Tuesday, November 5th, 2:00 PM - 5:00 PM
Location: Hilton Baltimore, Peale Room (1st Floor)
Brought to you by the AMP Informatics Subdivision
This practical workshop will utilize the widely used open source Integrative Genomics Viewer (IGV; http://software.broadinstitute.org/software/igv/, Broad Institute) in conjunction with real-world clinical cases to explore common problems and solutions encountered in clinical laboratory genomic testing with next-generation sequencing (NGS) panels. Participants will need to bring a laptop with working WiFi and Java installed: instructions and a test project will be available for viewing on the workshop website prior to the meeting. The workshop will start with basic bioinformatics resources and their use in IGV (FASTA/SAM/BAM/VCF), reference genomes, annotation tracks. Effective functional use of IGV will be covered with examples and practice with navigation, read coloring & sorting, vertical & horizontal compositions. Finally, real examples from clinical cases will be used to illustrate common challenges like allelic phasing, degenerate alignments, and distinguishing platform sequencing artifacts from true variants, as well as the effective use of IGV to draw conclusions about ground truth.
Objectives of the workshop:
Review basic bioinformatics file types used in NGS and how they can be loaded/viewed
Develop or enhance familiarity with IGV as a prototypic genomic viewer
Become comfortable with IGV parameters and controls and how they influence the viewing of sequence alignments
Review some top stumbling blocks encountered in clinical NGS and how to find answers with IGV
Requirements for participants:
Laptop with WiFi and Java installed (Java Runtime Environment)
Working familiarity with basic clinical genomics concepts such as the genetic code, exon/introns, and types of mutations
Pre-Registration for this event is now closed. On-Site registration will be available.