Collaborative effort led by Greg Zaric at the University of Western Ontario:
Identification and survival outcomes of a cohort of patients with cancer of unknown primary in Ontario, Canada. Kim CS1, Hannouf MB, Sarma S, Rodrigues GB, Rogan PK, Mahmud SM, Winquist E, Brackstone M, Zaric GS. Acta Oncol. 2015 Mar 31:1-7. (link)
Videos are now available describing how to use and interpret results from the different components of the MutationForecaster system. Credits: Ben Shirley, Shannon Brown.
Please go to this link to view them all: link
For example, this is a general overview of the system:
Our paper, “Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis,” and video, ”Interpreting genomic variants in rare and common diseases,” have been highlighted by F1000Research on their home page.
SHARCNET Scientific Computing Seminar Series
Wednesday 11 March, 11am-12pm, ERC 1056
Peter K. Rogan, CRC (Tier I) in Genome Bioinformatics, Department of Biochemistry & Department of Computer Science, University of Western Ontario, and
Cytognomix Inc, London ON
Mutation Forecaster, a software resource for genome-scale analysis of complete genes and human genomes
Complete genome sequencing is now feasible, becoming cost effective, and increasingly an essential component of cancer discovery and patient genomic analyses. This has created a bottleneck in interpretation of gene variants, partly because the effects of most variants remain unknown (variants of unknown significance, VUS), and also because interpretation is confounded by the lack of corresponding genetic information from closely related family members. The VUS problem is now exacerbated by the discovery of massive numbers of variants in each genome, many never before seen. Technologies that prune variants in an individual are essential to perform any large scale gene panel, exome or genome analysis. The variant analysis approaches I will describe improves complete gene and genome sequence analyses and by detecting dysregulated biochemical pathways. We stratify variants by mutation severity, which can suggesting or exclude particular therapeutic options (Shirley et al. 2013 <http://www.sciencedirect.com/
Revised version of our review article on mRNA splicing in F1000Research has been highlighted in the Faculty of 1000 blog:
The blog entry includes links to our YouTube video:
Short version (3:42)
Long version (9:41)
Since our release of the Mutation Forecaster system in January, we have been gratified to see the level of interest by the biomedical and clinical research communities. There have been 32 registrants from 18 countries. One subscription has been activated, and others are in progress.
Our fees are reinvested to improve and expand this resource. For example, we are developing a completely automated workflow for genome scale coding and splicing mutation analysis, and which will automatically prepare written report summaries. Our plans for this product will meet your future needs for mutation interpretation.
February 25, 2015. Release of updated plugin Shannon splicing mutation pipeline software for Qiagen-CLC bio products
Cytognomix has released version 2.0.2 of the Shannon splicing mutation pipeline for the Qiagen-CLCbio Genomics Workbench versions 7.5.2 and 8.0 and for Genomics Server versions 6.5.3 and 7.0. Please contact Qiagen-CLCbio to purchase a license to this software.
Cytognomix is pleased to announce the sale of annual subscriptions of our MutationForecaster system to a molecular diagnostics laboratory at a public hospital in the Toronto metropolitan area in Ontario, Canada. The client is a long time paid subscriber of our ASSEDA product, who now has an express need for higher throughput software to handle results of next generation sequencing studies. MutationForecaster™ is the only efficient and accurate platform for comprehensive, on-demand coding and mRNA splicing mutation analysis on the market.
We find and validate mutations that others cannot.
Contact us or register at mutationforecaster.com.
MutationForecaster is our new, comprehensive genome interpretation suite to interpret and validate mutations that affect mRNA splicing and protein coding. Our products can find and validate mutations that others cannot.
(Click any of the images below to view the paper)
MutationForecaster brings together our world class software in a single easy-to-use interface:
- The popular Automated Splice Site and Exon Definition server (ASSEDA)
- The Shannon pipeline for genome scale mRNA splicing mutation analysis
- Veridical, the first solution for validating splicing mutations by RNASeq
- Variant Effect Predictor for identification of coding changes and predicting their impact
- Cytognomix User Variation Database, to store and compare results obtained with these tools with other sources of genomic variation
- Our Visual analytics Decision Support Tool, for cytogenomic interpretation, and single copy hybridization genomic reagent design
We will be announcing our new MutationForecaster system imminently.
You can register now for a subscription. Sign up!
Veridical is now hosted by Cytognomix. The previous Veridical.org website has been migrated to Veridical.cytognomix.com.
This software product has been integrated into our new MutationForecaster webservice. To validate splicing mutations predicted by the Shannon pipeline, a set of gene variants (in vcf format) and RNASeq data (in bam format) are uploaded for the same individual. Control data are built in, the analysis is automated, and results are returned directly to users. Subscriptions to MutationForecaster will be available from Cytognomix in early 2015.
The standalone software is also available from Cytognomix, which licenses it and provides installation support. To further inquire, contact us at email@example.com.
We have published a new manuscript which has implications for metaphase chromosome epigenetics. The citation is:
Title: Localized, non-random differences in chromatin accessibility between homologous metaphase chromosomes
Authors: Khan A Wahab, Rogan K Peter, Knoll Joan,
Journal: Molecular Cytogenetics.2014, 7:70
We have published a review of the literature on information theory-based splicing mutations. The review includes a large dataset, comprehensive bibliography, and new software – the Splicing Mutation Calculator – for determining the impact of mutations at natural splice sites, based on the published literature. There are multiple citations of this work -
for the Review paper: Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis [v1; ref status: awaiting peer review, http://f1000r.es/4nq] (doi: 10.12688/f1000research.5654.1), 2014.
for the Dataset: F1000Research: Dataset 1. Dataset for mRNA splicing mutations in genetic disease, (doi: 10.5256/f1000research.5654.d382482)