Author Archives: Peter Rogan

January 25, 2024. Appreciation of Cytognomix’s COVID-19 research studies by the government of Ontario

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Peter Rogan, President of Cytognomix,  accepted a Certificate of Appreciation from Hon. Sylvia Jones, Deputy Premier and Minister of Health of the Province of Ontario for our work on community COVID-19 outbreaks and their risk factors. This work was carried out in response to the Ministry’s Challenge Questions initiative to researchers, clinical professionals, hospitals and companies addressing how to approach this disease.  Our work contributed to answering the challenge questions: Can we better predict the trajectory of COVID-19 across multiple pandemic waves? What are the drivers of future pandemic waves?

 In the letter that accompanied the certificate, the Minister wrote:

Thanks to your research, we are able to understand the importance of early identification of probable COVID-19 hotspots and the available mitigation strategies to limit rapid spread of COVID-19. Having contributions such as yours allows us to get the right information to the right people at the right time to support the COVID-19 pandemic response.

Our geostatistical epidemiology analyses of incidence and locations of infected individuals during Waves 1-3 provided the Ministry with key insights to support Ontarians during the COVID-19 pandemic.

Our published findings are described in:
Mucaki EJ, Shirley BC and Rogan PK. Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada. F1000Research 2022, 10:1312 (https://doi.org/10.12688/f1000research.75891.2).
We are grateful that the Ministry will be able to make use of our research findings and software for management of future disease outbreaks.
Certificate of Appreciation - Ministry of Health Ontario

Oct. 4, 2023. Radiobiology textbook published

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We have contributed our work on transcriptomics to the chapter on Molecular Radiation Biology in:

Radiobiology Textbook (editor Sarah Baatout), published by Springer in October 2023 (open access; link: https://link.springer.com/book/10.1007/978-3-031-18810-7). The citation for the chapter is:

Judith Reindl, Ana Margarida Abrantes, Vidhula Ahire, Omid Azimzadeh, Sarah Baatout, Ans Baeyens, Bjorn Baselet, Vinita Chauhan, Fabiana Da Pieve, Wendy Delbart, Caitlin Pria Dobney, Nina Frederike Jeppesen Edin, Martin Falk, Nicolas Foray, Agnès François, Sandrine Frelon, Udo S Gaipl, Alexandros G Georgakilas, Olivier Guipaud, Michael Hausmann, Anna Jelinek Michaelidesova, Munira Kadhim, Inês Alexandra Marques, Mirta Milic, Dhruti Mistry, Simone Moertl, Alegría Montoro, Elena Obrador, Ana Salomé Pires, Roel Quintens, Nicholas Rajan, Franz Rödel, Peter Rogan, Diana Savu, Giuseppe Schettino, Kevin Tabury, Georgia I Terzoudi, Sotiria Triantopoulou, Kristina Viktorsson, Anne-Sophie Wozny (2023). Molecular Radiation Biology. In Radiobiology Textbook (pp. 83-189). Cham: Springer International Publishing.

Sept. 19, 2023. Democratizing ADCI as cloud-based software

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We have published a new article describing use of the Automated Dicentric Chromosome Identifier and Dose Estimator (ADCI) as a web-based application:

Ben C Shirley, Eliseos J Mucaki, Joan H M Knoll, Peter K Rogan, Radiation exposure determination in a secure, cloud-based online environment, Radiation Protection Dosimetry, Volume 199, Issue 14, September 2023, Pages 1465–1471, https://doi.org/10.1093/rpd/ncac266

Imagine working with ADCI just by bringing your own metaphase image data.  We’ve developed a system where your data can be stored securely in your local region. This product is offered by term-length subscriptions, which can significantly reduce cost for short term projects.  The dosimetry can either be carried out by yourself or through consultation (fee-based) with CytoGnomix.

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI on dedicated computer hardware. Image processing and selection, calibration curve generation, and dose estimation of 9 test samples completed in < 2 days. ADCI Online has the capacity to alleviate analytic bottlenecks in intermediate-to-large radiation incidents. Multiple cloned software instances configured on different cloud environments accelerated dose estimation to within clinically relevant time frames.

Nov. 15, 2022. New US Patent on radiation biodosimetry

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The US Patent and Trademark office as issued our patent number 11,501,545 titled “Smart Microscope System for Radiation Biodosimetry.”  It has the same title as our previous patent no. 10,929,641, but there are some important differences. This one claims a broader spectrum of applications for estimation of absorbed radiation dose because it doesn’t require the microscope itself, just the data produced by the microscope. Also, it includes a claim for estimation of whole or partial body ionizing radiation (the latter of which is commonly used to treat patients in radiation oncology).

US Patent 11,501,545

Smart Microscope System for Radiation Biodosimetry

September 9, 2022. Update on US Patent Application “Smart microscope system for radiation biodosimetry”

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Our patent application, US Patent Application Serial Number 17/137,317,  has had all claims allowed by the US Patent and Trademark office. This application covers the method underlying our ADCI Radiation biodosimetry software system. New claims cover partial body exposures, which are typical in radiation therapy. In addition, this invention covers applications of the technology which do not require interaction with the microscope system software, and can be used as a standalone system. The patent should be issued within the next several months.

Dec. 8, 2021. New preprint about detecting COVID19 transmission earlier

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The #Omicron variant of SARS-CoV-2 spreads fast and contact tracing may prove difficult. Here is our new preprint introducing a new geostatistical approach to find disease hotspots earlier:

Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada.
 
Authors:Eliseos J. Mucaki, Ben C. Shirley, Peter K Rogan
 
medRxiv 2021.12.06.21267360; 
doi: https://doi.org/10.1101/2021.12.06.21267360
 

Figure 8.  Multi-node Directional Networks of Closely Situated Clustered Postal Codes. Directional acyclic graphs (left) organize adjacent high-case clustered PC streaks within the same FSAs ordered according to their occurrence. Panels indicate PCs within (A) M4H and (B) M9V in Toronto during wave 2. Each connection (or ‘edge’) linking two PCs represents a pair of clustered streaks occurring within 30 days of each other (all significant PC pairs are indicated in Extended data29, Section 1 – Table S6). Labels on each edge indicate the duration (in days) separating adjacent PC pairs and the number of cases which occurred in the combined streaks (“dates.cases”). Negative values, when present, indicate the number of overlapping days of concurrent streaks in pairs of PCs. Arrows indicate the temporal order of these paired streaks (from earlier to the later streak). Maps (right) show the physical locations of each PC within the corresponding networks.

October 21, 2021. New article on radiation gene expression signatures in press

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We have updated our preprint:

Improved radiation expression profiling in blood by sequential application of sensitive and specific gene signatures (biorxiv.org/content/10.110

This version of the article has now been accepted for publication in the International Journal of Radiation Biology. (link to: Improved radiation expression profiling…pdf)

October 5, 2021. New conference summary article from ConRad 2021 published

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Patrick Ostheim, Sally A. Amundson, Christophe Badie, Dimitry Bazyka, Angela C. Evans, Shanaz A. Ghandhi, Maria Gomolka, Milagrosa López Riego, Peter K. Rogan, Robert Terbrueggen, Gayle E. Woloschak, Frederic Zenhausern, Hanns L. Kaatsch, Simone Schüle, Reinhard Ullmann, Matthias Port & Michael Abend (2021) Gene Expression for Biodosimetry and Effect Prediction Purposes: Promises, Pitfalls and Future Directions – Key Session ConRad 2021 -, International Journal of Radiation Biology, DOI: 10.1080/09553002.2021.1987571