CARTaGENE_RMGA_16juin2016
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CARTaGENE's presentation at the Réseau de Médecine Génomique Appliqué. Montreal. Palais des Congrès 2016.
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CARTaGENE_RMGA_16juin2016
- 1. The largest prospective health study in Québec 43 000 participants !
- 2. Is biobanking a smart investment ?
- 3. EBIC (2005-2008) Economic Burden of Illness in Canada http://www.phac-aspc.gc.ca/publicat/ebic-femc/2005- 2008/assets/pdf/ebic-femc-2005-2008-eng.pdf 11.7 11.4 5.8 5.5 5.1 Direct costs in billion dollars Cardiovascular Neuropsychiatric Musculoskeletal Digestive Injuries The Global Burden of Disease Study The economic impact of disease
- 4. Source: CIHI Demographic change in Canada
- 5. http://blog-epi.grants.cancer.gov/2013/04/15/combined-environmental-exposures/ HEALTH VS. DISEASEEXPOSOME GENOME Genes + Life Style + Environment = Health
- 6. Mandate Provide a deeply phenotyped ressource of data and biosamples Strong expertise in epidemioloy, molecular biology, bioinformatics and drug development Reduce considerably research costs Provide a fast, easy and open access The CARTaGENE project Mission To facilitate scientific innovation and research projects, while ensuring the longitudinal mandate of the cohort
- 7. Open and fast access USE IT, IT’S YOURS ACCESS@CARTAGENE.QC.CA SDAC
- 8. 2008 2009 2010 2011 2012 2013 2014 2015 Optimisation Phase A Environment Nutrition Wave 2 Physical measures Consent Open consent long-term engagement Right to withdraw Sampling Based on Probability proportional to size (PPS) Random selection from the Health Insurance registry Men and women ages 40 to 69 living in one of six CMAs 20 000 22 000 The CARTaGENE project
- 9. > 300 000 participants Blood samples> 140 000 Physical measures> 90 000 $140 million invested Go big or go home
- 10. Data and biosamples collected
- 11. Data and biosamples collected DNA Extracted = 15 223 (done/upcoming in 2016) Genotyped ≈7500 (done/upcoming in 2016) Illumina OMNI 2.5 array (1029) Affymetrix Axiom array (1000) Illumina OMNI express (2842) Illumina MEGA array (upcoming) ≈ 1000 RNA seq Gene Expression ≈ 1000 Deep Sequencing – whole transcriptomic
- 12. CARTAGENE: COHORTE REPRÉSENTATIVE DE LA POPULATION Quality control
- 13. Awadalla P., Boileau C., 2012 Chronic diseases in CaG cohort 0 2000 4000 6000 8000 10000 12000 14000 Diabète Désordrethyroidien Hypercholestérolémie Hypertension Angine AVC IM Bronchitechronique Asthme Insuffisancerénale Calculsrénaux Infectionsrénales Ostéoarthrite Arthriterhumatoide Ostéoporose Glaucome Cataractes Dégénérescencemaculaire Cirhose Hépatitechronique Cholecystite Ulcère/refluxacide Syndromecôlonirritable Polype Diverticulite MaladiedeCrohn Eczéma Psoriasis Lupusérythémateuxdisséminé Dépressionmajeure Épilepsie Migraine Scléroseenplaques MaladiedeParkinson Schizophrénie Cancers Nombredeparticipants Maladies Cardiométaboliques ~50%
- 14. Factor Analysis Revealed 6 major comorbidity clusters. Ward Hierarchical clustering for the 64 chronic conditions based on their respective factor loadings (Jean-Philippe Goulet, Bioinformatique) Comorbidity in CaG cohort
- 15. Projects using CaG data and biosamples
- 16. GENOTYPING LONGITUDINAL CaG-FAMILY ENVIRONMENT CARTaGENE BIOBANKING ACCESS SERVICE PROJECT MANAGEMENT CURRENT AND FUTURE PLANS
- 17. Pan Canadian Sample of men and women DNA methylation ≈ 2000 (upcoming in 2017) Histone Acetylation, ChIPseq ≈ 1000 (upcoming in 2017) Pan Canadian Sample of men and women Cytokines and adhesion molecules (TBD) ≈ 10,000 (upcoming in 2017) Upcoming data from CARTaGENE and CPTP
- 18. CARTaGENE– The Canadian alliance for healthy hearts and minds Recontact Project “$16 million investment in first of its kind Canadian chronic disease research project” The Canadian Partnership Against Cancer (CPAC) • 10 000 Canadians from existing cohorts (1500 CARTaGENE) • Collect detailed information on vascular disease, cardiac disease, and cognitive function using MRI scans • Evaluate the impact of different environmental determinants on Cardiovascular Health.
