The Shannon Human Splicing pipeline is software for genome-scale mutation analysis and predicts variants affecting mRNA splicing. Individual information contents (in bits) of reference and variant splice sites are compared and significant differences are annotated and prioritized. Annotation indicates the context of novel mutations as well as common and rare SNPs with splicing effects. Potential natural and cryptic mRNA splicing variants are identified, and null mutations are distinguished from leaky mutations. Mutations and rare SNPs were predicted in genomes of three cancer cell lines (U2OS, U251 and A431), which were supported by expression analyses. For more information on these analyses and other pipeline functionality please refer to the paper: "Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences" on PubMed, or in downloadable pdf format.
This resource accepts a standard VCF (Variant Call Format) file as input and generates a lists of variants predicted to alter splicing. Generally the resultant list will contain and ~0.01-0.02% (natural) and ~0.05% (cryptic) of the total number of variants submitted. These percentages depend heavily on the nature of the variants submitted. It is our hope researchers who use this service will make use of this reduced subset of variants to guide their future research efforts towards those splicing variants most likely to be potentially pathogenic.
Click here to view a video discussing Shannon pipeline results formats. This video is a good place to start to understand the types of results you can expect to receive when examining variants on this server.
This website is deprecated and is now a part of MutationForecaster.