Brain-CODE. OBI s Data Integration Platform. Shiva Amiri, PhD

Transcription

1 Brain-CODE OBI s Data Integration Platform BIAC 2014 September 24, 2014 Shiva Amiri, PhD

2 OBI s Innovation System Collaboration and Partnership

3 OBI Values Patient-centred attack salient disorders Maximize neuroscience excellence across Ontario through integration and collaboration Standardize all assessments and diagnoses Build on past investments A partnership approach: government, researchers, clinicians, patients/advocacy groups & industry 3 3

4 OBI s Innovation System Outreach Research Putting patients at the centre of a multi-dimensional approach to the investigation of critical brain disorders. Training Improve brain health Data Products Partnerships 4

5 OBI s Innovation System Outreach Research Training Improve brain health Data Products Standardizing clinical data to accelerate discovery, improve patient care and foster healthcare efficiencies. Partnerships 5

6 OBI Values and Big Data Data sharing is critical to science and innovation today how do we create knowledge from data? Data sharing is key for effective collaboration, partnership, and discovery 6 6

7 A different look at brain disorders Brain disorders, like many other disorders are linked from genes to proteins to social and individual expression Research system must allow investigation not only within a disease, but across diseases 7 7

8 Complexity of Brain Disorders Disorder X

9 Complexity of Brain Disorders Disorder X Disorder Y

10 Productivity in Neuroscience Recognizing that neuroscience is not, of course, really a single field is important. Rather, it is a multidisciplinary enterprise including diverse fields of biology, psychology, neurology, chemistry, mathematics, physics, engineering, computer science and more. If scientists within neuroscience and related disciplines could unite around a small set of goals, the opportunity for advancing our understanding of brain and mental function would be huge. -- US National Academy of Sciences, 2008 The data integration imperative 10

11 Integrated Discovery System

12 Integrated Discovery Programs ID Program Focus Researchers & Clinicians Industry Partners Patient Groups Patients Expected Phase 1 & 2 Phase 2 Cerebral Palsy Epilepsy Neurodevelopmental Neurodegeneration Depression Total :

13 ID Programs: Numbers 5 Integrated Discovery Programs ~200 Researchers 35+ Institutions 40+ Companies 5+ Data Types Patients (expected) 1 3

14 OBI s Big Data Opportunity Integrated Discovery Programs Data Modalities Neuroimaging Clinical Genomics Proteomics Other Cerebral Palsy Epilepsy Neurodevelopmental Disorders Neurodegeneration Depression Other Brain Disorders 14

15 OBI s Big Data Opportunity Brain-CODE is an extensible large-scale informatics platform that manages the acquisition, storage, processing and analytics of multidimensional data collected from patients with a variety of brain disorders 15

16 Brain-CODE: OBI s Multidimensional Platform for Neuroscience

17 Brain-CODE: Core Principles Security and Privacy: Designated Privacy by Design ambassador by IPC/Ontario Open Access: Data holdings available to researchers globally Infrastructure: Extensible and user friendly data storage and management platform Standardization: Enabling efficient analysis of data Federation: Linking with autonomous databases to leverage existing resources Health Impact: Amplifying research outcomes, allowing for curiosity and hypothesis driven approaches Expertise: International Advisory Committee, InDOC Consortium - building Brain- CODE on OBI s behalf 17

18 Brain-CODE Brain-CODE: Inputs and outputs $$$ Brain-CODE Neurodegeneration POND Epilepsy CP-NET Depression Concussion Addiction ID programs Federation with existing databases researchers 18

19 Integrating Data Across the Province CAN-TBI CP-NET Brain-CODE 19

20 Expert Leadership International Advisory Committee Name Dr. Daniel Marcus Dr. Rodrigo Lopez Dr. Charles Peck Dr. Ann Cavoukian Dr. Sean Hill Institution Washington University at St. Louis European Bioinformatics Institute Neuroinformatics consultant Institute for Privacy and Big Data International Neuroinformatics Coordinating Facility, Karolinska Institute 20

21 Brain-CODE Portal

22 Privacy and Security

23 Privacy and Security The OBI and Brain-CODE adhere to high levels of data privacy and security: Physical, technical, and process security: Encryption and de-identification tools, security of data transfer and storage infrastructure. The path of data: Updated zone-based infrastructure Privacy systems: OBI has been designated Privacy By Design ambassador. Privacy Impact Assessment (PIA) completed (October 2012). Updated PIA March 2014; Threat and Risk Assessment (TRA) completed May Governance: Extensive policy framework and governance apparatus ensures ongoing compliance with regulatory and REB requirements. 23