- 19. Quantitative data with 7 000 variables per participants Prospective cohort Harmonized data Public infrastructure (open access) Accelerate personalized medicine Take home message
- 20. Founders Claude Laberge Bartha Maria Knoppers Scientific directors Anne-Monique Nuyt Sébastien Jacquemont Executive Alexandra Obadia-CEO Team Catherine Boileau – Epidemiology Nolwenn Noisel – Operations Joseph Tcherkezian-Access Yves Payette – Data manager Thibault de Maillard – Bioinformatics Gabrielle Thauvette – Analyst Geneviève David – Communications Maria Barone – Human ressources and finance Charles Rivard – Finance analyst
Notes de l'éditeur
- Hello everyone, it’s a pleasure to be here. in the next 15 min or so, I would like to give you a brief overview of what we do at CARTaGENE. So Despite all the advancements in detection and treatment of several chronic diseases, chronic disease-related deaths worldwide continue to increase at an alarming rate, therefore prevention and personalized medicine are gaining in popularity when it comes to disease control. Regardless of how we approach this problem it is generally necessary to identify the causes and for most chronic diseases the cause is either unknown or controversial. However what we do know is that chronic diseases are caused by a combination of an individual's genetic predisposition and their exposure to certain environmental risk factors. CARTaGENE was created to find solutions to these very complex diseases. And we do that, by collecting a lot of health data and biosamples on a lot of people. In fact we are conducting the largest prospective health study on men and women in Québec. It is one of the few population cohorts in the world where blood is stored not only for DNA and proteind-based science but also for gene expression analysis, which opens the door for multiple systems genomics approaches that identify genetic and environmental factors associated with disease-related quantitative traits.
- What is biobanking ? Well, I like to think of biobanks as organic bank accounts. You put your in your data and biosamples and earn medical interest in the form of knowledge and therapies that grow out of that deposit. Human biospecimens are a limited resource that are not subject to short-term depreciation unlike many other research tools. In fact, many collections tend to grow in value over long periods of time with the emergence of new methods to analyze biospecimens. Several high income countries have already invested huge sums of money in biobanks. So what’s fueling this motivation ?
- 9 out of the top 10 causes of mortality in high income countries are due to chronic diseases and almost half of the deaths are due to cardiovascular diseases; obesity and diabetes are also showing worrying trends, not only because they already affect a large proportion of the population, but also because they have started to appear earlier in life. It is estimated that by 2020, common chronic diseases will account for almost three quarters of deaths worldwide. Collectively chronic diseases have have an important economic impact.
- And this is particularly relevant for Canada at a time when it faces numerous challenges from its aging population and ever increasing health care costs. In fact, more than half of provincial and territorial governments’ health care expenditure is spent on seniors, yet this group accounts for only 16% of the population.
- As I mentioned earlier, chronic diseases are multifactorial and only by integrating multiple layers of information about individual profiles of health, such as health records, clinical data and family history combined with environmental determinants can we capture a full spectrum of risk, and come up with better diagnosis, treatment and prevention. Obviously this type of information can only be obtained through large cohort studies.
- Our mission is to facilitate scientific innovation and research projects, while ensuring the longitudinal mandate of the cohort. And we do that by providing a deeply phenotyped ressource of data and biosamples, as well as a strong expertise in edidemioly, molecular biology, bioinformatics, and drug development. By reducing research costs and providing letters of support to researchers for funding opportunities and by providing a fast and easy access ans are one for the few biobanks in the world to offer an open access.
- The application process is very staightforward. Applications are submitted through our web portal the SDAS, applications are then reviewed by our ethics commitee the SDAC and upon approval data and biosamples are sent to applicants. We also offer professional services for recontact projets and will soon have a web portal where past and futur participants can register to participate in future studies and help us fufill our longitudinal mandate. Also very importantly, CARTaGENE no longer has a principal investigator which facilitates the open access policy, hence our new slogan use it, its yours.
