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Early Experience of Gene Sequencing Classifier Compared to Gene Expression Classifier


Interview with Jennifer A. Sipos, M.D., The Ohio State University

Dr. Jennifer Sipos is a professor and endocrinologist at The Ohio State University’s Division of Endocrinology where she sees patients and specializes in research on thyroid nodules and thyroid cancer. Her institution has been an early adopter of the Afirma Genomic Sequencing Classifier and, before that, of the first-generation Gene Expression Classifier (GEC). Here she spoke with us about her team’s investigation of the next-generation Afirma test’s performance compared to the original.

Q: What was the purpose of your study?

Dr. Sipos: We wanted to see if the Afirma Genomic Sequencing Classifier increased the benign call rate on thyroid nodules evaluated at our institution and, if so, to what degree. We began using the next-generation test in August of 2017 and, before that, used the GEC since it became available in 2011, so we had a good amount of data to compare the two test versions.

Q: How did you go about doing the comparison?

Dr. Sipos: We studied prior GEC testing to determine how many indeterminate cases in the Bethesda III and IV categories the GEC identified as benign versus suspicious for cancer. We then compared this information to patients in the same Bethesda categories who were tested with the GSC. We also did a chart review of the GSC cases that were called suspicious to see what their surgical pathway and results were.

Q: And what did you find?

Dr. Sipos: There were 47 indeterminate cases that had GSC testing and were included in our study. Of these patients, the GSC called nearly three fourths (72.3 percent) benign. This was significantly higher than the nearly half (48.4 percent) that were called benign previously by the GEC. Ten of the 13 GSC-suspicious cases went to surgery and, of these, six – or 60 percent – were cancers.

Q: What is the significance of these findings to clinicians and their patients?

Dr. Sipos: We know that the Afirma GSC has a high negative predictive value that’s similar to the GEC. So, with the GSC, it’s really nice to have a test that gives high confidence in its benign calls, while also calling a lot of patients benign. The high NPV gives physicians and patients confidence that they are making the right decision when they decide not to go to surgery. As a physician, it’s very rewarding because I don’t want to send patients to surgery if they don’t need it and now I can help even more patients avoid this route.

Q: Do you have any thoughts on the overall impact to your institution of being able to identify more benign cases?

Dr. Sipos: Yes, because of our high patient volume, we have a lot of indeterminate cases. In reviewing our old datasets, we’ve had nearly 500 patients get tested using either the GEC or – now – the GSC. If you think about all of the unnecessary surgeries being avoided, in addition to helping patients, we’re helping reduce healthcare costs because that represents a lot of money being saved.