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