During this webinar, speakers from the Center for Personalized Diagnostics at Penn Medicine discuss the design and technical validation of a custom next-generation sequencing panel to detect mutations in a wide array of tumor types.

Next-generation sequencing of tumor-derived DNA has revolutionized clinical cancer genomic diagnostics by directing molecularly targeted therapies. The accurate detection of mutations at low allele frequencies is essential for wider adoption of this approach due to high levels of stroma and tumor-infiltrating lymphocytes diluting the detectable alterations.

The Center for Personalized Diagnostics began clinical NGS of solid tumors in 2013 using a 47-gene panel covering clinically relevant genes and hotspots. This was an early success with over 3,500 solid tumors sequenced in the laboratory over three and a half years.

However, the demand to increase gene content and to detect mutations in a wider array of tumor types led the team to explore molecular barcoding to bioinformatically eliminate duplicate reads and detect variants at lower allele frequencies. The team developed a custom 153 gene Agilent HaloPlexHS NGS panel to address this need. Dr. Jennifer Morrissette and her colleague Karthik Ganapathy share details of this work and discuss key considerations for the design, technical validation, and performance of this panel. Ashkan Bigdeli, an informaticist in the CPD demonstrates that in addition to Agilent’s SureCall software, a lab can choose to write a custom script for the analysis of HaloPlexHS NGS data.