Browsing articles by " Peter Rogan"

May 22, 2015. MutationForecaster receives US Trademark

May 24, 2015   //   by Peter Rogan   //   News  //  Comments Off

On May 12, the US Patent and Trademark Office awarded CytoGnomix a trademark for:



Registration of supplemental mark

May 21, 2015. Platform presentation at Compute Ontario Research Day

May 16, 2015   //   by Peter Rogan   //   News  //  Comments Off

Dr. Peter Rogan’s laboratory at the University of Western Ontario will present:

 Discovery of Primary, Cofactor, and Novel Transcription Factor Binding Site Motifs by Recursive, Thresholded Entropy Minimization

by Ruipeng Lu 1, Eliseos Mucaki 2, and Peter Rogan 1,2,3.    Departments of (1) Computer Science and (2)Biochemistry, University of Western Ontario, and (3)Cytognomix Inc., London ON

at Compute Ontario (abstract), Conestoga College, Cambridge Ontario, Canada. The presentation is in Room A2107 at 13:55 at the Conestoga College Institute of Technology and Advanced Learning.

May 14, 2015. Presentation at the Great Lakes Chromosome Conference

May 13, 2015   //   by Peter Rogan   //   News  //  Comments Off

Dr. Joan Knoll, Chief Scientific Officer of Cytognomix, will present:

Localized, Structural Differences in Condensation of Homologous Metaphase Chromosomes and the Underlying Mechanism

at the 53rd Annual Great Lakes Chromosome Conference at the University of Toronto, Ontario, Canada.

April 30. Sale of MutationForecaster subscription

May 3, 2015   //   by Peter Rogan   //   News  //  Comments Off

Cytognomix has sold an annual subscription to MutationForecaster, our comprehensive solution for next generation sequencing based mutation interpretation, to a hospital in Toronto, Ontario Canada. This customer was a previous subscriber to the Automated Site and Exon Definition Server, which is embedded in MutationForecaster and no longer available as standalone software.

April 30, 2015. Sale of Shannon mRNA splicing mutation pipeline software license

May 2, 2015   //   by Peter Rogan   //   News  //  Comments Off

Cytognomix’s standalone version of the Shannon mRNA splicing mutation analysis pipeline is distributed through Qiagen CLC bio as a plug-in for their Genomics Workbench and Server software.This product was recently purchased by Dr. Hidetaka Eguchi at the Research Center for Genomic Medicine, Saitama Medical University, Japan.

April 6, 2015. New paper published on cancer of unknown primary

Apr 7, 2015   //   by Peter Rogan   //   News  //  Comments Off

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 MBSarma SRodrigues GBRogan PKMahmud SMWinquist EBrackstone MZaric GS.  Acta Oncol. 2015 Mar 31:1-7.   (link)

April 3, 2015. Video tutorials available for MutationForecaster

Apr 4, 2015   //   by Peter Rogan   //   News  //  Comments Off

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:

Feb. 20, 2015. Presentation at Schulich School of Medicine and Dentistry

Mar 26, 2015   //   by Peter Rogan   //   News  //  Comments Off


March 11, 2015. Invited presentation at the University of Ontario Institute of Technology

Mar 22, 2015   //   by Peter Rogan   //   News  //  Comments Off
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 <>; Dorman et al. 2014 <>; Mucaki et al. 2011 <>; Mucaki et al. 2013 <>, Viner et al. 2014 <>).Our patented software computes changes in information content in DNA or RNA sequences. These changes tell us which sequences disrupt the regulation of genes and how severe these changes are.   Our methods have been validated in hundreds of published studies (Caminsky et al. 2014 <>), and use proven information theory, one of the most important scientific advances of the last century. I will introduce a single system that amalgamates several of our software products, and which also queries existing public databases and store results for users. MutationForecaster <> provides basic capabilities offered by others, but also offers proven mutation interpretation  methods not available elsewhere. This leads to more comprehensive mutation results and ultimately, a more complete understanding of the dysregulation of disease genomes.

March 17, 2015. Review article on mRNA splicing mutations highlighted on F1000Research blog

Mar 18, 2015   //   by Peter Rogan   //   product, Software  //  Comments Off

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)

March 5, 2015. Interest in Mutation Forecaster™

Mar 5, 2015   //   by Peter Rogan   //   News  //  Comments Off

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

Feb 25, 2015   //   by Peter Rogan   //   News  //  Comments Off

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.

February 8, 2015. Early adoption of the MutationForecaster system

Feb 8, 2015   //   by Peter Rogan   //   News  //  Comments Off

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

February 2, 2015. The Cytognomix MutationForecaster system

Feb 3, 2015   //   by Peter Rogan   //   News  //  Comments Off

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.

Here`s proof:

(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
Contact us about obtaining a subscription or sign up at