Processing Ion AmpliSeq™ Cancer Panel Data using NextGENe Software

The Ion AmpliSeq™ Cancer Panel uses highly multiplexed PCR in order to generate amplicons from 46 different cancer genes. These amplicons are sequenced on the Ion PGM™, allowing for rapid turnaround and low cost. NextGENe® software allows for a customized analysis of the results, including detection of novel alleles, alleles found at lower frequencies (less than 5%), or alleles in regions with less than 500x coverage. NextGENe includes many useful features, such as quality control reports, functional prediction scoring, and advanced project comparison.

An AmpliSeq Cancer Panel dataset can be processed in less than 15 minutes with NextGENe on a desktop computer. All analysis steps are performed with an easy-to-use point-and-click interface. The software provides a highly accurate and sensitive analysis of the Cancer Panel. Results as well as quality control metrics such as per Amplicon coverage, coverage no meeting user set criteria by Amplicon, mutation confidence score can quickly be assessed within the software.

Found variants are reported in the software’s mutation report which includes complete annotation, including Amino Acid Change and Causative Prediction information from dbNSP and the Sanger Centre’s COSMIC (Catalogue of Somatic Mutations in Cancer) database. The linked graphical viewer allows quick review and confirmation of found variants.

For user convenience SoftGenetics has created two .bed files one for the entire sequence and one for the loci only. See bottom of page for download link.

NextGENe includes a variant comparison tool which allows for comparison of up to 10 separate analysis using the same reference. Differences and similarities are quickly ascertained by using the reports embedded filtering capabilities.