Studying copy number variations using a nanofluidic platform

Qin, Jian; Jones, Robert C.; Ramakrishnan, Ramesh

One of the important applications of the digital array is absolute quantitation (14, 15) . The DNA molecules in each mixture are randomly partitioned into the 765 chambers of each panel. The chip is then thermocycled on Fluidigm's BioMark system and the positive chambers that originally contained one or more molecules will generate fluorescent signals and can be counted by the Digital PCR Analysis software. Since the volumes and dilution factors of the DNA samples are known prior to loading into the digital array, the DNA concentrations can be accurately calculated. The precision of this test is only dependent upon the sampling randomness and, like any biological experiments, will improve with multiple tests (panels). Digital array has been routinely used by us to quantitate DNA samples of unknown concentration and, especially, cDNA samples whose concentrations of the sequences of interest are hard to determine otherwise.