- Since 2007, over 42 million dollars in public money have been invested in the CARTAGeNE project to collect heatlh data and biological samples from 43 000 participants accross 6 major cities. In population-based cohorts, individuals are not selected for a particular disease but rather represent a random selection among the population which minimizes the need for correcting for bias in measured phenotypes. We chose participants in the 40 to 69 age group because they are the most at risk for developing chronic diseases. We also obtain an open consent from participants that allows us to use their information, including RAMQ health records and biosamples for any projects we deem ethical and valuable for health research
- To stay competitive with the rest of the world and to increase the statistical power of its data, CARTaGENE has joined forces with 4 other CANADIAN cohorts to create the Canadian Partnership for tomorrow project (CPTP) that collectively have detailed health information and biosamples on more than 300 000 participants. More than 140 million dollars of public money have been invested in this pan canadian project.
- The next two slides showcase what we can offer in terms of data and biosamples, we have collected over 7000 variables for each participant. In if my calculations are right, that is more than 300 000 million variables in our entire cohort which I believe qualifies as big data. So in our detailed health questionnaire we collected information about our participant’s demographic and socio economic factors, lifestyle habits, mental health, psychosocial environment, personal and family medical history, prescribed medications to name only a few. We also took many physical measurements including cognitive tests, body fat, bone density, blood pressure, lung function, arterial stiffness, ECG and several others.
- We have also complete blood count and biochemical profiles on 30 000 participants, environmental and nutritional variables. Genealogical data in partnership with balsac. We have more than 300 000 biological samples, including plasma, serum, blood for dna and rna based science, cells preserved for cell culture work. Importantly, we have genomic data and over 1000 participants, including genotyping, RNA seq, and exome seqencing.
- To assess whether the data collected from our participants was representative of the general population, we compared it to those collected by the Canadian Census. We found that in terms of age, gender and representation by region, our data was very similar to that of the census where the majority lived in Montreal at about a 50:50 ratio between men and woman and a wide range of ages with cardiovascular disease being the most prevalent.
- As I mentioned earlier, our primary mandate is to better understand the causes of chronic diseases and as you can see on this chart, the chronic diseases found in our cohort mirror those found in the general population, with cardiovascular diseases being the most prevalent. Importantly about 75 % of participants had some form of chronic disease and a significant number of those had more than one, suggesting an interaction between illnesses.
- In fact, bioinformatics analysis revealed six major comorbidity clusters , Allergies, Digestive, metabolic, cardiac, reperatory and asthmal.
- CARTaGENE data and biosamples are being used by a several research groups for different studies including but not limited to the discovery and validation of new biomarkers, Genetic association studies, environment association studies, fundamental research studies as well as several research programs on a number of diaseases, including cardiovascular, diabetes, cancer to name only a few. CARTAGENE is also now part of the INCPQ Biosurveillance program.
- Just a few words on our ongoing and future projects. We are are hoping to soon have genotyping data on most of our partiipants through collaborations with reseachers and recently obtained goverment funds. We are planning to lunch CARTaGENE family given that most of our participants have children and often more than one. This will allow us to better assess some of the hereditary determinants of chronic diseases. As I mentionned earlier, we will soon have a web portal where past and futur participants can register to participate in future studies and help us fufill our longitudinal mandate.
- Importantly, although genotyping data is very important it does not give you the full genomic picture. So we are participating in a pan canadian project that will soon provide epigenetic and inflamatory maker profiles on several thousand participants.
- CARTAGene is also participating in the Canadian alliance for healthy hearts and minds, a national research study aimed at understanding the causes and development of chronic diseases such as heart diseases, stroke and cancer, using MRIs. This 16 million dollar project is supported by the canadian partnership against cancer (CPAC) and will require 1500 participants form our cohort, People often come up to me after a talk and ask me if they can see the results of their scans, unfortunately or should I say fortunately all of CARTaGENE’s data is anonamyzed.
- Obviously tailored medicine is only relevant if we can predict which patients will benefit from a particular therapy. And topredict that we need to first determine the genetic and environmental determinants of diseases.