Kim Worley, Lindsay C. Burrage, Lisa T. Emrick, Lorraine Potocki, Monika Weisz Hubshman, Richard A. Lewis, Ronit Marom, Seema R. Lalani, Shamika Ketkar, Tiphanie P. Vogel, William J. Craigen, Jared Sninsky, Lauren Blieden, Sandesh Nagamani, Hugo J. Bellen, Michael F. Wangler, Oguz Kanca, Shinya Yamamoto, Christine M. Eng, Patricia A. Ward, Pengfei Liu, Adeline Vanderver, Cara Skraban, Edward Behrens, Gonench Kilich, Kathleen Sullivan, Kelly Hassey, Ramakrishnan Rajagopalan, Rebecca Ganetzky, Vishnu Cuddapah, Anna Raper, Daniel J. Rader, Giorgio Sirugo, Anne Slavotinek, Christopher Mayhew, Eneida Mendonca, Ziyuan Guo, Allyn McConkie-Rosell, Kelly Schoch, Mohamad Mikati, Nicole M. Walley, Rebecca C. Spillmann, Vandana Shashi, Alan H. Beggs, Calum A. MacRae, David A. Sweetser, Deepak A. Rao, Edwin K. Silverman, Elizabeth L. Fieg, Frances High, Gerard T. Berry, Ingrid A. Holm, J. Carl Pallais, Joan M. Stoler, Joseph Loscalzo, Lance H. Rodan, Laurel A. Cobban, Lauren C. Briere, Matthew Coggins, Melissa Walker, Richard L. Maas, Susan Korrick, Jessica Douglas, Cecilia Esteves, Emily Glanton, Isaac S. Kohane, Kimberly LeBlanc, Shamil R. Sunyaev, Shilpa N. Kobren, Brett H. Graham, Erin Conboy, Francesco Vetrini, Kayla M. Treat, Khurram Liaqat, Lili Mantcheva, Stephanie M. Ware, Kathleen Page, Paul Auwaerter, Yuka Manabe, Carlos A. Pardo-Villamizar
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.