Transcriptome Sciences Inc

Transcriptome Sciences Inc Better clinical care through precision medicine

Our Vision:

To change care through molecular diagnostics.

Our Mission:

To develop novel molecular diagnostic tools that will change how healthcare providers manage their patients.

Transcriptome Sciences Inc

About Us

  • History

    Transcriptome Sciences Inc. (TSI), a privately held Alberta company incorporated in 2008, is the commercial spin-off of the Alberta Transplant Applied Genomics Centre (ATAGC) at the University of Alberta in Edmonton, Canada. Transcriptome (TSI) is dedicated to developing a new understanding of disease mechanisms through the molecular analysis of transplanted organ biopsies, and to the commercialization of these discoveries. The result is an extensive and growing proprietary database consisting of clinical, histological, and gene expression findings from these biopsies, supplemented with patient outcomes. Transcriptome’s (TSI) database forms the basis of the Molecular Microscopetm Diagnostic (MMDxtm) system, a novel central diagnostic process for the assessment of organ disease states with unparalleled accuracy.

  • Personnel

    Transcriptome (TSI) is dedicated to commercializing its unique capabilities in the molecular basis of disease states to provide improved treatments and outcomes for patients.

    • Philip Halloran

      CEO and CSO

      Dr. Halloran is a clinician scientist with extensive research experience in basic immunology, clinical research, and microarrays. He currently leads the Alberta Transplant Applied Genomics Center (ATAGC) and is a Professor of Medicine (Nephrology) at the University of Alberta in Edmonton. He has more than 400 peer reviewed publications in transplantation and inflammatory diseases. He is an officer of the Order of Canada, a Fellow of the Royal Society of Canada, was founding editor of the American Journal of Transplantation, the first recipient of the Paul Terasaki Prize, and an elected member of the American Society for Clinical Investigation.

      He holds an MD from the University of Toronto and a PhD from the University of London.

    • Robert Polakowski

      Business and Operations Manager

      Dr. Polakowski is an experienced life sciences professional with broad skills spanning R&D, Product Development, Technology Transfer and Business Development. He has worked in Alberta life sciences sector for over 14 years, including local health technology start ups. He possesses a solid understanding of health technology commercialization and innovation. At TSI he is responsible for daily company operations, business development, partner relations, finances and HR.

      He holds a BSc in Chemistry from McMaster University and a PhD in Chemistry from University of Alberta.

    • Michael Trites

      Research Technician

      Michael Trites is an experienced molecular biologist with a diverse research background encompassing immunology, parasitology, medicinal chemistry, and basic science. He also has broad experience working in private, academic, and government research programs over the past 10 years. At TSI he is responsible for the microarray preparation and analysis of tissue samples using MMDxtm. 

      He holds a BSc (Honors) in Biology and Chemistry with Biochemistry and Molecular Biology from Acadia University and an MSc in Biological Sciences from University of Alberta.

    • Michael Parkes

      Research Associate

      Holding an MSc in Medicine and a BSc with focus in immunology and infectious diseases from the University of Alberta, Michael commands an expert knowledge of processes that drive disease at a microscopic level.  Michael’s background in molecular biology complements the skills acquired doing scientific research for the past 4 years, which include statistical programming, interpretation of large clinical data sets, and diverse laboratory skills. As a Research Associate at TSI, Michael’s diverse roles include performing and publishing the scientific research that MMDxtm is founded upon, building and managing databases, and maintaining stakeholder relations.

    • Konrad Famulski

      Team Leader Transcriptomics ATAGC

      Dr. Famulski is an experienced research scientist and manager. In his role as Team Leader he oversees the daily operations of ATAGC and works closely with TSI.

      He holds a PhD and a DSc from the Nencki Institute of Experimental Biology at the Polish Academy of Sciences.

    • Jeff Reeve

      Team Leader Computational Biology ATAGC

      Dr. Reeve is an experienced programmer and computational biologist. In his role as Team Leader he designs and updates the analytical methods used to examine high dimensionality data from the TSI disease databases.

      He holds an MSc and a PhD in evolutionary biology and quantitative genetics from Concordia University in Montreal.

  • Board

    Transcriptome’s (TSI) Board is composed of recognized business and academic leaders:

    • Robert Foster

      CEO, Ciclofilin Pharmaceuticals
      Robert Foster

      Dr. Foster was the founding CEO of Isotechnika Pharma Inc. (Edmonton, 1993) and is the Founder and CEO of Ciclofilin Pharmaceuticals (San Diego). As a respected executive, he has served in multiple capacities in academia and the biotechnology industry in Canada and abroad. He is named as an inventor on 242 patents. He led the discovery of the immunosuppressive drug Voclosporin and the diagnostic test kit, Helikit, for the diagnosis of H.pylori.

