Informatics Core. Arthur Toga May 2014
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1 Informatics Core Arthur Toga May 2014
2 Informatics Core Status Website News and Activity Data Repository News and Activity Image QC Workflows
3 3 New Study Cohort bar graphs PPMI Homepage
4 PPMI New Study Cohorts Showing progress: new study cohort numbers
5 PPMI Data Inventory Live table of available data and specimens Imaging Data Table Biologic Specimens Table
6 Publications & Presentations PPMI investigators can submit a manuscript for review and related presentations online Available Database of Publications and Presentations
7 Repository News New neuroimaging data & docs CT & AV-133 scans, metadata, results & methods New genetic data SNPs & Priority genotypes New Clinical data Physical Activity Scale New cohorts Prodromal Genetic
8 Image Inventory 4,778 Image Series SPECT 25% DTI 23% PET 3% fmri 3% MRI 46%
9 Non-Image Inventory Data Categories (# of Items) Biospecimen (32) Enrollment (11) Incidents & Notifications (4) Internal (14) Motor Assessments (11) Non-motor Assessments (14) Medical History (16) Study Docs (8) Subject Characteristics (6)
10 Biospecimen Results Data Project PI Institution Test Count 101 Les Shaw University of Pennsylvania Total tau 120 p-tau181p 120 Abeta Les Shaw University of Pennsylvania Total tau 1299 p-tau181p 1296 Abeta Peggy Taylor Covance CSF Hemoglobin Peggy Taylor Covance CSF Alpha-synuclein Peggy Taylor Covance CSF Alpha-synuclein Clemens Scherzer Harvard Medical School FBXO7, SNCA, DJ-1 isoforms 104 Andrew Singleton National Institutes of Aging ApoE Genotype Andrew Singleton National Institutes of Aging 35 Priority genotypes
11 Genetic Data
12 Data Use Applications Applicants by Quarter Applicants by Sector Biotech, 55 Government, Other, University/Rese arch Institute, 725 Pharmaceutical, 86 Scanner Mfg, Q Q Q Q Q Q Q Q Q Q Q Q Q 2014
13 Data Download Activity Q2011 3Q2011 4Q2011 1Q2012 2Q2012 3Q2012 4Q2012 1Q2013 2Q2013 3Q2013 4Q2013 1Q2014 Clinical Imaging download activity showed a 141% increase over 2012 download activity. Cumulative image downloads: 131,067 Cumulative clinical downloads: 46,807
14 Biospecimen Process Online systems supports the entire process of receiving and tracking biospecimen requests, transferring and distributing analysis results data to PPMI investigators. Complete application Submit Requestor Reviewers Review application Approve Select Ship Samples Investigator Analysis Results QC identifiers Post LONI Investigator Download data
15 Biospecimen Requests 36 requests for biospecimens received via online application 15 Approved at LOI stage 5 Approved at Full Proposal stage
16 Website Metrics from Launch 2010
17 Website Metrics 2012/2013 comparison
18 TOTAL 2013 = = Website Page Views
19 TOTAL 2013 = = Website Unique Views
20 Website Metrics: Top Pages Through 2013 Homepage 17891(22%) Download Data 5653 (7%) Who We Are 2483(3%) Documents & SOPs 2469 (3%) Ongoing Analysis 1805 (2%)
21 Website Metrics: Geo
22 Investigator Activity 14 manuscript submissions via website for: Acta Neuropathologica Parkinsonism and Related disorders European Journal of Nuclear Medicine and Molecular Imaging PLOS ONE 18th International Congress of Parkinson's Disease and Movement disorders The MDS 18th International Congress of Parkinson's Disease and Movement Disorders Movement Disorder Society Conference 2014 Stockholm Postconference e-book 9. PFK in Poznań, Poland Movement Disorders Neurology JAMA
23 In Progress Biospecimen Inventory data transfer from Tel-Aviv Biorepository Data Harmonization (Global Schema development) Exome data distribution
24 Data Harmonization Canvassed common assessments in PPMI and ADNI Performed item-by-item comparison Asked CPATH to push for inclusion of missing questionnaires in the next CDISC release
25 Data Harmonization Canvassed common assessments in PPMI and ADNI including item-by-item comparison
26 Status Common Questionnaires Geriatric Depression Scale Short Integrated into IDA Search MOCA CDISC cannot obtain copyright approval to include in CDISC standard
27
28 Requirements Data Format Requirements DICOM image data (not NIFTI, Analyze or other lossy formats) Structural MRI (e.g. SPGR, MPRAGE) Functional MRI (BOLD EPI) Diffusion Tensor Imaging (DTI) System Requirements Internet access Recent Browser User Requirements IDA Account
29 Quality Control Results As the data owner, you have the final say on image quality. Using the computed LONI QC metrics and summary images you can rate your data according to the following Good Indicates your approval of the data and its readiness for further analysis Questionable The data needs further review and consideration before it can progress to further analysis Bad The image data are not suitable for further analysis
30 Sections for Evaluation Acquisition Parameters Linked Studies NIFTI QA Figures Additional Summary Stats FSL Mot. Outlier & MCFLIRT Summary Volume Means (input) Volume Means (w/mask) Means of mean volume diff. Running diff volume means Outlier voxel percentages fmri Human FWHM in X dimension FWHM in Y dimension FWHM in Z dimension Center of mass (X) (input) Center of mass (X) (w/mask) Center of mass (Y) (input) Center of mass (Y) (w/mask) Center of mass (Z) (input) Center of mass (X) (w/mask) Freq. spectrum (mean-mask) Freq. spectrum (max-mask) Per-slice variation Mean, SD, SFNR Overall Evaluation fmri Phantom Structural MRI DTI Acquisition Parameters Linked Studies Additional Summary Stats BXH Plots BXH Images Overall Evaluation Acquisition Parameters Linked Studies Additional Summary Stats Image Viewer Overall Evaluation Acquisition Parameters Linked Studies Additional Summary Stats Gradient Matrix Image Viewer Overall Evaluation
31 Normatives Normative Graphical Bars Dynamic normative bars show: The Minimum accepted Good value The Maximum accepted Good value Mean of all Good values The range of standard deviation
32 Charts Multimetric charts Difference chart Actual value chart
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