The Atlas of Science has published a simplified description for the lay public of our 2016 study of gene variants in hereditary breast and ovarian cancer in BMC Medical Genomics (citation below).
Please see: Focusing on the most relevant gene variants in inherited breast and ovarian cancer by Eliseos Mucaki and Peter Rogan.
Original technical paper: A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer. Mucaki EJ, Caminsky NG, Perri AM, Lu R, Laederach A, Halvorsen M, Knoll JH, Rogan PK BMC Med Genomics. 2016 Apr 11
Cytognomix has received a notice of allowance of all claims for US Pat. App. Ser. No. 13/744,459:
Stable gene targets in breast cancer and use thereof for optimizing therapy
Inventors: Peter K. Rogan and Joan H.M. Knoll
The patent is based on our previous publication:
August 31, 2016. New publication on predicting outcomes of hormone and chemotherapy in breast cancer
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?
- Adding to our Interactive Report generator to summarize key findings (currently available at MutationForecaster).
- Incorporating our Unified Analytical Framework for complete gene and genome sequence analysis.
- Bespoke Consulting Services to assist you with variant analysis using our software products
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.
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:
- Peter K. Rogan, Yanxin Li, Ruth Wilkins, Farrah Flegal, Joan HM Knoll. Radiation Dose Estimation by Automated Cytogenetic Biodosimetry, Great Lakes/Canadian Bioinformatics Conference (CCBC/GLBIO). May 16, 2016. University of Toronto (Platform Presentation).
- Peter K. Rogan. Radiation Dose Estimation by Automated Cytogenetic Biodosimetry. Platform presentation. Great Lakes Chromosome Conference. May 20, 2016. University of Toronto.
- Peter K. Rogan. Cisplatin Response Prediction in Recurrent Bladder Cancer using Biochemically-inspired Machine Learning. Oral and Poster presentations. 3rd International Molecular Pathological Epidemiology Meeting. May 13, 2016. Dana-Farber Cancer Institute, Boston.
- Rezaeian I, Mucaki E, Baranova K, Quang HP, Angelov D, Ilie L, Ngom A, Rueda L, Rogan PK. Predicting outcome of hormone and chemotherapy in the METABRIC breast cancer study. Great Lakes/Canadian Bioinformatics Conference (GLBIO/CCBC). May 16, 2016. University of Toronto.
- Baranova K, Mucaki EJ, Angelov D, Lizotte D, and Rogan PK. Cisplatin Response Prediction in Recurrent Bladder Cancer using Biochemically-inspired Machine Learning. Great Lakes/Canadian Bioinformatics Conference (GLBIO/CCBC). May 16, 2016. University of Toronto.
- Lu R and Rogan PK. Predicting cis-regulation in human promoters by information density-based clustering of heterotypic transcription factor binding sites. Great Lakes/Canadian Bioinformatics Conference (GLBIO/CCBC). May 16, 2016. University of Toronto.
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:
- Medical Xpress
- Science Newsline
- Science Codex
- Ovarian cancer and us
April 26, 2016. Grant funding received for chromosome structure studies using Cytognomix ab initio scDNA probes
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.
April 11, 2016. New paper on analysis of variants of uncertain significance in hereditary breast & ovarian cancer
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)
March 29, 2016. New publication on cost effectiveness of gene expression microarray testing in cancer diagnosis
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)
March 23, 2016. Final version of article about prioritizing mutations in inherited breast cancer is online
Peer-reviewed article in Early View in the journal Human Mutation: Link
- October 19, 2016. Publication in Atlas of Science for the layperson
- Sept. 23, 2016. Notice of Allowance of claims for US patent application
- August 31, 2016. New publication on predicting outcomes of hormone and chemotherapy in breast cancer
- August 8-12, 2016. Presentation about metaphase chromosome epigenetics