      He holds an MPharm and PhD from the University of Alberta.

    • Richard Fedorak

      Interim Dean, Faculty of Medicine and Dentistry,
      University of Alberta

      Dr. Fedorak is a recognized expert in inflammatory bowel disease having served in multiple roles in industry associations, editorial boards and advisory panels. He currently serves as Interim Dean of the Faculty of Medicine and Dentistry, Professor of Medicine (Gastroenterology), Director of the Centre of Excellence for Gastrointestinal Inflammation and Immunity Research (CEGIIR) and Director of the Northern Alberta Clinical Trials and Research Centre (NACTRC), all at the University of Alberta. He is also the President and CMO of Metabolomics, a University of Alberta spin-off company, the President of Canadian Digestive Health Foundation (CDHF) and Chairman of the Research Committee of the World Gastroenterology Organization. He has published more than 400 peer-reviewed manuscripts and book chapters.

      He holds an MD from the University of Alberta and a Gastroenterology Fellowship from the University of Chicago and Columbia University.

    • Phil Halloran

      CEO, TSI

      Dr. Halloran is a clinician scientist with extensive research experience in basic immunology, clinical research, and microarrays. He currently leads the Alberta Transplant Applied Genomics Center (ATAGC) at the University of Alberta in Edmonton. He has more than 400 peer reviewed publications in transplantation and inflammatory diseases. He is an officer of the Order of Canada, a Fellow of the Royal Society of Canada, the first recipient of the Paul Terasaki Prize, and an elected member of the American Society for Clinical Investigatiton.

      He holds an MD from the University of Toronto and a PhD from the University of London.

    • Jennifer Halloran

      Associate, Dentons

      Ms. Halloran is a commercial litigator with a primary focus on contractual disputes, product liability and risk management. She has extensive experience in a number of industry sectors, including energy, professional services and insurance. She is a Member of the Law Society of Alberta, the Law Society of Upper Canada and the Canadian Bar Association.

      She holds an LLB from the University of Alberta, an MA from Brock University, and a BA (with Distinction) from the University of Alberta.

    • TSI's Professional Advisors

      Legal Advisors:
      Dentons LLP
      2900 Manulife Place
      10180-101 Street
      Edmonton, AB T5J 3V5
      Phone: (780) 423-7100

      Bankers:
      Royal Bank of Canada
      10107 Jasper Avenue
      Edmonton, AB T5J 1W9
      Phone : (780) 448-6611

      Patent Attorneys:
      Fish & Richardson P.C.
      3300 Dain Rauscher Plaza
      60 South Sixth Street
      Minneapolis, MN 55402
      Phone: (612) 337-2565

      Insurance Broker:
      AON Reed Stenhouse Inc.
      #900, 10025 102A Avenue
      Edmonton, AB T5J 0Y2
      Phone: (780) 423-9801

      Accountant:
      Stephen Wildfang, CA
      Stephen D Wildfang Professional Corporation
      #201, 7309 50 Street NW
      Edmonton, AB T6B 2J9
      Phone: (780) 440-4428

  • Careers

    Transcriptome (TSI) is always interested in hearing from qualified candidates seeking work in the molecular diagnostics sector, and welcomes resumes and CVs sent to info@transcriptome.com

    Please check back regularly for new job postings and information on available positions.

MMDX

  • Unmet Need

    The current standard for diagnosing and detecting organ disease from tissue biopsies is histology, the microscopic examination of processed tissue samples using various stains. This process is highly subjective and prone to relatively high error rates and disagreement among observers. Moreover many types of changes in disease states are molecular but not microscopically detectable. These high error rates often result in inappropriate treatments for patients, leading to higher costs and poor outcomes.

    In the post-genomic era, molecular diagnostics are being developed to address the unmet need for precision in diagnostics. Gene expression data can now be used to objectively assess disease states, adding predictive value to conventional methods.

    Microarrays (gene chips) are the best established method for studying gene expression in biopsies. Coupled with sophisticated statistical and machine learning methods, microarrays can identify gene expression patterns relatively specific for different disease states. Changes in gene expression are early indicators of changes in a tissue, and can be measured objectively and quantitatively, unlike opinion-based microscopic assessment of biopsies.

