About this Class

Fundamentals of DNA copy number analysis using Nexus
Learn the basics of copy number analysis and its application to genomic research. Fundamental concepts such as copy number measurement methods, quality assessment, and different approaches/algorithms used for detecting copy number changes and allelic events as well as unique complications encountered in cancer data will be presented. You will also learn how to apply this knowledge to common research objectives such as identification of significant aberrations, comparisons between sub-populations, and identification of biomarkers.

1. Introduction and course overview
2. Fundamentals of DNA copy number analysis
   1. Review of copy number measurement methods
      • BAC arrays
      • Oligo two color arrays
      • SNP Arrays (with and without CNV probes)
      • MIP Array data
      • Next-Gen data
   2. Review of unique complications in cancer data
      • Aneuploidy
      • Sample heterogeneity due to surrounding tissue contamination as well as colonal diversity
      • DNA fragmentation in FFPE samples
   3. Data preprocessing and quality assessment
   4. Approaches for detecting copy number and allelic event changes
      • Differences between copy number and allelic event data
      • HMM methods, CBS, ADM, ASCAT
3. Research objectives attained with the data
   1. Identification of recurrent events in a population
   2. Identification of statistically significant aberrations (STAC/GISTIC)
   3. Comparisons between groups
   4. Grouping samples based on copy number profiles
   5. Identification of biomarkers that are predictive of events such as survival