Parkinson’s Progression Markers initiative Informatics Core Arthur Toga

Informatics Core Supporting the informatics needs of the study Data integration Customized data ingress/egress flows Investigator ready datasets Biostats datasets Biologics datasets Secure data repository Broad data sharing and dissemination effort Comprehensive public-facing website PPMI Informatics Study Leadership Biostatistics Core Biospecimen Core Researchers Imaging Core LONI meets the ongoing needs of the other centralize the data collection by integrating data from several sources including the clinical EDC, the biospecimen repository, the imaging core.

PPMI @ LONI http://www.ppmi-info.org/ PPMI Website PPMI Repository PPMI Online The website and the repository work hand-in-hand to provide interested parties with information about the study, study data and progress in a relatively seamless fashion. http://www.ppmi-info.org/

Data Acquisition PPMI Repository Imaging Core (IND) Quality Control Image Pre-processing Image Acquisition Clinical Core (CTCC) Quality Control Study Management Clinical Data Acquisition Biorepository Core (IUSM) Sample Storage / Quality Assessment Biological Acquisition Biological Samples Biosample Analysts (Various) FOUND Substudy Data Collection FOUND Sub Study (UCSF) Enrollment status Self-reported Dx Survey data Genetic Samples Genetics Investigators New Data Source: UCSF for FOUND sub study Needed Soon: Pathology data dataflow ppmi@loni Study Information Data Access Investigator Resources Data Sharing Tools Biospecimen Requests Cell Line Requests Publications Inventory Results Results Sample-Subject Relinking File QC & Organization

Downloadable Datasets Amendments & sequestration requirements have resulted in an increased number of available datasets *Internal datasets support the data quality/management needs of core project managers and team leads.

Available Images

Recent Additions Integration of data from FOUND Gait & arm swing data Enrollment status Self-reported health status (coming soon) Risk factors questionnaire (coming soon) Gait & arm swing data We’ve done the data integration work, but have received only a sampling of data thus far. UCSF continues to work through data quality processes.

New Biospecimen Analysis Results Project# Project Name 123 Blood biomarker for Parkinson's disease 124 Total alpha-synuclein measurements in longitudinal CSF samples from de novo PD, Control, SWEDD, Prodromal and Genetic Cohorts 125 A-beta, tau, and p-tau measurements in longitudinal CSF samples from de novo PD, Control, SWEDD, Prodromal and Genetic Cohorts 129 Miro1, a Biomarker for Parkinson's Disease 130 The role of cell-free mitochondrial DNA in neurodegenerative disease 134 Hemoglobin measurements in longitudinal CSF samples from de novo PD, Control, SWEDD, Prodromal and Genetic Cohorts 138 Hemoglobin Biospecimen Analysis

Biospecimen Results Results for 1,004 unique participants Majority of subjects data have been used in 3 different analyses 12 subjects’ data have been used in 17 different analyses How to read: Assuming all participants could be included in each biospecimen analysis (not true), this shows a breakdown of how many different projects subjects’ samples were included. For example the majority of subjects are represented in the results for 3 different projects.

Data Use Applications

Over 1.9 million data downloads download activity Not shown on this chart, genetic downloads have spiked this year and are already at 8,215 which is a 400% increase over last year. Over 1.9 million data downloads

New Genetic Data NeuroX SNP Data for Prodromal and Genetic Cohorts WGS hg38 aligned data 24 Cohort Variants PLINK files 74 sets of final report TXT files DNA Methylation Profiling Raw idat files Cell Normalization data Cell Composition data

Whole Genome/Exome Data Sharing “Exome on a Disk” loaner drives Total requests: 17 BAM file requests: 10 FASTQ file requests: 14 Whole Genome data Requests for hs37d5 aligned FASTQ file requests: 3 New: hg38 aligned data Some requests were for both BAM and FASTQ files. This is a time-consuming process.

PPMI-Info Website Updates Cell Line Inventory & Requests Updated CRFs & Documents

The Global Alzheimer’s Association Interactive Network A Portal to Alzheimer’s Disease Research Data Connecting Scientists Worldwide GAAIN is a global cooperative for sharing, investigation & discovery for and by the Alzheimer’s research community. www.gaain.org Powered by the Laboratory of Neuro Imaging

Federated database system funded by the Alzheimer’s Association Global participation of Data Partners who host a GAAIN client at their location GAAIN clients interact with a central hub at LONI which aggregates query results for visualization

Architecture Addresses Data Partner Concerns Data Partners have a variety of study information and use different conventions for describing their data. Data can be cached in computer memory, but are never written to disk - protecting data ownership and privacy. Investigators can query and visualize harmonized Alzheimer’s disease data. Data are mapped to the GAAIN common data model. MAPPED DATA GAAIN SERVERS GAAIN PORTAL PARTNER DATA (Data Partners can switch ON/OFF if they wish to suspend communication with the GAAIN servers.) on off DATA EXPORT MAPPING TOOL DATA PARTNER CLIENT (A stand-alone client that sits at the Data Partner’s location.)

Our Data Partners 34 Data Partners up and running: NACC, NIAGADS, DIAN, N4U, BNA, ADNI, CNDR, LAADC, BIOCARD, WLS, Fundacio ACE, HELIAD, Tgen, etc. Signed Affiliates: QBIA to provide standardized terminologies for GAAIN and standardized imaging protocols Many more in discussion or with signed or verbal agreements GAAIN is in various stages of on-boarding over 80 global Data Partners.

GAAIN Data A collaborative effort to provide researchers around the globe with access to a vast repository of Alzheimer’s disease research data. A global hub for Alzheimer’s disease research data. We allow researchers to search across multiple data sources instantly and contact these Data Partners directly for data. Aggregates information about our Partners’ data and shares with researchers without infringing upon Data Partner data sharing policies and regulations. Data Partners always remain in control of their data.

Search Data in GAAIN GAAIN InteRrogator GAAIN Scoreboard Difficult to combine data across domains GAAIN InteRrogator A powerful interface to study relationships of variables in self-defined study cohorts across multiple sources. Access to the Interrogator requires a GAAIN Investigator Account. GAAIN Scoreboard A front-end tool to showcase the subject counts in GAAIN of a unique search. It is publicly available without a GAAIN account. GAAIN Cohort Scout A user-friendly tool to illustrate the breadth of variables in GAAIN and provides the option to share results. It is publicly available without a GAAIN account.

Interrogator: Exploration Each research study has its own data set. Explore variables shared by a Data Partner

Interrogator: Create Cohorts

Interrogator: Pool Data Across Studies

Interrogator: Review Results

Contact GAAIN Data Partners

Keywords: Human Fidelity, HuFi, Virtual Reality, Mixed Reality How can we track all the senses including proprioception and transfer that data to third party elements for them to have identical sensibilities? Keywords: Human Fidelity, HuFi, Virtual Reality, Mixed Reality

Keywords: Mind upload, Singularity, Future of death My research will focus on the upload of mind and how people are wrongly convinced that one day we will live forever inside the computers. Keywords: Mind upload, Singularity, Future of death