High-scale random access on DNA storage systems. Issue 1 (14th January 2022)

• Record Type: Journal Article
• Authors: El-Shaikh, Alex; Welzel, Marius; Heider, Dominik; Seeger, Bernhard
• Is Part Of: NAR genomics and bioinformatics. Volume 4:Issue 1(2022)
• Publication Date: 2022-01-14
• Subjects: Genomics -- Periodicals; Bioinformatics -- Periodicals; 572.8
• DOI: 10.1093/nargab/lqab126
• Languages: English
• ISSNs: 2631-9268

Abstract

ABSTRACT: Due to the rapid cost decline of synthesizing and sequencing deoxyribonucleic acid (DNA), high information density, and its durability of up to centuries, utilizing DNA as an information storage medium has received the attention of many scientists. State-of-the-art DNA storage systems exploit the high capacity of DNA and enable random access (predominantly random reads) by primers, which serve as unique identifiers for directly accessing data. However, primers come with a significant limitation regarding the maximum available number per DNA library. The number of different primers within a library is typically very small (e.g. ≈10). We propose a method to overcome this deficiency and present a general-purpose technique for addressing and directly accessing thousands to potentially millions of different data objects within the same DNA pool. Our approach utilizes a fountain code, sophisticated probe design, and microarray technologies. A key component is locality-sensitive hashing, making checks for dissimilarity among such a large number of probes and data objects feasible.