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SATuRN HIV-1 Genotyping System

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. SATuRN.

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SATuRN HIV-1 Genotyping System

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  1. 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

  2. SATuRN • A collaborative network of scientists and researchers working on HIV and TB drug resistance.

  3. 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: • No private patient information or public identification number is added to the database. • Data is owned by the researchers. • 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. • 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. • Publication of manuscripts from “public” area will include as authors up to two members of the group that deposited data.

  4. Data Entries at AC + clinical and treatment info RegaDB database at MRC Sequence Analysis At AC Lab

  5. RT-PCR Protocol Protease and RT Reverse transcription RT21 1st Round PCR MAW26 RT21 2nd Round PCR RT20 Pro1 1.3 kb fragment

  6. SATuRN Data Curation Stanford HIVDB SATuRN DB Collaborators • Input data • Sequences • Clinical data • Tx history • Viral load and CD4 results Data Curation Rega DB Data Curation At Stanford PASSWORD PROTECTION OF Rega DB HIVDB Mirror HIVDB

  7. REGA DATABASE (RegaDB) • 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

  8. 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

  9. Data Entities Event Therapy Attribute Patient Dataset Viral Isolate Test

  10. 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”)‏

  11. Viral Isolates Viral Isolates Nucleotide Sequence A N A L Y S E S Amino Acid Sequence Information automatically inferred Insertion Mutation Protein

  12. 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

  13. Synchronize auxiliary data • Auto-update services for • Drug definitions • New (versions of) resistance algorithms • Test types / Tests • Attribute types / Attribute groups

  14. Data Set Management

  15. Patient Management

  16. Patient Profile

  17. Management of Patient Measurements

  18. Management of Therapies

  19. Drug resistance report

  20. Patient Chart

  21. Thank You

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