Random access in large-scale DNA data storage

Lee Organick, Siena Dumas Ang, Yuan Jyue Chen, Randolph Lopez, Sergey Yekhanin, Konstantin Makarychev, Miklos Z. Racz, Govinda Kamath, Parikshit Gopalan, Bichlien Nguyen, Christopher N. Takahashi, Sharon Newman, Hsing Yeh Parker, Cyrus Rashtchian, Kendall Stewart, Gagan Gupta, Robert Carlson, John Mulligan, Douglas Carmean, Georg SeeligLuis Ceze*, Karin Strauss

*Corresponding author for this work

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Synthetic DNA is durable and can encode digital data with high density, making it an attractive medium for data storage. However, recovering stored data on a large-scale currently requires all the DNA in a pool to be sequenced, even if only a subset of the information needs to be extracted. Here, we encode and store 35 distinct files (over 200 MB of data), in more than 13 million DNA oligonucleotides, and show that we can recover each file individually and with no errors, using a random access approach. We design and validate a large library of primers that enable individual recovery of all files stored within the DNA. We also develop an algorithm that greatly reduces the sequencing read coverage required for error-free decoding by maximizing information from all sequence reads. These advances demonstrate a viable, large-scale system for DNA data storage and retrieval.

Original languageEnglish (US)
Pages (from-to)242-248
Number of pages7
JournalNature biotechnology
Volume36
Issue number3
DOIs
StatePublished - Mar 1 2018

Fingerprint

Information Storage and Retrieval
DNA
Data storage equipment
Oligonucleotides
Libraries
Decoding
Large scale systems
Recovery

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology
  • Molecular Medicine
  • Biomedical Engineering

Cite this

Organick, L., Ang, S. D., Chen, Y. J., Lopez, R., Yekhanin, S., Makarychev, K., ... Strauss, K. (2018). Random access in large-scale DNA data storage. Nature biotechnology, 36(3), 242-248. https://doi.org/10.1038/nbt.4079
Organick, Lee ; Ang, Siena Dumas ; Chen, Yuan Jyue ; Lopez, Randolph ; Yekhanin, Sergey ; Makarychev, Konstantin ; Racz, Miklos Z. ; Kamath, Govinda ; Gopalan, Parikshit ; Nguyen, Bichlien ; Takahashi, Christopher N. ; Newman, Sharon ; Parker, Hsing Yeh ; Rashtchian, Cyrus ; Stewart, Kendall ; Gupta, Gagan ; Carlson, Robert ; Mulligan, John ; Carmean, Douglas ; Seelig, Georg ; Ceze, Luis ; Strauss, Karin. / Random access in large-scale DNA data storage. In: Nature biotechnology. 2018 ; Vol. 36, No. 3. pp. 242-248.
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Organick, L, Ang, SD, Chen, YJ, Lopez, R, Yekhanin, S, Makarychev, K, Racz, MZ, Kamath, G, Gopalan, P, Nguyen, B, Takahashi, CN, Newman, S, Parker, HY, Rashtchian, C, Stewart, K, Gupta, G, Carlson, R, Mulligan, J, Carmean, D, Seelig, G, Ceze, L & Strauss, K 2018, 'Random access in large-scale DNA data storage', Nature biotechnology, vol. 36, no. 3, pp. 242-248. https://doi.org/10.1038/nbt.4079

Random access in large-scale DNA data storage. / Organick, Lee; Ang, Siena Dumas; Chen, Yuan Jyue; Lopez, Randolph; Yekhanin, Sergey; Makarychev, Konstantin; Racz, Miklos Z.; Kamath, Govinda; Gopalan, Parikshit; Nguyen, Bichlien; Takahashi, Christopher N.; Newman, Sharon; Parker, Hsing Yeh; Rashtchian, Cyrus; Stewart, Kendall; Gupta, Gagan; Carlson, Robert; Mulligan, John; Carmean, Douglas; Seelig, Georg; Ceze, Luis; Strauss, Karin.

In: Nature biotechnology, Vol. 36, No. 3, 01.03.2018, p. 242-248.

Research output: Contribution to journalArticle

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AU - Stewart, Kendall

AU - Gupta, Gagan

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Organick L, Ang SD, Chen YJ, Lopez R, Yekhanin S, Makarychev K et al. Random access in large-scale DNA data storage. Nature biotechnology. 2018 Mar 1;36(3):242-248. https://doi.org/10.1038/nbt.4079