Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona)
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Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona)

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Course: Bioinformatics for Biomedical Research (2014). ...

Course: Bioinformatics for Biomedical Research (2014).
Session: 3.1- Brief Overview to Amplicon Variant Analysis.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.

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Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona) Brief Overview to Amplicon Variant Analysis (UEB-UAT Bioinformatics Course - Session 3.1 - VHIR, Barcelona) Presentation Transcript

  • 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
  • 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
  • DISCLAIMER1 3Extracted from Dr Kassahn's publicly shared slides (2013)
  • 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 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
  • 6 3 NGS APPROACH
  • SOURCES OF ERROR 7 4
  • 454 SEQUENCING ERROR RATES 8 4
  • 454 SEQUENCING ERROR RATES 8 4
  • CLINICAL RELEVANCE 9 5
  • BAD NEWS / GOOD NEWS1 10 6
  • BAD NEWS / GOOD NEWS1 11 6