Choosing between closely matched technologies isn’t always easy, especially when it’s a decision as big as PGT-A platform. Adam Goodman, head of preimplantation genetic technologies at NxGen MDx, was in that position recently, and it provided him the opportunity to do a detailed research comparison study of ReproSeq and VeriSeq.
Adam Goodman works for NxGen MDx, a genetic testing firm specializing in reproductive and women’s health genetics. NxGen MDx aims to provide “best-in-class services” in everything they do, including all forms of preimplantation testing, and thus places a very high priority on quality when choosing a PGT-A platform.
NxGen MDx was a long-time user of the VeriSeq platform, but recently switched to Thermo Fisher Scientific’s ReproSeq. Describing his experience with VeriSeq, Goodman explains that its manufacturer “wasn’t always the best company to work with for smaller labs.” NxGen MDx considered SNP array technology as an alternative but was not impressed with its trade-offs relative to other platforms, leading them to the Ion ReproSeq instead. Goodman and NxGen MDx were not willing to switch without a careful comparison of the two platforms, which finally convinced them that Ion ReproSeq was their way forward.
Goodman notes that, “up until the point you’re starting to do whole-genome amplification, the protocols are virtually the same. However, post-amplification it is almost completely automated using the Ion Chef robotics, greatly reducing the learning curve for new technicians. Although on paper the protocols have similar hands-on time, in practice only the fully automated Chef protocol provides a ‘set it and forget it’ type solution in which technicians can work on other tasks.” However, an improved workflow would not be enough reason to retool a laboratory as sensitive as one dedicated to preimplantation testing, so Goodman and his team carefully compared the two platforms’ results as well.
Goodman’s team compared test outcomes for a selection of embryo biopsies previously predicted to be aneuploid by third-party SNP testing. Each of the two platforms produced identical results compared to each other and to reference methods: “We found nothing different between the two assays. Every prediction was exactly the same.” This gave NxGen MDx confidence that the Ion ReproSeq PGS kit and Ion GeneStudio S5 system are as good as the VeriSeq platform. Interestingly, both the VeriSeq and Ion ReproSeq fared better than the SNP-based assay that was also included in the study, which showed as many as six false positives out of 50 samples.
Next, they wanted to compare the limits of detection, or how small a segmental deletion they could successfully detect with each method. Here, they used carefully counted sub-samples from known aneuploid cell lines designed to simulate trophectoderm biopsies. After testing for segmental deletions ranging from 40 megabase all the way down to 1 megabase, they found complete concordance between the VeriSeq and ReproSeq. In fact, they found that “they both outperform their manufacturer-stated resolution, which is about 10 megabase pairs” by successfully recognizing 5-megabase segmental deletions.
As their third test, Goodman’s team tested the platform’s ability with regard to mosaicism precision. Mosaic samples were a part of the first test performed and both platforms made accurate calls. However, as Goodman puts it, “What we were more interested in is if you run the exact same sample and fill an entire run with it, so 24 samples, what kind of variation will we see in terms of percent mosaic in the results?” Using genomic DNA and large runs consisting of identical samples, they checked for inter-sample variability to establish how trustworthy each test’s mosaicism readings could really be. Here, as before, VeriSeq and ReproSeq again proved identical to one another, each showing ± 10% as the maximum variability in an entire run.
With these confirmations that the ReproSeq is as good as their current platforms and better than an SNP-based assay, Goodman and his team then focused on practical utility. In their estimation, for the same sample throughput, the ReproSeq workflow is easier and requires far less trained technician time in comparison to the VeriSeq workflow. Additionally, Ion Reporter software used for PGT-A data analysis allows Goodman’s team to be more involved in data analysis in terms of customizing the software to their needs. In the end, in Goodman’s words, “the decision was clear that the ReproSeq assay was the best way forward for our lab.”
To find out more, please visit thermofisher.com/ionreproseq.
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