Development of a microfluidic platform for integrated DNA sequencing protocols

Abstract

This thesis describes the design and development of a microfluidic platform to reduce costs and improve the quality of in the DNA sequencing methodology currently implemented at the Broad Institute in Cambridge, Massachusetts. The Sequencing Center at the Broad Institute currently generates an average of 130 million bases per day with an average read length of 800. This is enabled by the successful preparation and detection of over 97,000 unique samples. Most of the cost per sample is tied up in expensive proprietary reagents utilized in the various reactions comprising the preparation process. Through the application of microfluidics, the possibility of drastically scaling down the amount of proprietary reagents is explored. Stamp-sized elastomeric polydimethylsiloxane (PDMS) microfluidic devices were developed and microfluidic sample manipulation techniques were standardized. Using these devices and techniques, an attempt was made to adapt the various components of the sequencing process to the microfluidic platform. Work within the scope of this thesis is focused on the adaptation of the commercial sequencing protocols, which are labor intensive, consume costly reagents and serve as limitations for high-throughput parallelization of the process.

(cont.) The first is the amplification reaction. By scaling down the process from a plate-based format to an integrated microfluidic device, amplification reagent consumption was reduced by two orders of magnitude while maintaining the quality and length of the sequencing reads (with the subsequent sequencing reaction run off chip). As a follow up project, an attempt was made to scale down the Sequencing Reaction, which, in spite of limitations, suggested a good path toward the eventual development of an integrated microfluidic device for the preparation of running the complete sequencing reaction protocol on-chip.