Dr. Peter K. Rogan presented “Reversing chromatin accessibility differences that distinguish homologous mitotic meetaphase chromosomes,”at the Gordon Research Conference on DNA Topoisomerases in Biology and Medicine at Sunday River in Newry, ME, United States.
MutationForecaster is catching on. Researchers, clinicians and commercial laboratories are realizing the value of being able to detect and interpret mutations that other platforms miss. Cytognomix has picked up multiple new subscribers from Germany, Switzerland, Australia, China, and Canada this year, and subscription renewals from last year. Cytognomix continues to push the envelope, for the first time publishing papers describing a Unified framework for analyzing gene variants in non-coding and coding gene regions and applying this framework in a large clinical study of inherited breast and ovarian cancer. These reports have led to invitations to contribute our unique expertise to interpretation of results of large inherited cancer genetic studies in the United States and in France. These ongoing projects are showing that the effects of mutations we predict by information theory-based approaches can be confirmed with corresponding gene expression studies in collaborators’ laboratories. What are we working on next for the MutationForecaster suite?
This will give our customers will have access to our latest for analysis, filter and interpret their own data. Wouldn’t you like access to these capabilities? Subscribe! NGS sequencing itself may be more accessible and economical today than it has ever been. What we’ve learned from our complete gene sequencing projects is that this success comes with rapidly expanding collections of gene variants, many of which have never been reported before or have been found only rarely. Comprehensive sequencing significantly magnifies the challenges of accurate genome interpretation. Our approach allows you to focus these large collections on only the most functionally relevant variants for review, experimental validation, and prioritization. See what others think of MutationForecaster to gain access to our patented technologies. They are only available from Cytognomix.
The paper can be accessed at: abstract or full text (web), or downloadable pdf .
Please contact us if you would like a copy for non-commercial use.
Our previous preprint in bioRxiv on centromere detection has been published in F1000Research:
Subasinghe A, Samarabandu J, Li Y et al. Centromere detection of human metaphase chromosome images using a candidate based method. F1000Research 2016, 5
Our paper, “Radiation Dose Estimation by Automated Cytogenetic Biodosimetry” by Peter K. Rogan, Yanxin Li, Ruth Wilkins, Farrah N. Flegal, and Joan H. M. Knoll, has been accepted for publication in the journal Radiation Protection Dosimetry.
Figure 1. Representative processed metaphase image in ADCI:
Video interview with Eliseos John Mucaki and Peter K Rogan by Cara Campbell on CTV News-London Ontario. April 29, 2016.
(http://london.ctvnews.ca/video?clipId=857860&binId=1.1137789&playlistPageNum=1)
The University of Western Ontario has issued a press release about our studies describing a unified framework for prioritization of mutations in breast and ovarian cancer. 
Other press outlets:
Discovery Grant from Natural Sciences and Engineering Research Council received for “Unravelling the metaphase epigenome: Differences in DNA accessibility between homologous chromosomes.” Joan Knoll, Principal Applicant and Peter Rogan, Co-applicant have been awarded 5 years of funding (2016-21) for this project.
Our paper, which describes a generalized information theory-based approach for mutation analysis of protein-nucleic binding sites, has been published:
Mucaki, E, Caminsky N, Perri A, Lu R, Laederach A, Halvorsen, M, Knoll, JHM, Rogan PK. A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer, BMC Medical Genomics, 9:19, 2016. DOI: 10.1186/s12920-016-0178-5. (link to paper) (PubMed citation)
Through a pan-Canadian collaboration led by Greg Zaric, we have published:
Cost-effectiveness of using a gene expression profiling test to aid in identifying the primary tumour in patients with cancer of unknown primary. M B Hannouf, E Winquist, S M Mahmud, M Brackstone, S Sarma, G Rodrigues, P Rogan, J S Hoch and G S Zaric.
The Pharmacogenomics Journal advance online publication 29 March 2016; doi: 10.1038/tpj.2015.94 (Link)
Cytognomix pre-qualifies for funding from Build in Canada Innovation Program. Our proposal to test the Automated Dicentric Chromosome Identifier with Health Canada and Canadian Nuclear Laboratories has been approved by Public Works and Government Services Canada (link).
Our paper:
“A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer,” by
Eliseos J. Mucaki; Natasha G. Caminsky; Ami M. Perri; Ruipeng Lu; Alain Laederach; Matthew Halvorsen; Joan H.M. Knoll; and Peter K. Rogan
has been accepted for publication in the journal, BMC Medical Genomics.
A preprint of this article is currently available at BioRxiv: http://biorxiv.org/content/early/2015/11/11/031419.
Our new paper on interpretation of gene variants in inherited breast and ovarian cancer has been accepted for publication in the journal, Human Mutation as a Research Article.
“Prioritizing variants in complete Hereditary Breast and Ovarian Cancer (HBOC) genes in patients lacking known BRCA mutations,” by Natasha G. Caminsky1, Eliseos J. Mucaki1, Ami M. Perri1, Ruipeng Lu2, Joan HM. Knoll3,4 and Peter K. Rogan1,2,4,5.
1Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada, N6A 2C1, 2Department of Computer Science, Faculty of Science, Western University, London, Canada, N6A 2C1, 3Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Canada, N6A 2C1, 4Cytognomix Inc. London, Canada, 5Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, Canada, N6A 2C1
A preprint of this article is published at http://biorxiv.org/content/early/2016/02/09/039206
We have added new capabilities to Variant Effect Predictor. Exome sequencing reveals many variants that have little or no effect on phenotype. You can remove these variants in MutationForecaster with our new stringency filters. Different default levels of filtering are offered. These can also be customized based on allele frequencies, predicted SIFT, Polyphen, variant type (eg. synonymous change), or protein coding domain containing the variant.
