Browsing articles by " Peter Rogan"

December 5, 2014. Scheduled downtime for ASSEDA (Automated Splice Site and Exon Definition Analysis) server

Dec 5, 2014   //   by Peter Rogan   //   News  //  Comments Off

On December 12, 2014, the ASSEDA server will be migrated to a new location and will be unavailable for about 8 hours. The migration is scheduled to begin at 11 PM EST and should be completed by the morning of December 13th.  The migration will ensure the reliability of the hardware that hosts ASSEDA. We appreciate your patience during this process.

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


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,] (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 Source code:

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!

September 3, 2014. Technical presentation to US Patent and Trademark Office

Sep 7, 2014   //   by Peter Rogan   //   News  //  Comments Off

Peter Rogan gave an invited presentation titled: ”Interpreting pathogenic human genome variation: methods, applications and implications,” at the Patent Examiner Technical Training Program at the US Patent and Trademark Office. The presentation was webcasted  to all USPTO offices across the United States.  The program is focused on providing technical training to Patent Examiners, in this case to the Patent Examiners of Technology Center 1600 that examines patent applications on various aspects of biotechnology inventions.

The patent office recognized his contribution: link

August 13, 2014. New Patent Application published

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

US-Patent-Web US Pat. App. No. 13/744459 has been published by the US Patent and Trademark Office. 

The invention is entitled: Stable gene targets in breast cancer and use thereof for optimizing therapy.

Peter Keith RoganJoan Helen Knoll

July 30 2014. Invited presentation at Next Generation Sequencing conference

Jul 31, 2014   //   by Peter Rogan   //   News  //  Comments Off

Peter Rogan, President of Cytognomix has been invited by Oxford Global to present at the 6th Annual Next Generation Sequencing Congress at the Queen Elizabeth II Conference Center in London, UK on Nov. 21, 2014. The oral presentation is titled: “Impact Of Non-coding Mutation Analysis In Hereditary and Somatic Breast Cancer.” In the talk, Dr. Rogan will showcase results of the use of Cytognomix’s software and genomic reagents to obtain new insights into the genomic abnormalities present in breast cancer.

July 23, 2014. New US patent application published on exon definition mutation analysis

Jul 23, 2014   //   by Peter Rogan   //   News  //  Comments Off

US-Patent-WebUS Pat. Application No. 14/154,905 describes our method of predicting cryptic and exon skipping isoforms in mRNA produced by splicing mutations from the combined information contents and the distribution of the splice sites and other regulatory binding sites defining these exons.  Results obtained are highly concordant with result of expression studies.  A paper has been published in Human Mutation

July 13, 2014. Presentations at the 2014 American Society of Human Genetics Conference

Jul 13, 2014   //   by Peter Rogan   //   News  //  Comments Off

Cytognomix will be presenting several papers at the upcoming ASHG annual meeting (October 18-22, 2014, San Diego):

Using information theory to analyze and predict splicing mutations in rare and common diseases: performance and best practices. N.GCaminsky, E. Mucaki and P.K. Rogan

Reversing differences in chromatin accessibility that distinguish homologous mitotic metaphase chromosomes. W.A. Khan, P.K. Rogan, J.H.M. Knoll

Automated Dicentric Chromosome Identification by Machine Learning-based Image Processing. P.K. Rogan, Y. Li, A. Subasinghe, J. Samarabandu, R. Wilkins and J.H. Knoll

Towards the minimal breast cancer genome and its relevance to chemotherapy. S.N. Dorman, J.H. Knoll, K. Baranova, C. Viner, P.K. Rogan

The FANCM c.5791C>T nonsense mutation (rs144567652) induces exon skipping and is a risk factor for familial breast cancer. Paolo Peterlongo ,  Francesca Damiola, Eliseos Mucaki,  Valentina Dall’Olio ,Sara Pizzamiglio  , Irene Catucci ,  Anders Kvist , Paolo Verderio, Mara Colombo , Loris Bernard ,  Hans Ehrencrona, Laura Caleca, Valeria Pensotti , Sylvie Mazoyer, Peter K. Rogan ,Paolo Radice


Please contact us if you would like to meet or discuss this work.

June 12, 2014. New product announcement

Jun 12, 2014   //   by Peter Rogan   //   News  //  Comments Off

MutationForecaster™ ( is Cytognomix’s new web-portal for analysis of all types of mutations, interpretation, comparison and management of genetic variant data.  It is an integrated suite of software products where coding, non-coding, copy number variant analyses can be carried out, compared with published or your own databases, maintained or downloaded.

Stay tuned for more developments about this exciting product…

May 23, 2014. A Comment about Variant Databases

May 24, 2014   //   by Peter Rogan   //   News  //  Comments Off

Variant databases are an essential resource for both clinical and research genomics. Has the variant been reported previously in a patient and if so, what was their phenotype? They are used to exclude benign or common variants as pathogenetic, based on their high frequency in asymptomatic individuals. Many researchers curate variant databases of specific loci, regularly contribute known and new to public databases, and several companies release products aimed at compiling and visualizing this data. Determining the frequency and recurrence of variants can only be done through this compilation procedure.  Clinical labs maintain their own databases and regularly query public and commercial variant repositories to make sense of newly generated sequencing findings. Of course, it’s a lot easier to write up a variant if all one has to do is look it up in a database.

There is a fundamental problem with this approach: in a genome of 3.2 billion nucleotides, there are an infinite number of  possible mutations (single and oligo nucleotide changes on each chromosome). There is no database in existence that can catalog all of these effects, nor predict these effects based on prior knowledge of all of the mutation combinations. Only computational modeling of sequence variant effects can possibly provide a means of evaluting newly discovered mutations without explicit reference to a database of prior variants.  The approaches that Cytognomix has developed complement existing databases by confirming evidence of selection against predicted pathogenic variants (low allele frequencies), but more importantly, can predict deleterious effects when the mutation has not been observed previously.


May 19, 2014. Veridical wins best paper award at two conferences!

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

Coby Viner presented our F1000 paper on the Veridical algorithm and software at the 2014 Compute Ontario 1st Annual Research Conference (Waterloo, Ontario, May  7)  and at the 9th Annual Great Lakes Bioinformatics Conference (Cincinnati, Ohio, May 17). At these conferences, he received the Best Oral Presentation and Best Highlights Presentation award, respectively. This is an impressive achievement, and a testament to the originality and impact of the science.

Watch his presentation at the Compute Ontario conference:

May 14, 2014. Upcoming presentation at the 9th Annual Great Lakes Bioinformatics Conference

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

Coby Viner will be presenting our paper, Validation of Predicted mRNA Splicing Mutations Using High Throughput Transcriptome Data at GL Bio on Saturday May 17th, at 2:30 PM in Rooms 203-204 of Cincinnati Childrens’ Medical Center, Cincinnati Ohio.  The paper was selected as an oral presentation in the Highlights session of the meeting.