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Cytognomix Shannon Pipeline

The splicing mutation pipeline plugin finds and interprets genomic variants that alter mRNA splicing in human exome, targeted sequencing, or complete genome data.

Cytognomix genome-scale human splicing mutation analysis.

Shannon pipeline from Cytognomix was initially created to address the vexing problem of assessing the many variants of unknown significance that are detected in cancer genetic testing. The Shannon human splicing mutation plug-in uses a proven approach to predict mRNA splicing abnormalities based on single nucleotide variant data from human sequencing. The Cytognomix plugin can be deployed on CLC Genomics workbench either as a standalone application or to CLC Genomics server using the Genomics Workbench client.


The Cytognomix Shannon plugin identifies splicing mutations with industry-leading sensitivity and specificity. It is based on a legacy of peer-reviewed literature confirming validated mutation predictions using our patented information theory based technology. Changes in information content in splice sites correspond to actual differences in binding affinity. Input can either be CLC bio SNP objects, in standard VCF, or an indexed simple SNP format. Results are based on sensible default parameters, are sortable and intuitive, and exportable to spreadsheets or genome browsers.

Summary of changes in version 2.0

  • Runs on Windows Vista, 7, or 8 (64 bit)
  • Is approximately 12 times faster than version 1.0
  • Handles insertions and deletions (beta)
  • Performs gene set (or pathway overrepresentation analysis) on mutated gene lists
  • Simplifies post-run analysis with preset filters for functionally significant variants
  • Updated to include RefSeq gene annotations


The Shannon pipeline has been used to reanalyze the Breast Cancer Information Core identifying many splicing mutations, most of which were previously unrecognized (Mucaki et al. 2011) .

Splicing mutations in 3 complete cancer cell line genomes were identified with the Shannon pipeline and were validated by transcriptome analysis (Shirley et al. 2013) .

Learn more about the Shannon pipeline plugin in this video from Cytognomix:

Versioning and Requirements

The Cytognomix Shannon human mRNA splicing plugin runs in standalone mode on either the CLC Genomics Workbench V6.5, or with both the Workbench Client and CLC Genomics Server V6.5 (as a standalone server or grid-enabled). Released for the following 64 bit operating systems: Windows (Vista, 7, 8), Linux, and MacOSX. This plugin requires at least 4Gb of RAM. To facilitate variant annotation and information analysis, a dependency plugin must be installed for the appropriate genome build (GRCh37/hg19 or NCBI36/hg18).


  • Hones in on a limited number of variants that potentially affect mRNA splicing
  • Variants categorized by whether they fully or partially inactivate natural splice sites or activate cryptic sites
  • Predicts variants missed by other bioinformatic methods
  • Changes displayed graphically as Manhattan-like plots or custom tracks
  • Mutations are sortable according to information content, proximity to natural splice site, relative strength of cryptic vs natural site, gene, and coordinate
  • Variants affecting SNPs are annotated and can be filtered by allele frequency
  • Rapid results generated from complete genome-wide, variant analysis of thousands of SNPs
  • Variant tracks can be used as input for the Shannon Pipeline
  • All variants in a full genome can be analyzed in approximately 15 minutes on an Intel I7-based CPU with 16Gb RAM