Microfluidic platform for next-generation sequencing library preparation with low-input samples

Advances in Next Generation Sequencing (NGS) have made available a wealth of information that had previously been inaccessible to researchers and clinicians. NGS has been applied to understand genomic, transcriptomic, and epigenomic changes and gained traction as a significant tool capable of accelerating diagnosis, prognosis, and biomarker discovery. However, these NGS assays have yet to be practical methods for patient stratification or diagnosis because of the gap between the tiny quantities of biomaterials provided by a clinical sample and the large DNA input required by most of these assays. Current library preparation methodologies typically require large input amounts of DNA and a long and complicated manual process. Here we present a microfluidic reactor system for NGS library preparation, capable of reducing the number of pipetting steps significantly, automating much of the process, while supporting extremely low DNA input requirement (10 pg per library). This largely automated technology will allow for low-input preparations of 8 libraries simultaneously while reducing batch to batch variation and operator hands-on time. We examined library preparation efficiency using various ChIP DNA amounts looking at genome wide H3K4me3 profiles of GM12878 cell line. The system was further validated using ChIP DNA samples prepared from prefrontal cortex (PFC) of 10-week old male CD-1 mice, exploring different histone modifications: H3K4me3, H3K9me3, H3K36me3, and H3K79me2.