SATuRN HIV-1 Genotyping System Justen Manasa Africa Centre for Health and Population Studies Virology laboratory based at the Nelson R. Mandela School of Medicine University of KwaZulu Natal
Jan 03, 2016
SATuRN HIV-1 Genotyping System
Justen ManasaAfrica Centre for Health and Population Studies
Virology laboratory based at the
Nelson R. Mandela School of Medicine
University of KwaZulu Natal
SATuRN
• A collaborative network of scientists and researchers working on HIV and TB drug resistance.
Collaborative SATuRN version (currently 3000 patients with genotype information).Users:
• AC-UKZN (Dr. Tulio de Oliveira).
• MRC and Jembi Health Systems (Dr. Chris Seebregts)
• HPP Virology, University of KwaZulu-Natal (Dr. Mitchell Gordon)
• Stellenbosh Univ. (Dr. Gert Van Zyl),
• NICD (Prof. Lynn Morris, Dr. Gillian Hunt),
• NHLS, Witts University (Prof Wendy Stevens/Prof Maria Papathanasopoulos)
• Inkhosi Albert Luthuli Department of Virology Laboratory NHLS (Dr. Pravi Moodely)
• UFS (Dr. Cloete van Vurren, Dewald Stein),
• Pretoria Univ. (Prof. Sharon Cassol and Theresa Russouw),
• Dept of Medical Virology, University of Pretoria (Prof. Sheila Bowyer/Prof Lynne Webber)
• Ministry of Health (Botswana) (Dr. Madisa Mine and Dr. Avalos)
• AIDS and TB Unit -Ministry of Health (Zimbabwe)
• Stanford-UZ (Prof. David Katzenstein),
Policy:
1. No private patient information or public identification number is added to the database.
2. Data is owned by the researchers.
3. Database is password protected and datasets and dataset access is exclusive to the researcher. Researcher can give access to part of the data to its collaborators.
4. After publication researchers can choose to deposit the data in a collaborative area “public area” of the database where other participants of the network have access to the data.
5. Publication of manuscripts from “public” area will include as authors up to two members of the group that deposited data.
Sequence AnalysisAt AC Lab
RegaDB database at MRC
Data Entries at AC
+ clinical and treatment info
RT-PCR Protocol
Protease and RT Protease and RT
Reverse transcription
Reverse transcriptionRT21RT21
RT21RT21MAW26
MAW26
1st Round PCR
1st Round PCR
RT20RT20Pro1Pro12nd Round
PCR2nd Round
PCR
1.3 kb fragment1.3 kb fragment
SATuRN Data Curation
CollaboratorsSATuRN DBStanford HIVDB
Mirror HIVDB
HIVDB
Data Curation Rega DB
Data Curation At Stanford
Input data
•Sequences
•Clinical data
•Tx history
•Viral load and CD4 resultsPASSW
ORD
PROTECTION OF Rega
DB
– A medical informatics database dedicated to HIV management
– Linked to a some of the leading HIV drug resistance analysis tools
– Can be used as either a clinical or research tool
– The online version provides a very good collaborative platform
– To be used by• Clinicians
• Researchers
– Data is password protected
– All data is de-identified
– Data can be published thus accessible to other members of the consortium or unpublished-access limited to the owners only.
Developed by: REGA Institute, Leuven and Mybiodata
REGA DATABASE (RegaDB)
RegaDB Objective
• A free and open-source database system
• Facilitate research collaborations
– Easily interchange data, keeping track of data origin
– Create collaborative databases keeping track of dataset versions
– Easily publish data sets to Stanford HIVDB
• Empower clinicians with analysis tools
– Patient history graph
– Sequence analyses
• HIV typing and subtyping
• Genotypic analyses for resistance interpretation
• Third party analyses as “web services”
– Resistance reports
Data Entities
Patient
Therapy
Dataset
Test
Viral Isolate
Attribute
Event
Attributes
• Annotate Patient with information
– Adapts to “your (research) interest”
– Typically clinical and epidemiological information
• Examples
– Gender
– HIV transmission risk group
– Most of information collected in Collaborative projects
• Attributes may be grouped (like “SATuRN or SPREAD”)
Viral Isolates
Viral Isolates
Insertion
NucleotideSequence
Amino AcidSequence
Mutation
Protein
Informationautomaticallyinferred
ANALYSES
Analysis Services
• Built-in services– REGA Subtype tool
– Stanford ASI genotypic resistance algorithms
• ANRS, HIVDB, REGA
– Resistance report generation• Using your own template documents
• Integrate with external analysis services– Using “web services”
– e.g. connect to geno2pheno or Stanford
Synchronize auxiliary data• Auto-update services for
– Drug definitions
– New (versions of) resistance algorithms
– Test types / Tests
– Attribute types / Attribute groups
Data Set Management
Patient Management
Patient Profile
Management of Patient Measurements
Management of Therapies
Drug resistance report
Patient Chart
Thank You