HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints.

Area of Science:

• Biotechnology
• Bioinformatics
• Information Science

Background:

• Synthetic DNA offers a durable, high-density information storage solution.
• High error rates during DNA synthesis and sequencing pose a significant challenge for DNA data storage.

Purpose of the Study:

• To introduce HEDGES (Hash Encoded, Decoded by Greedy Exhaustive Search), a novel error-correcting code for DNA data storage.
• To demonstrate HEDGES' capability to repair insertion, deletion, and substitution errors in synthetic DNA.

Main Methods:

• Developed HEDGES, an error-correcting code designed for DNA synthesis and sequencing errors.
• Integrated HEDGES with Reed-Solomon codes and strand interleaving for enhanced error correction.
• Incorporated user-defined sequence constraints, including repeat avoidance and GC content regulation.

Main Results:

• HEDGES successfully repairs all basic DNA error types (insertions, deletions, substitutions).
• The code converts complex errors into substitutions, enabling correction by standard outer codes.
• Simulations and experiments show HEDGES can achieve error-free data recovery from DNA with up to 10% errors.

Conclusions:

• HEDGES significantly advances the reliability of DNA-based information storage.
• The developed statistical model predicts error-free recovery of exabyte-scale data.
• HEDGES is poised for large-scale applications as DNA synthesis and sequencing costs decrease.