Browsing articles by " Peter Rogan"

Sept. 23, 2016. Notice of Allowance of claims for US patent application

Sep 24, 2016   //   by Peter Rogan   //   News  //  Comments Off

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:

 Park et al. Structural and genic characterization of stable genomic regions in breast cancer: relevance to chemotherapy 2012.

graphicalabstractParketal

 

 

 

 

 

 

 

 

August 31, 2016. New publication on predicting outcomes of hormone and chemotherapy in breast cancer

Aug 31, 2016   //   by Peter Rogan   //   News  //  Comments Off
Rezaeian I, Mucaki EJ, Baranova K et al. Predicting Outcomes of Hormone and Chemotherapy in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study by Biochemically-inspired Machine Learning. F1000Research 2016, 5:2124 (doi:10.12688/f1000research.9417.1)
Figure 2

August 8-12, 2016. Presentation about metaphase chromosome epigenetics

Aug 13, 2016   //   by Peter Rogan   //   News  //  Comments Off

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.

July 29, 2016. The MutationForecaster Value Proposition

Jul 29, 2016   //   by Peter Rogan   //   News  //  Comments Off

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.

July 13, 2016. New publication on Automated Estimation of Radiation Exposure

Jul 13, 2016   //   by Peter Rogan   //   News  //  Comments Off

RoganetalRPD2016cover

 

 

 

 

 

 

 

 

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.

 

July 1, 2016. Article published on Centromere Detection in Human Metaphase Chromosomes

Jul 1, 2016   //   by Peter Rogan   //   News  //  Comments Off

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, 5:1565 (doi:10.12688/f1000research.9075.1)   URL Link.

June 6, 2016. New paper on automated biodosimetry to be published

Jun 4, 2016   //   by Peter Rogan   //   News  //  Comments Off

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:

Picture1

May 6, 2016. Upcoming public presentations

May 7, 2016   //   by Peter Rogan   //   News  //  Comments Off
  • 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.

April 28, 2016. Press release

Apr 28, 2016   //   by Peter Rogan   //   News  //  Comments Off

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. PressreleaseApril282016JPG

Other press outlets:

 

April 26, 2016. Grant funding received for chromosome structure studies using Cytognomix ab initio scDNA probes

Apr 26, 2016   //   by Peter Rogan   //   News  //  Comments Off

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

Apr 11, 2016   //   by Peter Rogan   //   News  //  Comments Off

BMCMedGenomics

 

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

Mar 30, 2016   //   by Peter Rogan   //   News  //  Comments Off

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

Mar 23, 2016   //   by Peter Rogan   //   News  //  Comments Off

Peer-reviewed article in Early View in the journal Human Mutation:   Link

Earlyview

March 15, 2015. Funding from the Build-in-Canada Innovation Program

Mar 16, 2016   //   by Peter Rogan   //   News  //  Comments Off

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).

BCIP announcement