CCNA LORIS - Data Dissemination Oct. 21st Workshop Zia Mohades - - PowerPoint PPT Presentation

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CCNA LORIS - Data Dissemination Oct. 21st Workshop Zia Mohades - - PowerPoint PPT Presentation

Oct 01, 2022 13 likes •574 views

CCNA LORIS - Data Dissemination Oct. 21st Workshop Zia Mohades (CCNA LORIS Data Manager) Jessica Callegaro (CCNA LORIS Developer) , Rolando Acosta Names Names INTRO - LORIS Overview Goal: - strengthen research groups to better manage the

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CCNA LORIS - Data Dissemination

  • Oct. 21st Workshop

Zia Mohades (CCNA LORIS Data Manager) Jessica Callegaro (CCNA LORIS Developer) , Rolando Acosta Names Names

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INTRO - LORIS Overview

Goal:

  • strengthen research groups

to better manage the causes,detection, and treatment of AD.

  • Help Advance findings and

understanding of AD Longitudinal Online Research & Imaging System “...is a modular and extensible web-based data management system that integrates all aspects of a multi-center study: From heterogeneous data acquisition (imaging, clinical, behavior, genetics) to storage, processing and ultimately dissemination.”

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INTRO - LORIS Overview

LORIS: Heterogeneous Data Management

data management system that integrates all aspects of a multi-center study

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INTRO - Data Acquisition

LORIS: Heterogeneous Data Management

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INTRO - Data Acquisition

Uploading/collecting heterogeneous data-sets

(imaging, clinical, behavior, genetics)

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INTRO - Data Acquisition - BVL

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INTRO - Data Acquisition - BVL

  • Registration of a candidate
  • Creation of a visit
  • Uploading the Scanned copy of the assessment/Instrument
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INTRO - Data Acquisition - Stats

Candidates (total) Candidates (CND only) Sites Configured Timepoints Cohorts (and sub-studies) 1423 1115 61 (22 of which are imaging sites) 39 22

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INTRO - Data Acquisition - BVL

  • Repeated for all the instruments at the given visit
  • Requirement for setting the entire visit to approval and uploading to DQT
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INTRO - Data Acquisition - Stats

Instruments /Forms Coded Fields Candidates with Baseline Visits Started Candidates with Baseline Visit Completed Candidates with Follow Up Visit Started Candidates with Follow Up Visit Completed 247 (165 translated) 12 506 1339 (out of 1423) 413(out of 1423) 865 382

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INTRO - Data Acquisition - Biosample

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INTRO - Data Acquisition - Biosample

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INTRO - Data Acquisition - Biosample

  • Biobanking tool/module to import and track

the collection process

  • Tracking tool to streamline interaction with

Canadian Biosample Repository (CBSR) Database

  • Allow import of analyzed and processed data
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INTRO - Data Acquisition - Biosample

Blood CSF Saliva Buccal Urine Fecal Raw 1014 125 1072 767 1037 633

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INTRO - Data Acquisition - Biosample

Blood CSF Saliva Buccal Urine Fecal Raw 1014 125 1072 767 1037 633 Analysis 313 72

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INTRO - Data Acquisition - Imaging Overview

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INTRO - Data Acquisition - Imaging

Scout 3D T1 Sagittal PD/T2 Axial FLAIR Axial T2* Axial DTI 30 dirs BOLD Resting 7 mins 5 mins 7 mins 5 mins 6 mins 11 mins

1 hour acquisition to acquire scans for different modalities

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INTRO - Data Acquisition - Imaging

Scout 3D T1 Sagittal PD/T2 Axial FLAIR Axial T2* Axial DTI 30 dirs BOLD Resting 7 mins 5 mins 7 mins 5 mins 6 mins 11 mins X mins Y mins Z mins

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INTRO - Data Acquisition - Imaging

Subject Scans Uploaded Phantom Scans Uploaded Modalities Scans Undergone QC (phantoms + subjects) Scans Passed QC (phantoms + subjects) 1103 228 11 1140 1053

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INTRO - Data Acquisition - Genetics

Work in Progress

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INTRO - Data Acquisition - Genetics

