Exome Analysis with Ion AmpliSeq and Ingenuity Variant Analysis

Cancer genomics represents one of the most active and exciting areas of clinical research.  Particularly important is the work being done to generate genetic signatures for cancers, an advance that will enable better risk assessment and treatment decision making.

Ion Torrent recently hosted an exome webinar series on the use of Ion AmpliSeq™ which included a presentation by Jeremy Stuart, Vice President of Selah Genomics and Adjunct Professor in the Department of Biological Sciences at University of South Carolina.

Stuart and his colleagues conducted a proof of demonstration project where exome and Comprehensive Cancer Panel (CCP) sequencing was performed on three types of cancer mutations with the goal of identifying an approach that offers the most relevant mutation data at a reasonable cost. In his talk, Stuart discussed how he used Variant Analysis to identify disease-causing variants for use in the development of new gene screening service.

Performing a filtering cascade using Ingenuity Variant Analysis, they were able to quickly narrow down 60,000 variants to the 376 associated with some sort of pharmcogenetic response.  The Variant Analysis Filter Cascade works by eliminating common and non-deleterious variants using a basic set of filters that quickly reduce the number of variants significantly. Users can then apply additional filters based on their knowledge of the disease being studied, to further reduce the number of variants allowing them to go from millions or tens of thousands to hundreds of interesting variants for follow on studies.

With this more targeted set of genes, Stuart and his colleagues were able to validate a subset which are now being piloted in Selah Genomic’s PrecisionPath™ service, a range of clinically validated biomarker assays that support stratification and management of patients diagnosed with cancer.

If you are interested in hearing the whole presentation, Ion Torrent has archived the webinar for viewing at your convenience.