December 5, 2014. Scheduled downtime for ASSEDA (Automated Splice Site and Exon Definition Analysis) server
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.
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)
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.
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!
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
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.
|Inventors||Peter Keith Rogan, Joan Helen Knoll|
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.
US 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
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.G. Caminsky, 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.
MutationForecaster™ (http://www.mutationforecaster.com) 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…
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.
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:
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.
- December 18, 2014. Best poster award for cytogenomics visual analytics decision support tool
- December 5, 2014. Scheduled downtime for ASSEDA (Automated Splice Site and Exon Definition Analysis) server
- November 18, 2014. Differential accessibility of scFISH probes to metaphase chromosomes published.
- November 18, 2014. New review article on splicing mutation information analysis