A microfluidic droplet platform for multiplexed single nucleotide polymorphism analysis of an array plant genomic DNA samples

A programmable droplet-based platform which performs multiplexed single nucleotide polymorphism analysis on an array of plant genomic DNA samples is presented. This device has the potential to meet the demand for flexible and cost-effective tools that can perform high throughput genetic screening for applications such as allelic variation detection in agriculture. The microfluidic droplet-based device accepts an unlimited number of sample plugs containing genomic plant DNA from a multi-well plate. Each plug is separated by a fluorinated immiscible carrier fluid to prevent cross-contamination. Once plugs are loaded on to the device, mechanical chopping of these sample plugs is performed to digitize them into smaller daughter droplets. The device then performs subsequent synchronization-free, robust injection of multiple single nucleotide polymorphism interrogating probes in to the sample daughter droplets on-demand. This microfluidic platform combines the excellent control of valve-based microfluidics with the high-throughput capability of droplet microfluidics. Furthermore, generation of a one-dimensional array of combinatorial mixtures of DNA-probe droplets in which the sequence of drops is maintained throughout the device leads to automatic spatial indexing of these droplets, precluding the need for barcoding to identify droplet contents. We expect this flexible platform to expand the range of applications of droplet microfluidics to include applications requiring high degrees of multiplexing as well as high throughput screening of arrays of samples.