Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona)
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The document provides a brief overview of amplicon variant analysis in biomedical research, emphasizing the importance of characterizing viral populations for understanding diseases like HIV-1 and HCV. It covers concepts such as next-generation sequencing (NGS), sources of error, and the clinical implications of identifying mutations associated with drug resistance. The presentation outlines the potential of NGS to enhance the accuracy and throughput of viral strain analysis.
Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona)
- 1. Hospital Universitari Vall d’Hebron Institut de Recerca - VHIR Institut d’Investigació Sanitària de l’Instituto de Salud Carlos III (ISCIII) Bioinformàtica per la Recerca Biomèdica http://ueb.vhir.org/2014BRB Ferran Briansó ferran.brianso@vhir.org 20/05/2014 BRIEF OVERVIEW TO AMPLICON VARIANT ANALYSIS
- 2. 1. DISCLAIMER 2. BASIC CONCEPTS 3. NGS APPROACH 4. SOURCES OF ERROR 5. CLINICAL RELEVANCE 6. BAD NEWS / GOOD NEWS 5 1 2 3 5 6 PRESENTATION OUTLINE 4
- 3. DISCLAIMER1 3Extracted from Dr Kassahn's publicly shared slides (2013)
- 4. BASIC CONCEPTS2 4 2 * Being able to characterize viral populations rapidly and accurately is important for understanding pathogenesis, interplay between viruses and humoral responses, and the evolution of drug resistance * Both HIV-1 and HCV exist as viral quasispecies in a host, i.e. many distinct viral strains are circulating at any given moment in time * NGS has the potential to directly sequence many such strains * Using multiplexing (multiple samples/run), high throughput can be achieved
- 5. 5 2 BASIC CONCEPTS * Which mutations are real? - Sequencing error - Assay error / reproducibility * What frequency of mutations matter clinically? * DRAMs = Drug resistance associated mutations * Cloning/Single genome sequencing generates ~10-100 sequences; how representative is this of the entire population? * NGS approach obtain 1000s of reads/sample from a single run
- 8. 454 SEQUENCING ERROR RATES 8 4
- 9. 454 SEQUENCING ERROR RATES 8 4
- 11. BAD NEWS / GOOD NEWS1 10 6
- 12. BAD NEWS / GOOD NEWS1 11 6