Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.

TitleQuantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.
Publication TypeJournal Article
Year of Publication2014
AuthorsZhang R, Li X, Ramaswami G, Smith KS, Turecki G, Montgomery SB, Li JBilly
JournalNat Methods
Volume11
Issue1
Pagination51-4
Date Published2014 Jan
ISSN1548-7105
KeywordsAlleles, Brain, DNA Barcoding, Taxonomic, DNA, Complementary, Gene Expression Profiling, Genotype, High-Throughput Nucleotide Sequencing, Humans, Multiplex Polymerase Chain Reaction, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, RNA, RNA Editing, Sequence Analysis, RNA, Transcriptome
Abstract

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.

DOI10.1038/nmeth.2736
Alternate JournalNat. Methods
PubMed ID24270603
PubMed Central IDPMC3877737
Grant ListGM102484 / GM / NIGMS NIH HHS / United States
P30 CA124435 / CA / NCI NIH HHS / United States
R01 GM102484 / GM / NIGMS NIH HHS / United States
T32 HG000044 / HG / NHGRI NIH HHS / United States

  • Douglas Hospital
  • Dobell Pavillion
  • Brain imaging centre