Read the summary and the most important questions on Cancer Genomics

• 1 Day 1: Introduction Cancer Genomics

• 1.1 Introduction

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• Strict defenition of cancer genomics

  The study of genome-wide DNA changes in cancer cells

• Wider definition of cancer genomics 

  Using genome-wide technologies to understand and treat cancer cells

• Cancer cells accumulate somatic mutations over time in differnt ways

  1. Intrinsic mutations
  2. Environmental and lifestyle exposures
  3. Mutator phenotype
  4. Chemotherapy

• Tumor mutation burden (TMB) varies by?

  Cancer type, age and environmental exposure

• Tumor mutation burden (TMB)

  The total number of mutations found in the DNA of cancer cells

• Cancer genomics plays a huge role in?

  Identifying novel targets and identifying eligible patients

• Molecular drugs are often given in combination for?

  Increased effectiveness (synergistic drug effect). But even then resistance frequently arises.

• 1.2 Working with sequencing data

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• Typical NGS pipeline

  1. Sequence reads (fastq)
     
  2. Aligment to genome (sam, bam, cram)
  3. Variant calling 
  • SNVs/indels (vcf)
  • SVs (vcf)
  • CNV (bed, seq)
  • Gene fusions (txt)

• Average depth of sequencing coverage

  (L * N) / G
  L = read length
  N = number of reads
  G = haploid genome length

• 2 Day 2: Somatic and Germline SNV calling

• 2.1 Calling Somatic SNVs

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• Several factors that complicate somatic SNV calling

  • Intra-tumour heterogeneity
    
  • Aneuploidy
  • Unbalanced structural variations
  • Normal contaminated with tumor DNA
  • Sequencing errors