mmPCR-seq – microfluidics-based multiplex PCR and deep sequencing

Researchers at Stanford University have developed a targeted RNA sequencing method that couples microfluidics-based multiplex PCR and deep sequencing (mmPCR-seq) to uniformly and simultaneously amplify up to 960 loci in 48 samples independently of their gene expression levels and to accurately and cost-effectively measure allelic ratios even for low-quantity or low-quality RNA samples. They applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.


Availability – A Perl script used to design the primers is available at

Zhang R, Li X, Ramaswami G, Smith KS, Turecki G, Montgomery SB, Li JB. (2013) Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing. Nat Methods [Epub ahead of print]. [abstract]