Forward Error Correction for DNA Data Storage

By Meinolf Blawat, K. Gaedke, I. Huetter, Xiao-Ming Chen, B. Turczyk, Samuel A. Inverso, Benjamin W Pruitt, George M. Church. International Conference on Conceptual Structures, 2016

344 citations recorded by the source corpus.

Abstract We report on a strong capacity boost in storing digital data in synthetic DNA. In principle, synthetic DNA is an ideal media to archive digital data for very long times because the achievable data density and longevity outperforms today's digital data storage media by far. On the other hand, neither the synthesis, nor the amplification and the sequencing of DNA strands can be performed error-free today and in the foreseeable future. In order to make synthetic DNA available as digital data storage media, specifically tailored forward error correction schemes have to be applied. For the purpose of realizing a DNA data storage, we have developed an efficient and robust forwarderror-correcting scheme adapted to the DNA channel. We based the design of the needed DNA channel model on data from a proof-of-concept conducted 2012 by a team from the Harvard Medical School [1]. Our forward error correction scheme is able to cope with all error types of today's DNA synthesis, amplification and sequencing processes, e.g. insertion, deletion, and swap errors. In a successful experiment, we were able to store and retrieve error-free 22 MByte of digital data in synthetic DNA recently. The found residual error probability is already in the same order as it is in hard disk drives and can be easily improved further. This proves the feasibility to use synthetic DNA as longterm digital data storage media.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/d77ea9a5082081ab0e69f1dfda40546ea332ec3d

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In Artificial Intelligence

1. Luis Ceze
2. Parikshit Gopalan
3. Konstantin Makarychev
4. Sergey Yekhanin
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In Molecular Biology

1. Karin Strauss
2. Luis Ceze
3. Konstantin Makarychev
4. Yuan-Jyue Chen
5. Georg Seelig

Citations in the corpus

• Random access in large-scale DNA data storage (2018, methodology): “After vortexing, the now milky-appearing product was split evenly into three PCR tubes and placed in a thermocycler with the following protocol: (1) 95 °C for 3 min, (2) 98 °C for 20 s, (3) 62 °C for 20 s, (4) 72 °C for 15 s, (5) go to step 2 a varying number of times depending on the proportion of ”