  • Transplants

    • Kidney

      There are limitations in the conventional opinion-based histology and laboratory-developed tests such as DSA and C4d staining, thus future biopsy assessment will require centralized molecular tests with evidence-based interpretation. The MMDxtm system incorporates strengths of each platform, both histology and molecular assessment.

      Gene expression measurements, or “classifiers”, were used to develop scores for diagnosing T cell-mediated rejection (TCMR), antibody-mediated rejection (ABMR), and all rejection. Each classifier generates a score indicating the probability of a conventional diagnosis, and these scores are then displayed on a report that is returned to the clinician. In addition, we developed a Risk Score classifier that predicts graft loss, and a gene set that quantifies acute kidney injury (AKI). The TCMR classifier correlates with the histologic lesions of TCMR (infiltrate, tubulitis). The ABMR Score correlates with ABMR microcirculation lesions and with donor-specific antibodies (DSA). The ABMR Score has also been shown to strongly predict future graft loss.

      MMDxtm for kidney transplants requires one additional kidney tissue needle biopsy core beyond the usual two to three biopsy cores obtained for routine histopathology as standard of care, and is expected to commercially launch in late 2016. Currently, the MMDxtm for kidney is in trial use in a number of transplant centers in North America and Europe.

    • Heart

      The current standard method for diagnosis of organ rejection in heart transplants is microscopic assessment of a tissue biopsy, using the International Society for Heart and Lung Transplantation (ISHLT) classification system. However, recent studies have indicated that this system can produce incorrect diagnoses with potential harm to patients due to inappropriate treatment.

      MMDxtm system for heart transplants addresses the need for a more quantitative and objective approach to heart biopsy assessment by introducing molecular and diagnoses. Biopsies are interpreted based on their molecular and clinical characteristics, plus clinical and laboratory parameters, to give the diagnosis. MMDxtm will detect and/or assess T cell-mediated rejection (TCMR), antibody-mediated rejection (ABMR), acute parenchymal injury (API), risk of failure, fibrosis, and cardiac allograft vasculopathy (CAV). MMDxtm system for heart is currently in clinical trials, and expected to commercialize in 2017/2018.

      MMDxtm for heart transplants requires one or two additional endomyocardial biopsy (EMB) bites beyond the usual five to seven EMB bites obtained for routine histopathology as standard of care.

    • Lung

      The current standard method for diagnosis of organ rejection in lung transplants is microscopic assessment of a tissue biopsy, using the International Society for Heart and Lung Transplantation (ISHLT) classification system. However, recent studies have indicated that this system can produce incorrect diagnoses with potential harm to patients due to inappropriate treatment.

      MMDxtm for lung transplants addresses the need for a more quantitative and objective approach to lung biopsy assessment by introducing a molecular and diagnostic system. Biopsies are interpreted based on their molecular and clinical characteristics, plus clinical and laboratory parameters, to give the diagnosis. MMDxtm will detect and/or assess T cell-mediated rejection (TCMR), antibody-mediated rejection (ABMR), risk of failure, and chronic lung allograft dysfunction (CLAD). MMDxtm for lung began clinical trials in late 2016, and is expected to commercialize in 2018.

      MMDxtm system for lung transplants requires one additional lung tissue bite beyond the usual two to three bites obtained for routine histopathology as standard of care.

  • Other Diagnostics

    • Melanoma

      More details on the upcoming MMDxtm for Melanoma coming soon.

    • Inflammatory Bowel Disease

      The current standard of care for diagnosing inflammatory bowel disease (IBD) and guiding IBD treatment is a combination of microscopic examination of intestinal tissue and measurement of markers in stool and blood. Conventional methods of diagnosis and monitoring are limited by turnaround times of 7+ days, and sometimes do not achieve a conclusive diagnosis for the patient.

      Accuracy and efficiency are unmet needs in IBD diagnosis and monitoring. MMDxtm would provide a more reproducible, timely assessment of IBD based on an integrated view of the molecular and clinical characteristics of biopsies. MMDxtm has the potential to improve diagnosis by developing a molecular classification system for IBD,   and enhance treatment guidance and monitoring by providing quantitative reports.

      MMDxtm will require fewer biopsies than the current histopathological standard of care. MMDxtm will streamline reporting with <48 hour turnaround times.

  • Theranostics

    High costs and long timelines in drug development are largely due to inefficient target identification and development models.

