Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data. Previous work has utilized ECCs that can correct substitution errors, but not insertion or deletion errors (indels), instead relying on sequencing depth and multiple alignment to detect and correct indels -- in effect an inefficient multiple-repetition code. This paper describes an ECC, termed "HEDGES", that corrects simultaneously for substitutions, insertions, and deletions in a single read. Varying code rates allow for correction of up to 10 nucleotide errors and achieve 50 or better of the estimated Shannon limit.
Church et. al @cite_16 synthesized oligomers of length 159, each of which contained both address information (ordering of oligomers in the message) and payload. There was no explicit ECC. The pool of oligomers was sequenced to a depth 3000x, allowing recovery of a consensus sequence with high probability. High-depth coverage can correct sequencing errors, but not synthesis errors. Indeed, the final results contained 10-bit errors.
@cite_16
2025383314
Digital information is accumulating at an astounding rate, straining our ability to store and archive it. DNA is among the most dense and stable information media known. The development of new technologies in both DNA synthesis and sequencing make DNA an increasingly feasible digital storage medium. We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing.