Genome-Scale Variant Interpretation

Automated Radiation Dose Estimation

Mission Statement

MutationForecaster® (mutationforecaster.com) is Cytognomix’s patented web-portal for analysis of all types of mutations – coding and non-coding- including interpretation, comparison and management of genetic variant data. It’s a fully automated genome interpretation solution for research, translational and clinical labs.

Run our world-leading genome interpretation software on your exome, gene panel, or complete genome (Shannon transcription factor and splicing pipelines, ASSEDA, Veridical) with the Cytognomix User Variation Database and  Variant Effect Predictor.  With our integrated suite of software products, analyze coding, non-coding, and copy number variants, and compare new results with existing or your own database.  Select predicted mutations  by phenotype using articles with CytoVisualization Analytics.  With Workflows,  automatically perform end-to-end analysis with all of our software products.  Download an 1 page overview of MutationForecaster® (link)

Subscribe and analyze your own data via the cloud or… Don’t want to run your own analyses on MutationForecaster®? Let us do it for you with our Bespoke Analysis Service.

Experience our suite of genome interpretation products through a free trial of MutationForecaster®. Once you register, we provide datasets from our peer-reviewed publications to evaluate these software tools.

Automated radiation biodosimetry

Ionizing radiation produces characteristic chromosome changes. The altered chromosomes  are known as dicentric chromosomes [DCs]). DC biodosimetry is approved by the IAEA for occupational radiation exposure, radiation emergencies, or monitoring long term exposures.  The DC assay can also monitor effects of interventional radiation therapies.

Cytognomix has developed  a novel approach to find DCs (TBME).  The Automated Dicentric Chromosome Identifier and Dose Estimator (ADCI) software  works on multiple platforms and uses images produced by any of the existing automated metaphase capture systems found in most cytogenetic laboratories. ADCI is now available for for trial or  purchase (link).  Or contact us for details (pricing).

ADCI* uses machine learning to distinguish monocentric and dicentric chromosomes (Try the Dicentric Chromosome Identifier web app). With novel image segmentation, ADCI has become a fully functional cytogenetic biodosimetry system. ADCI takes images from metaphase scanning systems,  selects high quality cells, identifies dicentric chromosomes, builds biodosimetry calibration curves, and estimates exposures.  ADCI fulfills the criteria established by the IAEA for accurate triage biodosimetry of a sample in less than an hour. The accuracy is comparable to an experienced cytogeneticist. Check out our online user manual: wiki.

We find and validate mutations and gene signatures that others cannot with advanced,  patented genomic bioinformatic technologies. Cytognomix continues our  long track record of creating technologies for genomic medicine. We anticipate and implement the needs of the molecular medicine and genomics communities.

Predict chemotherapy outcomes

Pharmacogenomic responses to chemotherapy drugs can be predicted by supervised machine learning of expression and copy number of relevant gene combinations. Since 2015,  CytoGnomix has used biochemical evidence to derive gene signatures from changes in gene expression in cell lines, which can subsequently be examined in patients that have been treated with the same drugs. We have derived signatures for 30 different commonly used drugs.  Try out out our online predictor:  https://chemotherapy.cytognomix.com. 

Quantifying responses to ionizing radiation with gene expression signatures.

Gene signatures derived by machine learning have low error rates in externally validated, independent radiation exposed data. They exhibit high specificity and granularity for dose estimation in humans and mice.  These signatures can be designed to avoid the effects of confounding, comorbidities which can reduce specificity for detecting radiation exposures. See: https://f1000research.com/articles/7-233/v2

Single copy genomic technologies

Latest Posts

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

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

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 […]

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

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 […]

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

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 […]

August 13, 2014. New Patent Application published

 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  

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

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 […]