Splice Variant Analysis using BaseScope™ Assay

Alternative splicing of exons in pre-mRNA can lead to the expression of multiple different mature mRNAs from an individual gene, known as splice variants. Splice variants have been shown to play significant roles in human disease, particularly cancer and neurological disorders and they often are differentially regulated across tissues and cells and during disease progression. However, the localization of the precise cells expressing specific splice variants in a complex tissue environment has been limited by the lack of sensitive and reproducible technologies.

While current RNA ISH techniques can detect splice variants, these methods may target exons that are present in both pre-mRNA and mature mRNA, due to the limited specific and unique sequence of that variant. Therefore, it is unknown if the RNA ISH signal being detected is from mature mRNA or pre-mRNA, precluding the reliable identification of specific splice variants within the tissue context. Detection of the exon-exon junction would ensure accurate detection of the mature mRNA variant.

The BaseScope™ Assay is a relatively new product from ACD, based on the same platform of proven and established RNAscope™ technology. It enables detection of exon junctions in FFPE tissue with morphological context by using only one ZZ probe uniquely designed on the specific exon junction of interest. These technological advantages enable:

  • Sensitive and specific detection of any exon junction
  • Detection of a specific RNA locus at single molecule detection sensitivity
  • Analysis of broad sample types, including FFPE tissue and fresh frozen tissues


Example of probe design for detection of a sequence with specific exon skipping: METΔ14 

Three probes are designed (image 1): one control probe designed for an exon junction present in all MET transcripts (exon junction 12/13), one probe designed for the exon junction with exon 14 (exon junction 14/15), and one probe designed for the exon junction with exon 14 skipping (exon junction 13/15).



FIGURE 1: Probe design for the detection of METΔ14 using the BaseScope™ assay. One ZZ probe (blue), designed to detect the junction between exons 12 and 13, is considered common and will detect both wild-type MET and METΔ14 mRNA. A second ZZ probe (orange) is designed to detect the junction between exons 14 and 15 and will detect only MET mRNA containing exon 14 (wild-type MET). A third ZZ probe is designed to detect the junction between exons 13 and 15 and will detect only MET exon 14 skipped mRNA (METΔ14). The 3 probes are tested in parallel (see next image).

FIGURE 2: Detection of METΔ14 using the BaseScope Assay. The cell lines H596 (METΔ14) and A549 (MET WT for exon 14) were used to examine METΔ14 status. The probe for exon junctions 12/13 showed expression of exons 12 and 13, which are present in both wild-type MET and METΔ14 cell lines. The probe for exon junctions 14/15 detected expression of wild-type MET in the A549 cell line only. The probe for exon junctions 13/15 detected expression of METΔ14 only in the H596 cell line.

Example of the BaseScope™ assay used for the detection of MET exon 14 status in lung cancer tissue.


FIGURE 3: The BaseScope assay is also applicable to FFPE tissue samples. Same probes used in cell lines are used here to detect MET exon 14 status. Signal is observed with the probe exon junctions 12/13 common for both wild-type MET and METΔ14. Signal is also observed with the wild-type MET-specific probe, exon junctions 14/15. Signal is not detected with the METΔ14 -specific probe exon junctions 13/15, indicating that the MET exon 14 status of this lung cancer sample is wild-type


BaseScope probes for Splice Variant List


  • AR
  • CD19
  • CTAG2
  • EGFR
  • ERBB2
  • FCGR2A
  • FCGR2B
  • FCGR3A
  • HOXB-AS3
  • IL4
  • IL6
  • LILRB1
  • LOC101927027
  • MAGEA2
  • MAGEA4
  • MAGEA8
  • MAGEA10
  • MAGEA11
  • MAGEA12
  • MET
  • MICA
  • SLC1A2
  • XBP1

Want to order a probe or don't find your gene of interest in this list? Contact your Account Manager 

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