    The Molecular Microscopetm (MMDxtm) can assist this process in several ways:

    1. Better understanding of potential targets in terms of “gene and protein” function
    2. Reliable gene expression information
    3. Accurate quantifiable clinical trial endpoints

    Transcriptome (TSI) is uniquely positioned to address all of these needs through its proprietary MMDxtm algorithms and database. Guiding the development of new and improved drugs is part of Transcriptome’s (TSI) mandate to foster an environment of enhanced patient care and better outcomes.

    (click image to enlarge)

    For more information on our products/services, please contact us at info@transcriptome.com

  • For Clinicians

    The current standard for diagnosing and detecting organ disease from tissue biopsies is by microscopic examination. This process, however, is highly subjective and error prone.

    In the post-genomic era, molecular diagnostics are being developed to complement histological practices. Gene expression data can now be used to objectively assess disease states, and add predictive value to conventional methods.

    Transcriptome (TSI) is uniquely positioned to address all of these needs through its proprietary technology.

    Patient care is of the utmost importance, both for the clinician and for Transcriptome (TSI). With a complementary test capable of supplementing current standard of care, better treatment plans can be developed. Through MMDxtm, Transcriptome (TSI) intends to provide health care practitioners with an improved understanding of diseases to augment diagnosis, treatment and monitoring.

    (click image to enlarge)

    For more information on our products/services, please contact us at info@transcriptome.com

    • Testimonials

      “…A powerful diagnostic strategy contributing to a better understanding of the specific causes of transplant injury. In ongoing intervention trials our group has learned that the Molecular Microscopetm (MMDxtm) has the potential to substantially improve the accuracy of biopsy-based rejection diagnosis…”
      Dr. Georg Bohmig and Dr. Farsad Eskandary
      VIETAC, Medical University Vienna, Vienna, Austria

      ***************

      “The Molecular Microscopetm (MMDxtm) has performed extremely well when compared with histology at our transplant center. Knowing this we have confidence in the MMDxtm when traditional diagnostic methods are ambiguous, such as in the case of ABMR.”
      Dr. Andrew Malone
      Washington University School of Medicine, St. Louis, MO, USA

      ***************

      “It is very exciting to see that Molecular Microscopetm (MMDxtm) is moving to clinical practice.”
      Enver Akalin, MD
      Montefiore Medical Center, Bronx, NY, USA

      ***************

      “We have been using MMDxtm (Molecular Microscopetm) for the past year and have been very impressed with the results. In general, there is a high concordance with pathology results which gives the treating clinician more confidence in the diagnosis and management. In many cases, MMDxtm has provided greater insight and granular detail to our biopsy evaluation which has significantly helped in patient care. I believe that MMDxtm will remain a valuable tool for the care of our kidney transplant patients.”
      Dr. Gaurav Gupta
      VCU, Richmond, VA, USA

      ***************
  • FAQs

    • What is MMDxtm and how does it work?

      A. The Molecular Microscopetm (MMDxtm) is a molecular system for tissue biopsy analysis. RNA is extracted from the biopsy, then analyzed using microarray technology. Gene expression results are statistically compared to an established reference set of known biopsies to produce a report and diagnosis. This system complements histology, by offering a quantitative and objective method for tissue biopsy analysis.

      (click image to enlarge)

    • What is a molecular classifier?

      A. A molecular classifier is a machine learning method that can predict something (e.g. diagnoses) based on the gene expression data output from the microarray analysis. This is done by the program ‘learning’ which expression patterns can recognize the differences between the samples, and combining these differences to generate a pattern that can be used to predict the diagnosis in future (unknown) samples.

    • How do I ship a sample?

      A. Samples are shipped to Transcriptome Sciences Inc. in Edmonton, Canada using approved packaging materials provided by Transcriptome (TSI).

      1. Biopsies are stabilized immediately after they are taken in a transport tube with RNAlater®
      2. The sample transport tube is wrapped in absorbent tissue, and placed in a small biohazard bag
      3. The biohazard bag is placed in a padded envelope
      4. The padded envelope is packaged in a FedEx Pak with appropriate paperwork and waybill affixed

      To request shipping materials or further information, please email us at info@transcriptome.com.

    • How does MMDxtm compare to histology?

      A. The Molecular Microscopetm (MMDxtm) has compared very favorably to clinical opinion and local conventional assessment, with accuracy of 90% in TCMR and 78% in ABMR. In 275 feedback forms thus far, clinicians have indicated that 86% agreed with clinical judgment (with or without disagreement with histology), 84% indicated that MMDxtm invited more confidence for management decisions and that in 1/4 of biopsies the MMDxtm report would alter therapy and/or investigations.

