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Robust data storage in DNA by de Bruijn graph-based de novo strand assembly

Author

Listed:
  • Lifu Song

    (Tianjin University
    Tianjin University)

  • Feng Geng

    (Binzhou Medical University)

  • Zi-Yi Gong

    (Tianjin University
    Tianjin University)

  • Xin Chen

    (Tianjin University)

  • Jijun Tang

    (Tianjin University
    Chinese Academy of Sciences)

  • Chunye Gong

    (National SuperComputer Center in Tianjin)

  • Libang Zhou

    (Nanjing Agricultural University)

  • Rui Xia

    (National SuperComputer Center in Tianjin)

  • Ming-Zhe Han

    (Tianjin University
    Tianjin University)

  • Jing-Yi Xu

    (Tianjin University
    Tianjin University)

  • Bing-Zhi Li

    (Tianjin University
    Tianjin University)

  • Ying-Jin Yuan

    (Tianjin University
    Tianjin University)

Abstract

DNA data storage is a rapidly developing technology with great potential due to its high density, long-term durability, and low maintenance cost. The major technical challenges include various errors, such as strand breaks, rearrangements, and indels that frequently arise during DNA synthesis, amplification, sequencing, and preservation. In this study, a de novo strand assembly algorithm (DBGPS) is developed using de Bruijn graph and greedy path search to meet these challenges. DBGPS shows substantial advantages in handling DNA breaks, rearrangements, and indels. The robustness of DBGPS is demonstrated by accelerated aging, multiple independent data retrievals, deep error-prone PCR, and large-scale simulations. Remarkably, 6.8 MB of data is accurately recovered from a severely corrupted sample that has been treated at 70 °C for 70 days. With DBGPS, we are able to achieve a logical density of 1.30 bits/cycle and a physical density of 295 PB/g.

Suggested Citation

  • Lifu Song & Feng Geng & Zi-Yi Gong & Xin Chen & Jijun Tang & Chunye Gong & Libang Zhou & Rui Xia & Ming-Zhe Han & Jing-Yi Xu & Bing-Zhi Li & Ying-Jin Yuan, 2022. "Robust data storage in DNA by de Bruijn graph-based de novo strand assembly," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-33046-w
    DOI: 10.1038/s41467-022-33046-w
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    References listed on IDEAS

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    1. Philipp L. Antkowiak & Jory Lietard & Mohammad Zalbagi Darestani & Mark M. Somoza & Wendelin J. Stark & Reinhard Heckel & Robert N. Grass, 2020. "Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    2. Kevin N. Lin & Kevin Volkel & James M. Tuck & Albert J. Keung, 2020. "Dynamic and scalable DNA-based information storage," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    3. Tom van der Valk & Patrícia Pečnerová & David Díez-del-Molino & Anders Bergström & Jonas Oppenheimer & Stefanie Hartmann & Georgios Xenikoudakis & Jessica A. Thomas & Marianne Dehasque & Ekin Sağlıcan, 2021. "Million-year-old DNA sheds light on the genomic history of mammoths," Nature, Nature, vol. 591(7849), pages 265-269, March.
    4. Howon Lee & Daniel J. Wiegand & Kettner Griswold & Sukanya Punthambaker & Honggu Chun & Richie E. Kohman & George M. Church, 2020. "Photon-directed multiplexed enzymatic DNA synthesis for molecular digital data storage," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    5. S. Kasra Tabatabaei & Boya Wang & Nagendra Bala Murali Athreya & Behnam Enghiad & Alvaro Gonzalo Hernandez & Christopher J. Fields & Jean-Pierre Leburton & David Soloveichik & Huimin Zhao & Olgica Mil, 2020. "DNA punch cards for storing data on native DNA sequences via enzymatic nicking," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    6. Karishma Matange & James M. Tuck & Albert J. Keung, 2021. "DNA stability: a central design consideration for DNA data storage systems," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
    7. Henry H. Lee & Reza Kalhor & Naveen Goela & Jean Bolot & George M. Church, 2019. "Terminator-free template-independent enzymatic DNA synthesis for digital information storage," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    8. Yuan-Jyue Chen & Christopher N. Takahashi & Lee Organick & Callista Bee & Siena Dumas Ang & Patrick Weiss & Bill Peck & Georg Seelig & Luis Ceze & Karin Strauss, 2020. "Quantifying molecular bias in DNA data storage," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
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    1. Afsaneh Sadremomtaz & Robert F. Glass & Jorge Eduardo Guerrero & Dennis R. LaJeunesse & Eric A. Josephs & Reza Zadegan, 2023. "Digital data storage on DNA tape using CRISPR base editors," Nature Communications, Nature, vol. 14(1), pages 1-10, December.

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