Journal Article

96 sample parallel acoustic fragmentation for high throughput next generation sequencing library preparation

Dayton, Paul A., Pattenden, Samantha G., Tsuruta, James K., Kim, Jinwook, Bautista, Kathlyne Jayne B., Mehrab-Mohseni, Marjan, Marron, James S., Zheng, Haofan, Hepperla, Austin J., Maldonado-Rosado, Erika E., Liu, Yusha, Carroll, Michell D., Niederhuber, Matthew J., Haaland, Perry D., Mieczkowski, Piotr A., Kasoji, Sandeep K., Rosen, Jonathan D., Velasco, Brian

2026

Overview

Random, unbiased fragmentation of genomic DNA is necessary for next generation sequencing (NGS), yet the process of DNA fragmentation is still a bottleneck in NGS pipelines. A technology that increases the efficiency and consistency of this step will be highly desirable for both research laboratories and in clinical diagnostics. Previously, we reported the development of a novel cavitation enhancement reagent that dramatically decreases the time and acoustic energy required for genomic DNA fragmentation. The inclusion of this reagent in standard protocols facilitates highly efficient sonication enabling the use of widely available and inexpensive equipment, including water bath-based sonicators. Here, we report that cavitation enhancement facilitates parallel fragmentation of up to 96 samples of genomic DNA in a modified sonication device. The parallel processing of multiple samples significantly reduces processing time, while maintaining fragment range reproducibility and preserving DNA quality for NGS. Consequently, this system removes a key bottleneck in standard NGS pipelines and facilitates efforts toward research and personalized genomics.

• Publisher: Public Library of Science,PLOS,Public Library of Science (PLoS)
• Subject: Acoustics / Analysis / Biology and life sciences / Cavitation / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - genetics / DNA Fragmentation / DNA sequencing / Ethylenediaminetetraacetic acid / Fragmentation / Gene Library / Gene sequencing / Genomes / Genomics / Health care / High-Throughput Nucleotide Sequencing - methods / Humans / Lipids / Methods / Multiprocessing / Next-generation sequencing / Nucleotide sequencing / Open source software / Parallel processing / Pipelines / Reagents / Reproducibility of Results / Research and Analysis Methods / Sequence Analysis, DNA - methods / Sonication / Sonication - instrumentation / Sonication - methods / Water baths / Yeast