title: A molecular inversion probe assay for detecting alternative splicing.
abstract: BACKGROUND
  A sensitive, high-throughput method for monitoring pre-mRNA splicing on a genomic scale is needed to understand the spectrum of alternatively spliced mRNA in human cells.
  
  
  RESULTS
  We adapted Molecular Inversion Probes (MIPs), a padlock-probe based technology, for the multiplexed capture and quantitation of individual splice events in human tissues. Individual MIP capture probes can be quantified using either DNA microarrays or high-throughput sequencing, which permits independent assessment of each spliced junction. Using our methodology we successfully identified 100% of our positive controls and showed that there is a strong correlation between the data from our alternative splicing MIP (asMIP) assay and quantitative PCR.
  
  
  CONCLUSIONS
  The asMIP assay provides a sensitive, accurate and multiplexed means for measuring pre-mRNA splicing. Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies.
authors.affiliation: Stanford Genome Technology Center, Department of Biochemistry, Stanford University School of Medicine, Palo Alto, CA USA. kjuneau@stanford.edu
authors.forename: Shengrong
authors.initials: S
authors.lastname: Lin
authors.forename: Wenyi
authors.initials: W
authors.lastname: Wang
authors.forename: Curtis
authors.initials: C
authors.lastname: Palm
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
authors.forename: Kara
authors.initials: K
authors.lastname: Juneau
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D015342:DNA Probes / Q000378:metabolism; D005091:Exons / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D015336:Molecular Probe Techniques; D015335:Molecular Probes / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D012372:ROC Curve; D012015:Reference Standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014335:Tropomyosin / Q000235:genetics / Q000378:metabolism
chemical_list: D015342:DNA Probes; D015335:Molecular Probes; C490775:TPM1 protein, human; C518659:TPM2 protein, human; D014335:Tropomyosin