Dr. Milan Radovich is an Assistant Professor of Surgery at the Indiana University School of Medicine and his current research focuses on the uses of archived breast tumor samples that had been previously determined as “triple negative”, which means genetically they are negative for expressing the estrogen receptor, progesterone receptor, and the Her2/neu genes thus making these tumor types recalcitrant for commonly used chemotherapy. Triple negative breast cancer (TNBC) comprises about 10 to 15% of all breast cancers and is a considerably more lethal with a poorer prognosis.
Dr. Radovich’s team is working on a large, integrative approach that not only uses sequencing to study the tumor gene expression of TNBCs to identify new molecular targets, but he also focuses on germline genetics, using both transcriptome sequencing and Ion AmpliSeq Whole Exome with the Ion Proton sequencer.
One of the most powerful applications of Dr. Radovich’s next-generation sequencing research is comparing TNBC to normal breast tissue. Indiana University happens to be home to the Susan G. Komen For the Cure Tissue Bank, the largest repository of normal breast tissues in the world. The bank contains 1,500 frozen specimens with matched blood, DNA, and plasma, and a full medical history. By comparing archived samples of triple negative versus normal laser micro-dissected breast tissue using both the ArcturusXT Laser Capture System combined with SOLiD Transcriptome Sequencing, he recently reported the transcriptional heterogeneity and gene disregulation of TNBC. He also uses Ion AmpliSeq Whole Exome sequencing from both tissue and plasma to look at germline variation that may affect drug response.
Dr. Radovich also is using sequencing to test new medications with an approach called tissue derived xenografts. These are tumors taken from subjects then implanted in mice, and novel compounds can then be tested against these xenografts for efficacy. Sequencing helps the team characterize these xenografts. “We actually get an idea of why, genomically, these different tumors are getting differential responses,” Dr. Radovich said.
When the team started, they evaluated a variety of platforms. First using SOLiD® sequencing and now the Ion Torrent™ platform, they now have the best balance of cost, effectiveness, breadth of coverage, and evolving automation. Since Dr. Radovich is sequencing many samples, the ability to automate libraries and the templating of emulsion PCR, and then sequence with a very quick turnaround time was a significant factor in their decision.
The main application of Ion Proton sequencing for Dr. Radovich has been RNA sequencing. His lab leverages the amount of reads on the Ion PI Chip, as well as longer read lengths, to interrogate gene fusions and alternative splicing. View Dr. Radovich’s YouTube video and see how Ion Torrent sequencing methods and analyses have helped his team arrive at new possibilities in cancer research. If you are interested in learning more about his research, watch the full presentation of his research using RNA-Seq and Exome-Seq to discover cancer biomarkers.