brief overview to amplicon variant analysis (ueb-uat bioinformatics course - session 3.1 - vhir,...
DESCRIPTION
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.TRANSCRIPT
Hospital Universitari Vall d’HebronInstitut 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[email protected]
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
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PRESENTATION OUTLINE
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BASIC CONCEPTS2
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* 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
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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