Identifying Damage Pathways Linking Sequence Composition to Storage Failure in DNA Data Storage via High-Dimensional Mediation Analysis

Abstract: DNA data storage offers extraordinary information density and long-term durability, but its reliability is limited by sequence-dependent errors introduced during synthesis and accumulated during storage. It remains unclear how sequence composition is associated with storage failure through specific molecular damage components. We develop a high-dimensional semiparametric mediation framework for survival outcomes. GC content is treated as the exposure, a high-dimensional baseline damage spectrum (a vector of per-read damage counts stratified by trinucleotide context and error type) as the mediator, and storage-quality failure as the outcome. Nonlinear covariate effects in both the mediator and survival models are approximated using deep neural networks. A three-step procedure combining product-of-coefficients screening, Smoothly Clipped Absolute Deviation (SCAD) penalized estimation, and joint significance testing is developed for mediator selection and inference. Applied to an aging experiment on electrochemically synthesized DNA, the method identifies 14 significant mediators, all corresponding to single-base deletions, with estimated mediated effects concentrated in trinucleotide contexts ending in C. These results reveal deletion-type damage as a major pathway linking sequence composition to reduced archival reliability and suggest candidate sequence features for future optimization and error-control strategies. The proposed framework thus offers a mechanism-oriented statistical approach for understanding and improving the reliability of DNA data storage.