NGS 2

clinical applications

Exercises

• Exercise 1: whole genome sequencing; WGS
  
  • Google search exercise: availability and prices.
  • Advantages and shortcomings of WGS.
  • Advantage over WES.
  • Clinical applicability of WGS.
• Exercise 2: whole exome sequencing; WES
  
  • Underpinnings of WES: target enrichment strategies
    • on Wikipedia
    • example: Roche
  • Google search exercise: availability and prices.
  • Clinical applications of WES.
  • Advantages and shortcomings of WES.
• Exercise 3: RNA sequencing; RNASeq - sequencing the transcriptome.
  
  • Transcriptome:
    • What is a transcriptome?
    • The problem of determining the haplotype ("phasing").
    • Gene fusion.
  • How does RNASeq work?
  • Clinical applications 1: RNASeq in tumors.
  • especially understanding Fig. 2
  • ignore protocols, bioinformatics etc
  • Clinical applications 2: older applications.
• Exercise 4: NGS in pathogen detection - clinical setting
  
  • Clinical metagenomics, review
    • especially understanding Fig. 2
  • FDA-ARGOS, reference genomes for diagnostic use and regulatory science
  • Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection
  • skip the intro - start with "Advantages of Metagenomic Next-Generation Sequencing for Pathogen Detection"
  • can skip the "Validation" section