Small Nucleotide Variant Analysis Using RNA Fusion Panel ( SMURF ): Making the Most of RNAseq Data in Solid Tumours

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BACKGROUND: RNA-based fusion panels using targeted next-generation sequencing of formalin-fixed paraffin-embedded tumour tissue specimens are used for various tumour types to detect rearrangements/fusions. Using bioinformatic approaches, the data obtained from RNA sequencing (RNA-Seq) can also be used for small nucleotide variants analysis (single nucleotide variants and indels). METHODS: The performance characteristics of applying Small nucleotide variant analysis Using RNA Fusion panel (SMURF) analysis to RNA-Seq (RNA sequencing) data obtained from an RNA-based fusion panel was evaluated and compared to results obtained from a dedicated DNA-based panel. RESULTS: This demonstrated that an RNA fusion panel can be enhanced to identify small nucleotide variants to maximise the utility of this panel. Although coverage depth across various genes, based on gene expression, was found to be quite variable, which is expected, there were certain genes found to consistently display coverage depth suitable for variant identification, such as GNAS, GNAQ, NRAS, and CTNNB1. CONCLUSION: This analysis suggests that the variants in these genes can be confidently reported from RNA-Seq data obtained from an RNA-based fusion panel.

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