    • What is a 'nearest neighbor'?

      A. MMDxtm is built on the Reference Set – a collection of biopsies that have already been fully characterized in terms of their molecules, histology, diagnoses, and outcomes. The molecular distribution of these biopsies is plotted in 3-dimensional ‘principal component’ space. The new biopsy (shown as a red triangle in the graphic below), whose histology status is unknown, is then projected into this space based on its molecular characteristics, and the characteristics of its 50 ‘nearest neighbors’ (defined by three-dimensional Euclidean distance) are found. Because the diagnoses and prognoses for these neighbors are known, we can assign a probabilistic diagnosis and prognosis for the new sample based on the averages in its neighbors. This can be seen as a typical example of case-based reasoning – solving new problems by observing the solutions found for similar problems in the past.

      (click image to enlarge)

    • Is MMDxtm safe for my patients?

      A. MMDxtm requires only one biopsy beyond the standard of care, and poses minimal risk to your patient.

    • What information is required for submitting a sample?

      A. The minimal information absolutely required for submitting a sample is the date of transplant and date of biopsy, though more information is useful and can make the diagnoses more relevant. Please email info@transcriptome.com for more details.

    • Is MMDxtm a central diagnostic system or a kit?

      A. MMDxtm is a central diagnostic system.

  • For Researchers

    For a current list of our publications, please click here.

Company Information

  • News & Events

    A video montage recognizing Dr. Phil Halloran's contributions to the field of organ transplantation presented during the Doctor Honoris Causa ceremony at the Sorbonne in Paris.


    TSI CEO and Founder Dr. Philip Halloran receives Doctor Honoris Causa award from Faculté de Médicine de University of Paris Descartes

    Transcriptome Sciences Inc. (TSI) is proud to announce that its CEO and founder, Dr. Philip Halloran, received the award of  Doctor Honoris Causa from Faculté de Médicine de University of Paris Descartes on December 14, 2016 in Paris, France. The ceremony took place in the historic Musee d’Histoire de Medicine, and the honorary doctorate from the Faculté de médecine de l’Université de Paris Descartes was presented by the Dean of Faculty of Medicine, Professeur Friedlander. Also in attendance were Prof. Denis Glotz,  Dean Friedlander, Prof. Xavier Jouven, Prof. Alex Loupy, Prof. Carmen Lefaucheur, and Prof. Christophe Legendre. Many congratulations!


    CEO Awarded with Prix Galien Award

    CEO and Founder Dr. Philip Halloran has been honored with the prestigious 2016 Prix Galien Canada Research Award in Toronto, in recognition of his work in transplantation.

    The Prix Galien is the most prestigious award in the field of Canadian pharmaceutical research and innovation. Referred to as the Nobel Prize of pharmaceutical research, it recognizes the efforts and achievements of pharmaceutical research and development. The Prix Galien Canada is organized by Innovation Life Canada, a non-profit organization whose mission is to celebrate Canadian innovation in the life sciences.” (Taken from http://innovativemedicines.ca/historic-honourees-celebrated-at-2016-health-research-foundation-research-awards-gala/, accessed November 23, 2016)

     

    Full article available here.

    Additional article here.


    TSI & ATAGC Presentation Schedule

    CEO and Founder Dr. Philip Halloran will be attending the 2017 Cutting Edge of Transplantation (CEOT) meeting in Phoenix February 23-25.

    The Transcriptome Sciences team and their ATAGC partners will be well-represented at the 2017 American Transplant Congress in Chicago April 29-May 3.

    For a list of our talks and posters presented at the 2016 American Transplant Congress in Boston, please view or download the attached file.

    click here to open


    TSI Launches New Website

    Transcriptome Sciences Inc. (TSI) is proud to launch its new website, designed to be more interactive with the intention of staying connected to clinicians, investors, and scientists. Feel free to let us know what you think by sending us your comments at info@transcriptome.com


  • For Investors

    Transcriptome Sciences Inc. (TSI) is a privately held company.

    For investment opportunities please contact info@transcriptome.com

  • Product Pipeline

    Product Pipeline

Contact Us

Please contact us at:

info@transcriptome.com

P. 780-492-5091
Twitter


TSI is located at:

Rm. 250
Heritage Medical Research Centre
University of Alberta
Edmonton, AB, Canada T6G 2S2