Synthetic DNA applications in information technology

Meiser, Linda C.; Nguyen, Bichlien H.; Chen, Yuan-Jyue; Nivala, Jeff; Strauß, Karin; Ceze, Luís; Grass, Robert N.

doi:10.1038/s41467-021-27846-9

Cited by 73 publications

(66 citation statements)

References 108 publications

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“…Synthetic DNA has now been proved to be a new potential storage medium for the exponentially growing data 1,2 . The total amount of data stored in synthetic DNA has reached the GB level; various practical automated read/write technologies for DNA storage have been proposed [3][4][5] .…”

Section: Introductionmentioning

confidence: 99%

A robust and efficient DNA storage architecture based on modulation encoding and decoding

Zan

Xie

Yao

et al. 2022

Preprint

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Thanks to its high density and long durability, synthetic DNA has been widely considered as a promising solution to the data explosion problem. However, due to the large amount of random base insertion-deletion-substitution (IDSs) errors from sequencing, reliable data recovery remains a critical challenge, which hinders its large-scale application. Here, we propose a modulation-based DNA storage architecture. Experiments on simulation and real datasets demonstrate that it has two distinct advantages. First, modulation encoding provides a simple way to ensure the encoded DNA sequences comply with biological sequence constraints (i.e., GC balanced and no homopolymers); Second, modulation decoding is highly efficient and extremely robust for the detection of insertions and deletions, which can correct up to ~40% errors. These two advantages pave the way for future high-throughput and low-cost techniques, and will kickstart the actualization of a viable, large-scale system for DNA data storage.

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Section: Introductionmentioning

confidence: 99%

A robust and efficient DNA storage architecture based on modulation encoding and decoding

Zan

Xie

Yao

et al. 2022

Preprint

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“…DNA, as the carrier of genetic information, is regarded as the most attractive representative of molecular-level storage for ultrahigh storage density, robust stability, easy amplification and low power consumption in the storage period. [14][15][16][17] More importantly, the current cost of synthesis and sequencing in DNA-based storage were only ~$0.8/KB and ~$10 À 3 -10 À 5 /KB, respectively, and has plummeted by few orders of magnitude in the last decades. [14,18] The relatively mature DNA synthesis and sequencing technologies also provide the important technical support for the development of DNA-based information storage systems.…”

Section: Introductionmentioning

confidence: 99%

Preservation and Encryption in DNA Digital Data Storage

et al. 2022

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The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.

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“…including their potential use in schemes for engineered DNA data storage [15,16]. For some applications, barcodes must function robustly in experimental situations subject to significant error rates (that is, the unintended occurrence of nucleotide substitutions, insertions, and deletions).…”

Section: Introductionmentioning

confidence: 99%

Fast trimer statistics facilitate accurate decoding of large random DNA barcode sets even at large sequencing error rates

Press

2022

Preprint

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Predefined sets of short DNA sequences are commonly used as barcodes to identify individual biomolecules in pooled populations. Such use requires either sufficiently small DNA error rates, or else an error-correction methodology. Most existing DNA error-correcting codes (ECCs) correct only one or two errors per barcode in sets of typically less than or the order of 10^4 barcodes. We here consider the use of random barcodes of sufficient length that they remain accurately decodable even with 6 or more errors and even at 10 or 20 percent nucleotide error rates. We show that length about 34 nt is sufficient even with as many as 10^6 or more barcodes. The obvious objection to this scheme is that it requires comparing every read to every possible barcode by a slow Levenshtein or Needleman-Wunsch comparison. We show that several orders of magnitude speedup can be achieved by (i) a fast triage method that compares only trimer (three consecutive nucleotide) occurence statistics, precomputed in linear time for both reads and barcodes, and (ii) the massive parallelism available on today's even commodity-grade GPUs. With 10^6 barcodes of length 34 and 10% DNA errors (substitutions and indels) we achieve in simulation 99.9% precision (decode accuracy) with 98.8% recall (read acceptance rate). Similarly high precision with somewhat smaller recall is achievable even with 20% DNA errors. The amortized computation cost on a commodity workstation with two GPUs (2022 capability and price) is estimated as between USD 0.15 and USD 0.60 per million decoded reads.

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Synthetic DNA applications in information technology

Cited by 73 publications

References 108 publications

A robust and efficient DNA storage architecture based on modulation encoding and decoding

A robust and efficient DNA storage architecture based on modulation encoding and decoding

Preservation and Encryption in DNA Digital Data Storage

Fast trimer statistics facilitate accurate decoding of large random DNA barcode sets even at large sequencing error rates

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