24 Standardization

25 Standardization» Efficient comparison of data (analysis) can only be done when the data is available in a homogeneous format, comparing apples apples» Standardized entry at data collection sites» The OBI has implemented several methodologies to ensure standardization including: Common data elements (CDEs): where applicable, the OBI ensures that researchers adopt existing CDEs (e.g., NIH, OHS) for data reporting. Demographic, Clinical, and Imaging CDEs developed through Delphi consensus process All available at: 25

26 Standardization Consensus-based process Percentage of respondents that rated an element as "Important/Very Important" Brain-CODE Goals Program Goals CHILD/ADOL ADULT CHILD/ADOL ADULT» Representatives from each ID Program filled out the survey to establish the Brain-CODE Demographic Common Data Elements (CDEs)» Keeping the CDEs manageable for our researchers» Recently completed Clinical CDEs and first steps on Imaging CDEs» Brain Data Harmonization - Standardization project with other brain databases across Canada» Workshops held for clinical, imaging and more generally brain data harmonization.

27 Linkages and Analytics

28 Federation Secure linkages of Brain-CODE s data with other databases Leverages existing resources Augments our data Richer data for analytics We will be federating with multiple strategic partners and plan to expand Pilot with ICES using encrypted health card numbers Research data Administrative data CLSA NDAR OHS Brain-CODE ICES Others 28 Others 28

29 Analytics Drawing value from integrated Data Features:» Diverse toolset for multiple neuroscience data types» Tools for integrated data analysis» Facilitate sharing and tracking of research data» Training of Data Scientists» Advisory service for researchers» Clinical trial recruitment operations» Encryption and data security services» Resources for SMEs Outcomes:» Cross modality discoveries» Augmented data sets» Clinical trial recruitment» Partnerships and Collaborations Integration Layer Federation Secure Databases Analytics Workspace Research Data Brain-CODE Portal Analytics Results Researchers 29

30 Analytics Development Phases Phase 3 Autonomous Analytics Engine Phase 2 Integrated Data Analysis Developer Space Challenges Space Visual Analytics Phase 1 Data Specific Tools/Pipelines General Analytics Environments Data Search Engine Secure Analytics 30

31 Potential of Brain-CODE» Amplified research outcomes Enriched patient data Optimized clinical trials Enhanced analytics» Attract industry partnerships» Engage, educate, and empower the Patient» Improve health care outcomes Enabling novel approaches to understanding CNS disease 31

32 Questions/comments Shiva Amiri, PhD Manager, Informatics and Analytics Francis Jeanson, PhD Program Lead, Informatics and Analytics Luca Pisterzi, PhD Program Lead, Informatics and Analytics Thank you

33 CDE Summary (Preliminary) DOMAIN SUB-DOMAIN Brain-CODE CDE Additional Supplemental Patient Characteristics Demographic Brain-CODE NONE Demographic Form SES Brain-CODE NONE Demographic Form Physical and Mental Health Quality of Life WHO-Qol (adult) KIDSCREEN (pediatric) SF-36 (adult) NEUROQOL (adult) Activities of Daily Living TBD TBD Medical Comorbidity NINDS Medical History NONE Form Psychiatric Comorbidity SCL-90 NONE Clinical Endpoints Depression PHQ-9 (adult) PROMIS-Depression CDI (pediatric) Anxiety GAD-7 (adult) PROMIS-Anxiety RCMS-2 (pediatric) Sleep PSQI (adult) PROMIS-Sleep TBD (pediatric) Other NONE PROMIS Cognitive TBD TBD TBD Disease-related (Program-specific) CAN-BIND TBD NINDS CDEs EpLINK Classification of Etiology NINDS CDEs (NINDS form) Classification of Seizures (NINDS form) Syndrome Age of Onset (NINDS form) Anti-Epileptic Drug Log (NINDS form) Neurological Exam (NINDS form) POND TBD NINDS CDEs CP-NET TBD NINDS CDEs Neurodegeneration In progress NINDS CDEs NEUROQOL (adult) Addictions TBD NINDS CDEs

34 Brain-CODE Data: Information Flow & Access Levels Single Research Lab OBI Program Research Access Linkage with External Databases Third Party Access