Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing

Nat Methods. 2014 Jan;11(1):51-4. doi: 10.1038/nmeth.2736. Epub 2013 Nov 24.


We 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. We applied mmPCR-seq to RNA editing and allele-specific expression studies. mmPCR-seq complements RNA-seq for studying allelic variations in the transcriptome.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alleles
  • Brain / metabolism
  • Brain / pathology
  • DNA Barcoding, Taxonomic
  • DNA, Complementary / metabolism
  • Gene Expression Profiling
  • Genotype
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Multiplex Polymerase Chain Reaction / methods*
  • RNA / analysis*
  • RNA Editing
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction / economics
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Sequence Analysis, RNA / economics
  • Sequence Analysis, RNA / methods*
  • Transcriptome


  • DNA, Complementary
  • RNA

Associated data

  • SRA/SRP029341