Course Details

  • Date: February 27th, 2020 - February 27th, 2020
  • Time: 1:00 pm - 3:00 pm
  • Location: Building 37, Room 4041/4107
  • Presenter(s): Anney Che (NCI/OD-F/Advanced Biomedical Computational Science), Hue Reardon (NCI/OD-F/Advanced Biomedical Computational Science), Uma Mudunuri (NCI/OD-F/Advanced Biomedical Computational Science)

The Annotation, Visualization and Impact Analysis (AVIA) is an application developed to guide, prioritize and summarize genomic variants. AVIA maintains and aggregates dozens of publicly available variant annotation databases and predictions from impact analysis algorithms, allowing users to investigate functional significance of their genetic alterations across samples, genes, and pathways.

This demonstration will cover:

  • Variant annotation and impact analysis
  •  Variant representation formats and standards
  • Analyze variants using AVIA
    • Submit variant lists
    • Understand annotation categories
    • Include or exclude variants based on
      • genes of interest
      • genic features – intronic, exotic, splice
      • public databases – 1000 genomes, TCGA, ClinVar
      • region features – repeat regions, mappability
      • custom annotations
    • Impact analysis
      • levels of impact – pathogenic to benign
      • prediction algorithms on pathogenicity
      • clinical annotations from sources such as ClinVar
    • Variant, gene, protein and pathway analysis
    • View related literature
    • Overview profiles
      • variant landscape using vcf.iobio
      • gene variant profile using gene.iobio
      • frequency of variant occurrence by genes and samples
    • Comparative Analysis
      • overlap with public data sources such as TCGA
      • assess type of damage and compare with cancer mutational profiles using SAMM
      • between sample comparisons
    • Share data with collaborators
    • Reannotate – new genome versions or new samples

 

Link to WebEx recording: https://cbiit.webex.com/cbiit/ldr.php?RCID=838671822befaaf2bf504f85a5fb897b

 

 

 

 

 

 

Course Material 1: PDF icon AVIA_BTEP_27Feb2020.pdf