Design and Analysis of Two-Layer Coding Scheme for DNA-Based Data Storage

Area of Science:

• Biotechnology
• Information Science
• Computer Science

Background:

• DNA data storage offers high density and stability but faces high read costs due to errors in synthesis, storage, and sequencing.
• Current methods struggle to balance reliability and redundancy, hindering practical DNA data storage deployment.

Purpose of the Study:

• To propose a read-cost-efficient coding framework for DNA data storage that enhances reliability without increasing total redundancy.
• To mitigate base-level and sequence-level errors in DNA data storage systems.

Main Methods:

• Developed a novel two-layer intra-oligo coding scheme using Bose-Chaudhuri-Hocquenghem (BCH) codes to protect index and data bits separately.
• Introduced a semi-analytical optimization method for optimal redundancy allocation between index and data bits under a fixed total code rate.
• Implemented inter-oligo protection using low-density parity-check (LDPC) codes to address sequence-level errors.

Main Results:

• The proposed two-layer coding scheme with optimized redundancy allocation significantly reduces frame error rate (FER) compared to single-layer schemes.
• Analytical and numerical results demonstrate the effectiveness of the proposed coding framework and optimization method.
• The system achieves enhanced reliability under identical sequencing depth and total redundancy levels.

Conclusions:

• The novel two-layer coding scheme and optimization method are effective in improving the reliability of DNA-based data storage.
• This framework addresses the critical challenge of high read costs, paving the way for more practical DNA data storage solutions.
• The findings highlight the advantages of layered coding strategies for robust DNA data storage systems.