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

Aug. 31, 2020. Presentation at the 2020 American Society of Human Genetics meeting

We are giving a platform presentation at the upcoming American Society of Human Genetics virtual meeting #ASHG2020 Session: Personalized Medicine Approaches in Healthcare. Paper: Pathway-extended gene expression signatures integrate novel biomarkers that improve predictions of responses to kinase inhibitors P. K. Rogan(1,2), A. J. Bagchee-Clark(1), E. J. Mucaki(1). 1. Department of Biochemistry, University of Western […]

August 14, 2020. Interview on Scientific Sense podcast

Peter Rogan was interviewed by Gill Eapin for his daily podcast, Scientific Sense, focused on Science & Economics about our research projects about COVID19. Listen at the link below. https://anchor.fm/scientificsense/episodes/Prof–Peter-Rogan–Professor-of-Biochemistry-and-Biostatistics-at-Western-University-ei5i40 #medicine #sarscov2 #covidー19 #medicalsciences #epidemiology #health #geostatistics #hotspots #publichealth #genomics #molecularmechanism

August 7, 2020. Publication of novel molecular mechanism of severe RNA-viral lung infections

We have described and provide evidence for an explanation for how rapid onset, severe RNA viral infections, such as SARS-CoV-2 or Influenza, may develop: Rogan PK, Mucaki EJ and Shirley BC. A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections. F1000Research 2020, 9:943 (https://doi.org/10.12688/f1000research.25390.1) There is an accompanying infographic describing the mechanism, which is cited in […]

July 19, 2020. New analysis of SARS-CoV-2 cases in the United States

Version 3 of Geostatistical Analysis of SARS-CoV-2 in the United States dataset published (http://doi.org/10.5281/zenodo.3950057). Contains hotspot and cluster analysis of daily case counts across all US counties from Marcy 25-July 13, 2020.                             #covid-19 #SARSCov2 #geostatistics #hotspot

July 13, 2020. New article on Virtual Molecular Tumor Boards from the Variants in Cancer Consortium

CytoGnomix has coauthored a new article on collaborative gene variant interpretation applied to selection of cancer therapy: Shruti Rao, Beth Pitel, Alex H Wagner, Simina M Boca, Matthew McCoy, Ian King, Samir Gupta, Ben Ho Park, Jeremy L Warner, James Chen, Peter K Rogan, Debyani Chakravarty, Malachi Griffith, Obi L Griffith, Subha Madhava. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices.  DOI: […]

Geostatical Biodosimetry

We have consolidated our geostatistical biodosimetry contributions at Grow Kudos. We have been developing a new application of this technology for tracking hotspots of infections during the current COVID-19 pandemic. This animation shows geostatistically significant hotspot counties in the US relative to 3 nearest neighbors from March through June 2020.  Please stay tuned for more: