Scaling up with Ingenuity Variant Analysis for Ion Reporter at the University of Arizona Cancer Center

George Watts, PhD, has never been afraid to try something new.

George Watts, PhD University of Arizona Cancer Center

George Watts, PhD
University of Arizona Cancer Center

As a postdoctoral fellow at the Arizona Cancer Center in 1997, Dr. Watts became the first scientist in the state of Arizona to analyze the genetics of cancer cells using DNA microarray technology. Now as a Research Assistant Professor and Co-Director for the Genomics Shared Service at the University of Arizona Cancer Center, he is moving aggressively into Next-Generation Sequencing (NGS), first on the Ion PGM™ sequencer and most recently on the Ion Proton™ system.

“The objective of just about every study in our center is identifying variants in targeted genes that help explain tumorigenesis,” Dr. Watts explained.  “NGS gives us additional capabilities to identify rare variants that may help to explain the base mechanisms of cancer.”

But NGS also delivers a lot more data than traditional microarray approaches.  For this, Watts relies heavily on the Ion Reporter™ Software Suite and the integrated Ingenuity® Variant Analysis™ workflow.

Ion Reporter Software is a suite of bioinformatics tools that streamlines and simplifies the analysis, annotation, reporting and archiving of semiconductor sequencing data.  Ingenuity Variant Analysis is integrated into Ion Reporter, providing simple and secure access to the web-based Variant Analysis application, which helps researchers studying human disease to identify biologically relevant variants from Ion Torrent human sequencing data in just hours.

Dr. Watts is one of the most active users of the Ingenuity Variant Analysis integration into Ion Reporter and as an early adopter to this integration has been instrumental in optimizing the workflow.  “I recently loaded 92 samples to Variant Analysis from Ion Reporter.  These were for two separate projects using different tissue types but all running custom AmpliSeq panels that we have designed,” he described.

For Dr. Watts, the biggest value of Ingenuity Variant Analysis is the exclusive biological content.

“I remember an earlier breast cancer study that we did, prior to the Ion Reporter/Ingenuity Variant Analysis offering, in which 6 of the 15 had mutations in BRCA2,” stated Watts.  “We did our own PubMed searches and saw papers that associated these BRCA2 mutations with increased risk of cancer.  But when we dug deeper we saw that the meta-analysis refutes these claims and identified the mutations as fairly common SNPs.  The great thing with Variant Analysis is that it filters out these ‘false positives’ immediately.”

In addition to larger studies, Dr. Watts is also excited to begin generating more data per sample on their Ion Proton instrument as they move into whole exome analysis.

“We have some very interesting families for whom we are going to sequence their whole exomes,” he said.  “I am really excited to take advantage of the full capabilities of Ingenuity Variant Analysis to analyze and interpret these larger datasets.”

One thing we know for sure is that George Watts won’t shy away from trying out new and innovative approaches for unraveling the genetics of cancer.

Want to learn more about Ingenuity Variant Analysis for Ion Reporter?  Find out more here: