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WU ADRCDATA INTEGRATION AND SHARING:
PLAN & PROGRESS
http://nagarajanlab.wustl.edu
*Dr. Nagarajan is on the Scientific Advisory Board of Persistent Systems. Persistent Systems does not fund Dr. Nagarajan’s research.
Study Participant
Peripheral LeukocytesSerum / PlasmaFrozen Tumor BiopsyBone MarrowFFPE Block
RxPeripheral LeukocytesSerum / PlasmaFrozen Tumor BiopsyBone MarrowFFPE Block
Biospecimen Bank and
Informatics
Mutation Profiling
Proteomics
Gene Expression Microarray
FFPE qRT-PCR
Biomarker Validation
aCGH DB
DB
DB
DB
Clinical Data Molecular Data
IHC / Cell Assays
Integrative Analysis
Translational Research Paradigm
• Clinical Core– Patient demographic information, family history, health history, depression inventories,
physical examination, standard cognitive tests , and CDR
• Biomarkers Core– Fasting plasma and cerebrospinal fluid- Levels of total protein, hemoglobin A1C,
homocysteine, folate, Aβ, tau, apoE, and other biomarkers
• Genetics Core– Non-fasting blood, plasma, serum, buffy coat, and DNA during the initial visit and every 3
years thereafter for genotyping APOE and other genetic risk factors
• Neuropathology Core– Post-mortem frozen and fixed brain tissue- Quantitation of senile plaques, neurofibrillary
tangles, neuron counts, amyloid angiopathy, Lewy bodies, and vascular pathology
• Psychometric Core– Primary, working, episodic, and semantic memory, abstract reasoning,
visuospatial/visuoconstructive dysfunction, psychomotor deficits
• Neuroimaging Core– MRI (3D T1- and T2-weighted scans, diffusion-weighted scans, echo-planar imaging scans);
Amyloid PET scan data and derived images
WU Alzheimer’s Disease Research Center Cores
Core Participants Encounters BiospecimensClinical 3,489 11,486 N/APsychometric 3,036 9,554 N/ANeuroimaging 716 1,346 N/ANeuropathology 1,255 1,255 ~62,000Genetics 3,669 5,467 ~170,000Biomarkers 465 497 ~25,000
WU ADRC Data Integration Problem
BiomarkersCore
ClinicalCore
PsychometricCore
NeuroimagingCore
NeuropathologyCore
GeneticsCore
SAS
Excel
Filemaker Pro
MySQL
PostgreSQL ?
Translational Research Paradigm
Study Participant
Peripheral LeukocytesSerum / PlasmaFrozen Tumor BiopsyBone MarrowFFPE Block
RxPeripheral LeukocytesSerum / PlasmaFrozen Tumor BiopsyBone MarrowFFPE Block
Biospecimen Bank and
Informatics
Mutation Profiling
Proteomics
Gene Expression Microarray
FFPE qRT-PCR
Biomarker Validation
aCGH DB
DB
DB
DB
Clinical Data Molecular Data
IHC / Cell Assays
Integrative Analysis
Collection Site Specimen Bank Investigator Lab
Biospecimen Inventory
Collect Ship
Process Store
Distribute
Studies Database
Add ProtocolAdd Annotation
Accession SpecimenCreate SpecimenDistribute
SearchOrder
Workflow of a Translational Research Study
Intake Site
Register Participant
Register Participant
Add Collection Event
Exam Site #1 Exam Site #2 Exam Site #n…
Add Exam Site Details at Encounter Event
Collection Site Specimen Bank Investigator Lab
Biospecimen Inventory
Collect Ship
Process Store
Distribute
Studies Database
Add ProtocolAdd Annotation
Accession SpecimenCreate SpecimenDistribute
SearchOrder
Workflow of the WU ADRC
Intake Site
Register Participant
Register Participant
Add Collection Event
Exam Site #1 Exam Site #2 Exam Site #n…
Add Exam Site Details at Encounter EventClinicalCore
ClinicalCore
PsychometricCore
NeuroimagingCore
Biomarkers, Genetics, &
NeuropathologyCores
ClinicalCore
Collection Site Specimen Bank Investigator Lab
Biospecimen Inventory
Collect Ship
Process Store
Distribute
Studies Database
Add ProtocolAdd Annotation
Accession SpecimenCreate SpecimenDistribute
SearchOrder
Clinical Studies Data Management
Intake Site
Register Participant
Register Participant
Add Collection Event
Exam Site #1 Exam Site #2 Exam Site #n…
Add Exam Site Details at Encounter EventClinicalCore
ClinicalCore
PsychometricCore
ClinicalCore
Studies Database
ClinPortal: Representing & Storing Clinical Studies
• Robust and scalable clinical studies management system
• End user graphical design of clinical case reports
• Automatic generation of forms for data entry
• Graphical interface to query and download study data
PARTICIPANTAn individual who has consented to a study
1
many
PARTICIPANT STUDY REGISTRATIONAn event in which a
PARTICIPANT is registered to a CLINICAL
STUDY
CLINICAL STUDYA set of attributes that dictates how a study is
to be conducted
many
1
ENCOUNTER EVENTAn encounter with a
PARTICIPANT enrolled on a CLINICAL STUDY at a
point in time when data is captured
1
many
ANNOTATIONOne or more data
elements describing the PARTICIPANT
1 many
1 many
ClinPortal Concepts
ClinPortal Study Definition
• Define clinical study encounter events
• Define data elements (attributes or variables) to capture at each encounter event
• Model data elements as appropriate to the biomedical domain (e.g. group biomarkers together and organize physical exam findings per anatomic location)
• Create forms containing variables
• Associate form(s) to one or more encounter events
Encounter events and annotations
Participant demographics page
ClinPortal: Participant Registration
Encounter events and annotations
Data entry form(s)
ClinPortal: Encounter Event and Data Entry
Collection Site Specimen Bank Investigator Lab
Biospecimen Inventory
Collect Ship
Process Store
Distribute
Studies Database
Add ProtocolAdd Annotation
Accession SpecimenCreate SpecimenDistribute
SearchOrder
Workflow of the WU ADRC
Intake Site
Register Participant
Register Participant
Add Collection Event
Exam Site #1 Exam Site #2 Exam Site #n…
Add Exam Site Details at Encounter Event
Biomarkers, Genetics, &
NeuropathologyCores
Biospecimen Inventory
• Comprehensive biospecimen informatics system– Tissue bank functions
• Protocol Management• Inventory Tracking• Quality Assurance / Quality Control Parameters
– Annotation Features• Concept-coded surgical pathology reports• Discrete Clinical and Pathology Attributes
– Researcher functions• Graphical query interface• Biospecimen ordering system
Tissue Suite
Tissue Suite Concepts
PARTICIPANTAn individual from
whom biospecimens are collected
1
many
PARTICIPANT PROTOCOL
REGISTRATIONAn event in which a
PARTICIPANT is registered to a
COLLECTION PROTOCOL
COLLECTION PROTOCOL
A set of attributes that dictates how
biospecimens are to be collected
many1
SPECIMEN COLLECTION GROUPOne or more specimens collected at one point in
time from a PARTICIPANT enrolled on a
COLLECTION PROTOCOL
1
many
SPECIMENA tissue or fluid collected from a PARTICIPANT
1 many
DISTRIBUTION PROTOCOL
A set of attributes that dictates how
biospecimens are to be used for a correlative
science study
many1
1 many
Aliquot Derivative
Participant demographics page
CP registration page
Tissue Suite: Participant Registration
Creation of all expected specimens, derivatives, and aliquots based on CP definition
Calendar clock offset
Collection event (SCG) status
Tissue Suite: Add Specimen Collection Group
Label printing 1. Indicate expected specimens collected
2. Indicate expected derivatives / aliquots created
3. Pre-defined / editable labels, quantities, and storage destination
Tissue Suite: Add Specimen Collection Group
De-Identified Report Information
Category Highlighter
PROCEDURE ORGAN DIAGNOSIS Modifier [Report de-identified (Safe-harbor compliant) by De-ID v.6.14] [Final Diagnosis] Consult from CHLA, Los Angeles, CA: ***PATH-NUMBER[1] (**DATE[Nov 28 05])): Left parotid gland, resection: MUCOEPIDERMOID CARCINOMA, LOW GRADE (SEE NOTE). [Microscopic Description] Parotid gland contains a multilocular cystic lesion. Some of the smallercysts are filled with mucoid debris. The cystic lesion is embedded in a dense, collagenous pseudo-capsular reaction with entrapped smaller cysts within the dense collagen. There is extensive inflammation around the smaller peripheral cysts, and in places there is follicular lymphoid tissue around the larger cystic areas. The lining varies. Most of the larger cysts are lined by a mucoid layer rich in goblet cells that are very large and often ballooned with concretions. There are cuboidal and squamous areas admixed with oncocytic foci. In some areas, the lining is proliferative, and there are multiple layers that appear disorganized. The collagenous reaction that encompasses squamoid hyalines approaches within one high-power field of the inked margin of resection. The surrounding gland is locally atrophic, with a chronic periductal inflammatory component.
Tissue Suite: Other Features
Progress to Date
• Neuropathology Core migrated to Tissue Suite for prospective biospecimen collection; Creating forms for pathology annotation and NACC Neuropathology
• Genetics Core being migrated to Tissue Suite
• Clinical and Psychometric Core data elements being modeled
• Plan to engage Biomarkers Core in January 2009
• Neuroimaging Core integration by late 2009
Institution to Global IntegrationcaBIG: cancer Biomedical Informatics Grid
CTSA: Clinical and Translational Science Award
Summary: ADRC Data Integration and Sharing
TissueSuite ClinPortal XNAT
BiomarkersGenetics
Neuropathology
ClinicalPsychometric
Neuroimaging
TissueTissueSuiteSuite
ClinPortalClinPortal
caGrid BIRN
GRID
AcknowledgmentsOn-site TeamSunita KoulJoanne ZhaoGeorge JosephRekha MeyerYongkee ChoLi-Wei ChangHrishikesh DeshmukhMukesh SharmaBurr FontaineCaerie HouchinsDan FlasarJahangheer ShaikEdmond AbrahamianHaresh BhatiaDianne OliverAmmar HalawaDaniel FaresDavid MulvihillBijoy GeorgeRobnet Kerns
Software Engineers
Project ManagerSrikanth Adiga
Abhijit Naik Mandar Shahasrabudhe Sachin LaleAmit Bidkar Mandar Shidhore Sagar BaldwaAmit Doshi Milind Kulkarni Sakshi RaoAnup Agrawal Namita Hardikar Salil GavankarAshish Gupta Nitesh Marwaha Sanket AtreAtul Jawale Pawan Maheshwari Santhoshkumar ChintalaBaljeet Dhindhwal Pooja Arora Sarita SoniBhagyasree Chaudhuri Pooja Deshpande Seema GoswamiChandrakant Talele Poornima Gokhale Shailesh WaghChetan Patil Poornima Govindrao Shital LawhaleChitra Garg Pradhnya Unawane Siddharth ShahDeepak Shingan Prajakta Sakat Snehil GuptaDeepali Ahirao Prasanna Kashikar Srinath KrishnamurthyDeepti Shelar Prashant Bandal Sujay NarkarFalguni Sachde Prashant Kadam Sumit DeshmukhGanesh Naikwade Pratha Budhrani Sumit GauravHrishikesh Rajpathak Preeti Munot Sunil AgrawalJanhavi Hasabnis Rachana Dharpure Supriya DankhJasbir Sachdeva Rajesh Patil Swati ChavanJignesh Wala Rajesh Vyas Syed RizviJuberahamad Patel Rakhi Garg Taraben KhoiwalaKalpana Thakur Ravi Kumar Vaishali KhandelwalKiran Pinnamaneni Ravindra Jain Vijay PandeKunal Kamble Reena Athawle Vimal RawatLalit Chand Rinku Arora Vipin BansalLeena D'Almeida Rukhsana Sameer Virender MehtaMadhumita Shrikhande Rupali Ratnaparakhi Vishvesh MulayMadhurima Bhatacharjee Rushikesh Kanap Yogesh LeveMandar Deshmukh Rushikesh Subedar Yogesh Shetty
WU ADRCJohn MorrisADRC Core DirectorsADRC Personnel