A High-Throughput and High-Resolution Microfluidics System for SNP Genotyping

A single-nucleotide polymorphism (SNP) is a single base pair mutation at a specific locus, usually consisting of two alleles. SNP genotyping measures genetic variations of SNPs between members of a species. It has been widely used to measure genetic variation, and it is one of the most important tools for clinical, pharmaceutical, and agricultural gene analysis. Microfluidic measurement can provide high throughput with fast turnaround, low consumption of reagents, and an automated workflow for SNP genotyping. For many low-quality samples, a preamplification step is required. The preamplification step, however, could add extra cost, operator error, time, and risk of contamination in the lab.

Fluidigm has developed a High Precision integrated fluidic circuit (IFC) that integrates preamplification function into the high-throughput, PCR-based genotyping 96.96 Dynamic Array. The loading was greatly accelerated by combining open-channel loading with the typical dead-end filling for a PDMS-based microfluidic IFC. The IFC takes 96 different samples, tests for 96 different SNPs for each sample simultaneously, and delivers 9,216 datapoints within 2½ hours. Since both preamplification and genotyping reactions are performed within the closed IFC, the process is highly simplified and automated, with no risk of contamination from open vessels. Starting with 1 ng of human genomic DNA, the system generated an auto call rate of higher than 99.5% and accuracy of greater than 99.75%, thereby demonstrating the performance and power of the system.