What to Consider When Choosing a Preimplantation Genetic Testing (PGT) Platform

Adam Goodman is a graduate of the University of Michigan and trained for many years at the Reproductive Genetics Institute in Chicago under Yuri Verlinsky and Svetlana Rechitsky, two founding pioneers in preimplantation genetics. There he helped the lab become one of the first to utilize NGS technology for the detection of aneuploidy in human embryos. He is currently the director of preimplantation genetics at NxGen MDx and has been working in the PGT field for over a decade, playing an essential role in the adoption of evolving PGT technologies for multiple reference labs.

You recently conducted a study comparing the performance of Thermo Fisher Scientific’s Ion ReproSeq^TM platform with Illumina’s VeriSeq^TM platform for preimplantation genetic testing for aneuploidy (PGT-A). What did you find?

We found that both the assays performed identically. Moreover, they both outperform their manufacturer stated resolutions, of about 10Mbp. Using control samples with known deletions or duplications, we were able to discern that both can easily see down to about 5Mbp before we start to see some variability in what they can and cannot detect. 

How do the ReproSeq^TM and VeriSeq^TM platforms compare in their ability to detect mosaicism?

Both can detect as little as 20 percent mosaicism in a given sample. But what I really wanted to see, with regards to mosaicism, was precision. In other words, how much variability in percent mosaicism detected could be produced when the same sample was run multiple times. Here we filled two sequencing runs to capacity by running the same control sample 24 times and again the results were identical. Both platforms saw plus or minus 10 percent from the expected value of 40 percent mosaic.

Aside from performance, what other factors should researchers consider when choosing a platform for PGT-A?

With performance being equal, cost and ease of use become the most important factors when choosing a PGT-A platform. We found Ion ReproSeq^TM assay to be the clear winner in these departments. In addition to having slightly less expensive reagents, ReproSeq^TM use far fewer plastic consumables and does not require the use of a fume hood as does VeriSeq^TM. Moreover, the ReproSeq^TM protocol is more user friendly.

What makes the ReproSeq^TM platform easier to use than the VeriSeq^TM platform?

The biggest difference is that the lengthy and difficult process of preparing amplified samples for sequencing is fully automated on the Ion ReproSeq^TM platform. This essentially frees up five hours of technician time per run compared to VeriSeq^TM. Additionally, this lowers inter-run variable and decreased the chances of human error. 

How do the two systems compare in terms of throughput and turnaround time?

VeriSeq is based entirely on a 24-samples-per-run throughput. The ReproSeq^TM kit has 16, 24, and 96 capacity run options, depending on what size sequencing chip is used. We are currently using the 24-sample capacity most often at NxGen MDx, but at 96 samples per run the cost savings becomes even more significant.

This also has big implications for turnaround time. Because the maximum run size with the VeriSeq^TM platform is 24, if you’re doing 48 or 96 samples, you are essentially doubling or quadrupling the amount of time needed. With the ReproSeq^TM platform, whether running one or 96-samples, the amount of time required changes very little. 

To learn more about simplified PGT-A solutions, watch the on-demand webinar below: