Bayes and NGS

NGS process

• Library preparation
  • DNA pool (diversity, many cells)
  • Targeted (multiplexing PCR, Hybrid capture)
    
  • Adeptor ligation (ID, primer, platform adaptor)
• Sequencing
  • Amplification (to enhance signal)
  • Sequencing (capture photo, check electric current change)
• Alignment
  • SAM, BAM file
• Variant calling
  • Bayes approach
  \[\text{Posterior} = (\text{Prior} * \text{Likelyhood} )/\text{Normalizing constant}\]

Allele frequency (AF)

• Allele
  • Population
    
  • Cancer
• Somatic vs Germline
  • CNV
    
  • Minor allele frequency
    
  • Tumor cellularity

• CNV
  • CNV
    
  • Minor allele frequency
    
  • Tumor cellularity
• Markov Chain Monte Carlo (MCMC)
  • Hierachical model
    
  • Determine parameter distribution by simulation