NGS 2

Clinical applications

Exercises

• Exercise 1: Panel sequencing
  • Find a homozygous variant in intronic region of some gene in IGV. Make a pic for the presentation
  • WGS vs WES vs panel sequencing
  • NGS-based gene panel tests for the management of solid tumors the sections of interest 4, 5 i 9
  • How many genes are typically sequenced in a panel? (see the Genetic testing registry below)
  • TCGA i ICGC databases (TCGA data portal) the central cancer genome repository

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• Exercise 2: WES - whole exome sequencing
  • Find a homozygous variant in exonic region of some gene in IGV. Make a pic for the presentation
  • WGS vs WES vs panel sequencing
  • how big is exome compared to a genome
  • Exome sequencing in genetic disease (up until and including "shortcomings ..."; you can skip "studying rare variation")
  • what is a monogenic disease
  • what is a 'trio' in genetic diagnostics
  • what is the price of a clinical exome today? what is the price of a trio?

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• Exercise 3: WGS - whole genome sequencing
  • Find a heterozygous variant in exonic region of some gene in IGV. Make a pic for the presentation
  • WGS vs WES vs panel sequencing
  • Best practices ... (the introduction only)
  • What are structureal variants? (See the intro on wikipedia; copy number variation also intro only)
  • What are deep intronic mutations?
  • What are multifactorial (polygenic) diseases
  • What is the price a clinical genome today?

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• Exercise 4: Long reads in clinic
  • Find a heterozygous variant in intronic region of some gene in IGV. Make a pic for the presentation
  • What are structural variants?
  • What is methylation ?
  • Long reads (the introduction only)
  • A nicer illustration of the long reads technology (Fig 2. pls ignore the rest of the paper)
  • The application of long-read sequencing in clinical settings Rare diseases and oncology, pls ignore the rest