DNA Fountain enables a robust and efficient storage architecture

Erlich, Yaniv; Zielinski, Dina

doi:10.1101/074237

Cited by 144 publications

(337 citation statements)

References 37 publications

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“…Error correction coding is performed to correct errors within each oligonucleotide and to deal with missing oligonucleotides. Two of the state-of-the-art works [1] and [4] use very distinct schemes for the error correction and decoding and are discussed below.…”

Section: Previous Workmentioning

confidence: 99%

“…In [1], Fountain codes [11] are used to recover missing oligonucleotides, and Reed Solomon (RS) codes [12] are used to correct errors within each read. Since the RS code is applied on very short sequences, the scheme suffers from limitations of short block length codes [13].…”

Section: Previous Workmentioning

confidence: 99%

“…The size of these segments is determined by the capability of the synthesis technique (typically 150-200 bases). Other works ( [1], [4]) explored mappings that restrict homopolymers (e.g., AA) to reduce the synthesis error rate at the cost of higher redundancy. Instead, we randomize the binary data itself by compressing and encrypting it before the encoding.…”

Section: Encodingmentioning

confidence: 99%

“…Interestingly, the cost of DNA sequencing has been decreasing exponentially in the past ten years. DNA is a robust method of storing information as demonstrated by every living organism and offers exceptionally high storage densities (100s of Petabytes per gram [1]) and long-term durability (1000s of years [2]). The longevity of DNA-based storage makes it ideal as an archival medium to store the knowledge gained by humanity over the millennia.…”

Section: Introductionmentioning

confidence: 99%

“…Since both the DNA synthesis and sequencing processes are inherently error-prone, error correction coding based on the characteristics of this noise is critical for reliable decoding of data. There has been a series of recent works on DNA-based storage such as [1], [4], [5], [6], [7] and [8] which focus on error correction and random-access retrieval, among other aspects. Figure 1 shows a schematic of a typical DNA-based storage system.…”

Section: Introductionmentioning

confidence: 99%

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Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Chandak

Tatwawadi

Lau

et al. 2019

Preprint

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With the amount of data being stored increasing rapidly, there is significant interest in exploring alternative storage technologies. In this context, DNA-based storage systems can offer significantly higher storage densities (petabytes/gram) and durability (thousands of years) than current technologies. Specifically, DNA has been found to be stable over extended periods of time which has been demonstrated in the analysis of organisms long since extinct. Recent advances in DNA sequencing and synthesis pipelines have made DNA-based storage a promising candidate for the storage technology of the future.Recently, there have been multiple efforts in this direction, focusing on aspects such as error correction for synthesis/sequencing errors and erasure correction for handling missing sequences. The typical approach is to use separate codes for handling errors and erasures, but there is limited understanding of the efficiency of this framework. Furthermore, the existing techniques use short block-length codes and heavily rely on read consensus, both of which are known to be suboptimal in coding theory.In this work, we study the tradeoff between the writing and reading costs involved in DNA-based storage and propose a practical scheme to achieve an improved tradeoff between these quantities. Our scheme breaks with the traditional separation framework and instead uses a single large block-length LDPC code for both erasure and error correction. We also introduce novel techniques to handle insertion and deletion errors introduced by the synthesis process. For a range of writing costs, the proposed scheme achieves 30-40% lower reading costs than state-of-the-art techniques on experimental data obtained using array synthesis and Illumina sequencing.

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Section: Previous Workmentioning

confidence: 99%

Section: Previous Workmentioning

confidence: 99%

Section: Encodingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Chandak

Tatwawadi

Lau

et al. 2019

Preprint

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Controlling the structure of sequence‐defined poly(phosphodiester)s for optimal MS/MS reading of digital information

et al. 2017

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Digital polymers are monodisperse chains with a controlled sequence of co-monomers, defined as letters of an alphabet, and are used to store information at the molecular level. Reading such messages is hence a sequencing task that can be efficiently achieved by tandem mass spectrometry. To improve their readability, structure of sequence-controlled synthetic polymers can be optimized, based on considerations regarding their fragmentation behavior. This strategy is described here for poly(phosphodiester)s, which were synthesized as monodisperse chains with more than 100 units but exhibited extremely complex dissociation spectra. In these polymers, two repeating units that differ by a simple H/CH variation were defined as the 0 and 1 bit of the ASCII code and spaced by a phosphate moiety. They were readily ionized in negative ion mode electrospray but dissociated via cleavage at all phosphate bonds upon collisional activation. Although allowing a complete sequence coverage of digital poly(phosphodiester)s, this fragmentation behavior was not efficient for macromolecules with more than 50 co-monomers, and data interpretation was very tedious. The structure of these polymers was then modified by introducing alkoxyamine linkages at appropriate location throughout the chain. A first design consisted of placing these low dissociation energy bonds between each monomeric bit: while cleavage of this sole bond greatly simplified MS/MS spectra, efficient sequencing was limited to chains with up to about 50 units. In contrast, introduction of alkoxyamine bonds between each byte (i.e. a set of eight co-monomers) was a more successful strategy. Long messages (so far, up to 8 bytes) could be read in MS experiments, where single-byte containing fragments released during the first activation stage were further dissociated for sequencing. The whole sequence of such byte-truncated poly(phosphodiester)s could be easily re-constructed based on a mass tagging system which permits to determine the original location of each byte in the chain. Copyright © 2017 John Wiley & Sons, Ltd.

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DNA as a digital information storage device: hope or hype?

et al. 2018

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The total digital information today amounts to 3.52 × 10 bits globally, and at its consistent exponential rate of growth is expected to reach 3 × 10 bits by 2040. Data storage density of silicon chips is limited, and magnetic tapes used to maintain large-scale permanent archives begin to deteriorate within 20 years. Since silicon has limited data storage ability and serious limitations, such as human health hazards and environmental pollution, researchers across the world are intently searching for an appropriate alternative. Deoxyribonucleic acid (DNA) is an appealing option for such a purpose due to its endurance, a higher degree of compaction, and similarity to the sequential code of 0's and 1's as found in a computer. This emerging field of DNA as means of data storage has the potential to transform science fiction into reality, wherein a device that can fit in our palms can accommodate the information of the entire world, as latest research has revealed that just four grams of DNA could store the annual global digital information. DNA has all the properties to supersede the conventional hard disk, as it is capable of retaining ten times more data, has a thousandfold storage density, and consumes 10 times less power to store a similar amount of data. Although DNA has an enormous potential as a data storage device of the future, multiple bottlenecks such as exorbitant costs, excruciatingly slow writing and reading mechanisms, and vulnerability to mutations or errors need to be resolved. In this review, we have critically analyzed the emergence of DNA as a molecular storage device for the future, its ability to address the future digital data crunch, potential challenges in achieving this objective, various current industrial initiatives, and major breakthroughs.

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DNA Fountain enables a robust and efficient storage architecture

Cited by 144 publications

References 37 publications

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Improved read/write cost tradeoff in DNA-based data storage using LDPC codes

Controlling the structure of sequence‐defined poly(phosphodiester)s for optimal MS/MS reading of digital information

DNA as a digital information storage device: hope or hype?

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