Browsing articles by " Peter Rogan"

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

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

ssmdtalk

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 <http://www.sciencedirect.com/science/article/pii/S1672022913000296>; Dorman et al. 2014 <http://www.nature.com/srep/2014/141114/srep07063/full/srep07063.html>; Mucaki et al. 2011 <http://www.ncbi.nlm.nih.gov/pubmed/21523855>; Mucaki et al. 2013 <http://onlinelibrary.wiley.com/doi/10.1002/humu.22277/full>, Viner et al. 2014 <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983938.1/>).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 <http://f1000research.com/articles/3-282/v1>), 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 <http://mutationforecaster.com/> 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:

http://blog.f1000research.com/2015/03/17/interpreting-genomic-variants-in-rare-and-common-diseases/

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 mutationforecaster.com.

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 MutationForecaster.com.

January 17. MutationForecaster is launching…

Jan 17, 2015   //   by Peter Rogan   //   News  //  Comments Off

We will be announcing our new MutationForecaster system imminently.

You can register now for a subscription. Sign up!

December 30, 2014. Veridical software status update

Dec 30, 2014   //   by Peter Rogan   //   News  //  Comments Off

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  info@cytognomix.com.

November 18, 2014. Differential accessibility of scFISH probes to metaphase chromosomes published.

Nov 19, 2014   //   by Peter Rogan   //   News  //  Comments Off

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
DOI: 10.1186/s13039-014-0070-y

URL: http://www.molecularcytogenetics.org/content/7/1/70

November 18, 2014. New review article on splicing mutation information analysis

Nov 18, 2014   //   by Peter Rogan   //   News  //  Comments Off

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)

for the Software:   The Splicing Mutation Calculator (SMC) is available at http://splicemc.cytognomix.com. Source code: http://dx.doi.org/10.5281/zenodo.12422

November 14, 2014. New paper on lymph node metastatic breast cancer uses MutationForecaster system

Nov 14, 2014   //   by Peter Rogan   //   News  //  Comments Off

Cytognomix’s technology key to new publication on origin of metastasis in breast cancer:

Dorman S, Viner C, Rogan PK. Splicing mutation analysis reveals previously unrecognized pathways in lymph node-invasive breast cancer, Nature Scientific Reports, 4: 7063 (DOI: 10.1038/srep07063), 2014.

Press Release. Dorman et al. Nat. Sci. Reports 2014

October 14, 2014. New paper in press on the epigenetics of metaphase chromosomes

Oct 17, 2014   //   by Peter Rogan   //   News  //  Comments Off

Using our patented ab initio scFISH probes, Cytognomix and Western University researchers have discovered important differences between paired chromosomes. No other product on the market can detect these chromosome features. The following article has been accepted for publication in a leading open access journal:

Khan W, Rogan PK, and Knoll JHM. Localized, Non-random Differences in Chromatin Accessibility between Homologous Metaphase Chromosomes, Mol. Cytogenetics, in press.

Stay tuned for the URL of the published paper. It should be available shortly!

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