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
- Customized genomic microarrays
- Ultrahigh resolution FISH probes (article):
- Microarray-based comparative genomic hybridization (aCGH) can use SC technology to increase reproducibility and reduce cost per sample.
Latest Posts
January 21, 2013. Paper about Shannon pipeline accepted for publication in Genomics, Proteomics, and Bioinformatics.
Interpretation, stratification and validation of sequence variants affecting mRNA splicing in complete human genome sequences. Genomics, Proteomics, and Bioinformatics, 11:77-85, 2013. Ben C. Shirley, Eliseos J. Mucaki, Tyson Whitehead, Paul I. Costea, Pelin Akan, Peter K. Rogan. Information theory-based methods have been shown to be sensitive and specific for predicting and quantifying the effects of non-coding […]
November 12, 2012. Paper accepted for publication in Cytogenetics and Genomics
“Relating centromeric topography in fixed human chromosomes to alpha-satellite DNA and CENP-B distribution: apply for credit with bad creditpayday loan in calgary Authors: Khan W., Chisholm R., Tadayyon S., Subasinghe A., Norton P., Samarabandu J., Johnston LJ., Knoll JH., Rogan PK.
January 11, 2013. New paper accepted for publication in Nucleic Acids Research
“Expanding probe repertoire and improving reproducibility in human genomic hybridization” by S. Dorman, B. Shirley, J. Knoll, and P. Rogan has been accepted for publication by the journal Nucleic Acids Research. In this paper, we use Cytognomix’s patented ab initio sc probe technology to develop and validate a novel classes of FISH probes, genomic microarrays […]
January 4, 2013. Paper: “Predicting mRNA transcript isoforms derived from splicing mutations”, ASSEDA server
guaranteed lendingfast cash online payday loans “Prediction of mutant mRNA splice isoforms by information theory-based exon definition,” by Eliseos Mucaki, Ben Shirley and Peter Rogan has been accepted for publication by the journal Human Mutation. Abstract. Mutations that affect mRNA splicing often produce multiple mRNA isoforms, resulting in complex molecular phenotypes. Definition of an exon […]
November 7, 2012. Presentation at 2012 meeting of the American Society of Human Genetics.
Strategy for Identification, Prediction, and Prioritization of Non-Coding Variants of Uncertain Significance in Heritable Breast Cancer P. K. Rogan1,2,4, E. J. Mucaki1, A. Stuart3, N. Bryans2, E. Dovigi1, B. C. Shirley2, C. Viner2, J. H. Knoll3,4, P. Ainsworth4. Departments of Biochemistry1, Computer Science2, and Pathology3 Western University, and Cytognomix Inc4, London, ON N6A 2C1 Canada. […]
October 17, 2012. Automating cytogenetic biodosimetry
Cytognomix has established partnerships to develop advanced high throughput software and microscope systems to automate cytogenetic biodosimetry in the event of a mass casualty radiation event. Biodosimetry laboratory partners include Health Canada and Atomic Energy of Canada Ltd. Software development for image processing of chromosome images is being carried out at the Schools of Engineering […]
Oct 5, 2012. New Product: Shannon pipeline ….
… for Human mRNA splicing mutation analysis is now available through our distributor, CLC Bio LLC. payday loans online easy Try it now!
June 26, 2012. New US Patent
US Patent 8,209,129 has issued on single copy DNA probes which include divergent repetitive sequences, thus significantly extending the portions of the genome that can be used for such probes beyond traditional single copy sequences. bad credit loans guaranteed The technology also increases the density of genomic DNA probes for higher resolution genetic analysis beyond […]
