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How can MutationForecaster® help you pinpoint and interpret variants of interest?

MutationForecaster® is a system comprising several interlocking programs that analyze mutations in genes. The system's particular strength is in interpreting non-coding variants that alter recognition of binding sites in genomic DNA (transcription factors) and mRNA (splicing, RNA binding proteins).

Shannon pipeline
Identifies splicing and promoter mutations in gene panels, exomes, and genomes.
Uses HGVS designations for individual splicing mutations, including regulatory sequences.
Validates splicing mutations with RNA-Seq data
Analyze coding sequence changes
Combines results of other programs into a database and fetches publicly available info about variants.
Finds literature references for disease variants based on phenotype and gene
Overrepresented pathways in a gene list, Shannon pipeline, VEP, or Veridical results
Submits variants for interpretation by all or some of the program applications.
Interactively view variant results amalgamated from multiple sources

A more detailed description of each tool, related peer reviewed publications, documentation, tutorial videos, and presentations can be found within tool specific tabs below.

Shannon pipeline — Pinpoint potentially deleterious splicing mutations in full genomes

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 list of genomic variants as input and generates a list 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.

*Update* CytoGnomix has released a major update of this software called the Combined Shannon pipeline. It features several advancements over previous versions including:

  • Splicing regulatory binding sites can be examined using a selection of splicing regulatory Riw(b,l)s.
  • Transcription factor binding sites can be examined using a large selection of transcription factor Riw(b,l)s.
  • Ri,total (the total information content of an exon) is included for each reported variant.
  • "ASSEDA-like" visualizations are available for splice site variants.
  • More filtering options are available including the ability to report nearby binding sites which do not experience a change in information content.
Computational analysis of nucleic acid information defines binding sites. US Pat. No. 5,867,402
Method of predicting mutated mRNA splice isoforms. US Pat. App. Ser. No. 61/751,975; US Pat. App. Ser. Nos. 14/154,905, and 15/729,218

ASSEDA — Learn more about a specific variant

ASSEDA is a tool used to predict the effects of sequence changes that alter mRNA splicing in human diseases. It evaluates changes in splice site strength based on information theory-based models of donor and acceptor splice sites. Potential isoform structures and their relative abundance are predicted and reported.

Veridical — Compare predictions to RNA-Seq to determine statistical significance

Veridical is companion software to the article "Validation of predicted mRNA splicing mutations using high-throughput transcriptome data", Viner et al. published in F1000research. Veridical provides an in silico method for the automatic validation of DNA sequencing variants that alter mRNA splicing. Veridical performs statistically valid comparisons of the normalized read counts of abnormal RNA species in mutant versus non-mutant tissues.

VEP — Examine variation within coding regions

Predict of the effect of your variants on genes, transcripts, and protein sequence. SIFT and PolyPhen scores are also generated. Although this tool is freely available through Ensembl, we have included it to supplement our expertise in mRNA splicing variation. Like all other tools present on MutationForecaster®, VEP can be accessed in a hassle-free matter from our web interface and results can be automatically exported to CUVD.

Learn more about this tool at the VEP website.

Read about the inner-workings of VEP in their 2010 publication.

CUVD — Store your variants and compare with external resources

CUVD is based on the Leiden Open Variation Database with several significant modifications. Variants reported by any of our web tools can be imported into CUVD in bulk at the click of a button. Entrez e-utilities is utilized to provide additional information about each variant including related publications. Once your data is stored in the database, external resources such as HGNC, NCBI, EBI, and locus specific LOVD installations are automatically connected to each variant. The 'Variants' page has been modified to include results generated by each tool on MutationForecaster®. These additional columns can be hidden at the click of a button to reduce clutter if desired.

Learn more about LOVD or examine existing installations at the LOVD homepage.

Consult documentation for an unmodified LOVD here.

CytoVA — Accelerate literature searches

We have added a new resource to MutationForecaster® called CytoVA.

This is a cytogenomics visual analytics decision support tool with PubMed in the backend. Dr. Rogan and Dr. Knoll both contributed to designing it and it has been jointly developed with computer scientists at Western University.

The Cytolit tool allows you to search Pubmed for phenotype or gene (actually any) search terms. There is a dedicated link to search the Human Phenotype Ontology in the Advanced options. The program automatically classifies papers into subcategories, which you can then choose from to review abstracts. We find that it greatly expedites literature searches especially for genes and phenotypes where there is extensive literature available.

The CytoVA tool can accelerate finding literature references for intervals found by genomic microarray to harbor copy number changes. You select one or multiple chromosomes containing the changes. It then displays karyograms from which you can select bands, you can narrow the interval in the bands to specific coordinate ranges, then it displays genes and OMIM phenotypes in those intervals. Right clicking on the genes brings up links to the built-in genome browser and to a PubMed search on the gene.

The Jbrowse genome browser is also available separately. It contains ISCA, Cytognomix oligo and FISH probe designs and many other tracks.