High throughput system for preparing samples for genomic, epigenetic, transcriptomic, proteomic and metabolomic analysis

Abstract

Multi-omics considers the analysis of complex biological “omes” (genome, epigenome, transcriptome, proteome, metabolome, and others). This exponentially growing systems biology approach aims to better understand phenotypes in health and disease and as such identify biomarkers of disease and drug targets. The basic workflow is divided into an upstream sample preparation step, and corresponding downstream assays. To prepare samples for these assays biospecimen are treated to extract analytes such as chromatin, DNA, RNA, protein and metabolites. Often these sample preparation steps are done using cavitation. Current tools such as ultrasonic horns, and even many commercial sample preparation instruments, can be highly inconsistent, leading to unreliable assays. In order to overcome the problems of inconsistency, an instrument was designed and built with a transducer array (free field pressures P + = 30 MPa, P– = 12 MPa) capable of processing samples directly in standard 96-well microplates. An array of transducers is mounted below a microplate, coupled to a lens array that focuses acoustic energy into each well of a microplate. Intense cavitation is generated in each well. This process results in consistent analytes extraction that leads to consistently reproducible results. The authors have a financial conflict of interest. [Funded by NIH R33CA191135, R21GM111439, R01DK103849, R42HG010855, U01CA246503, and R44GM122097.]