  • Samples Genotyped at the University of Toronto
  • Sequencing on an IlluminaMiSeq platform with a NeuroX or Affymetrix UK Biobank chip
  • Aligned, annotated and variant calls at the analysis site
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INTRO - Data Acquisition - Genetics

  • Genotyped at the University of Toronto
  • Sequencing on an IlluminaMiSeq platform with a

NeuroX or Affymetrix UK Biobank chip

  • Aligned, annotated and variant calls at the

analysis site

  • Storage of raw and processed files/genetic

data in LORIS

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INTRO - Data Acquisition - Genetics

  • Genotyped at the University of Toronto
  • Sequencing on an IlluminaMiSeq platform with a

NeuroX or Affymetrix UK Biobank chip

  • Aligned, annotated and variant calls at the analysis

site

  • Storage of raw and processed files in LORIS
  • To view/QC through Genomic and SNP browser
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Request An Account

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Request Data Access

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Request Data Access

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Request Data Access Module

Data Access module was designed to facilitate the process of both requesting and granting access to data

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Request Data Access Module

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Request Data Access Module

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Request Data Access Module

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Request Data Access Module

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Request Data Access Module

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Request Data Access Module

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INTRO-How to access the data

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Data Query Tool (DQT)

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Data Query Tool (DQT) - What is it?

  • Query and retrieve data without technical expertise (or a programmer)
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Data Query Tool (DQT) - What is it?

  • Query and retrieve data without Technical expertise
  • Design, execute, and save queries in a simple and intuitive manner
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Data Query Tool (DQT) - What is it?

  • Query and retrieve data without Technical expertise
  • Design, execute, and save queries in a simple and intuitive manner
  • Selection of variables, and quick download in most commonly used formats
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Data Query Tool (DQT) - What is it?

  • Query and retrieve data without Technical expertise
  • Design, execute, and save queries in a simple and intuitive manner
  • Selection of variables, and quick download in most commonly used formats
  • Save and reload any query
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Data Query Tool (DQT) - Define Fields

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Data Query Tool (DQT) - Define Filters

Detailed examples During the Live Demo!

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Data Query Tool (DQT) - View Data

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Data Query Tool (DQT) - Download Data

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Data Query Tool (DQT) - Demo

Live Demo by Jessica Callegaro

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Data-Dictionary for DQT

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DQT - Demo Test Case 1

Compare MOCA assessments for hearing-impaired MCI vs hearing-impaired Controls. Tip: make sure to select ‘Longitudinal’ view when viewing data!

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Investigate the link between homocysteine levels and WMH burden in different cohorts (AD, Mixed, MCI, V-MCI). a) Using blood analysis data and MRI visual measurements related to WMH. b) Checking specifically for px that meet the vascular dementia / cognitive impairment criteria (ARWMC >= 2)

DQT - Demo Test Case 2

Tip: You can save your queries to retrieve and edit later!

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DQT - Stats

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Data Release

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Data Release

  • The Data Release Module can be used to easily distribute packaged data

releases of your study

  • Users can download customized subsets of data from this module
  • Scaling and transferring solutions were implemented for researchers

downloading large datasets

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Data Release

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Data Release

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ProFTP/sFTP

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Accessing Files Using FileZilla

  • Brain donation

○

  • An SFTP server is used to

securely transfer large data files over a remote system to users based on permission.

  • Easy setup and configuration
  • f FileZilla client using LORIS

credentials.

  • Gain access to and download

CCNA data release files.

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Acknowledgement

CCNA LORIS Dev Team

Camille Beaudoin Pierre Pac Soo Rolando Acosta

CCNA-LORIS User Support Team

Jingla Fri-Tunteng Charlie Henri-Bellemare

Protocol Implementation Team

Howard Chertkow Victor Whitehead Michael Borrie Natalie Phillips Jennifer Fogarty Randi Pilon Nimi Bassi Sarah Best Cynthia Di Prospero Celine Fouquet

Ace Lab

Alan Evans Samir Das Software Manager

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Questions

You can email us at ccna@mcin.ca if you have any further questions!