Infertility affects around one in six adults worldwide, according to the WHO. Determining the health of embryos prior to implementation is key to addressing infertility. Testing has become even more significant due to the aging population of pregnant women and medical tourism.
Next generation sequencing (NGS) has been widely adopted for pre-implantation genetic testing labs. Advantages of using NGS compared to traditional techniques such as FISH include higher sensitivity, throughput and versatility. A common pre-implantation genetic test is for aneuploidy, or PGT-A. “PGT-A screens for extra or missing chromosomes or parts of chromosomes,” explained Kathy Davy, VP & GM Clinical Sequencing Solutions at Thermo Fisher Scientific. PGT-A testing can reduce the risk of miscarriages and failure of IVF transfer.
NGS has been a method of choice for PGT-A for several years, according to Ms. Davy. She told IBO that NGS began to gain prominence in the field of PGT-A around the mid-2010s. For pre-implantation genetic testing, Thermo Fisher focuses on PGT-A, and also genetic variants linked to specific single-gene disorders, or PGT-M.
To address NGS-based pre-implantation genetic testing needs, Thermo Fisher recently released the Ion ReproSeq PGT-A Kit and the brand new Ion AmpliSeq Polyploidy Kit. The new kits complement Thermo Fisher’s existing NGS-based Ion ReproSeq PGS (pre-implantation genetic screening) solutions and workflow.
“These panels work together for what we’re calling premium PGT-A analysis. It’s leveraging two approaches for a more powerful test: whole genome sequencing for aneuploidy and then SNP sequencing with AmpliSeq.”
Regarding the new Ion ReproSeq PGT-A Kit and Ion AmpliSeq Polyploidy Kit. Ms. Davy explained, “These panels work together for what we’re calling premium PGT-A analysis. It’s leveraging two approaches for a more powerful test: whole genome sequencing for aneuploidy and then SNP sequencing with AmpliSeq.”
Based on Thermo Fisher’s Ion AmpliSeq amplicon-based enrichment method, the Ion AmpliSeq Polyploidy Kit provides additional quality control checks. “What this allows is for labs to offer a genetic test for ploidy status instead of having to rely on a visual check, improves their QC processes, and minimizes the risk of sample mix-ups or contamination,” noted Ms. Davy.
Describing the ReproSeq Kit, Ms. Davy commented, “ReproSeq is a low-pass whole genome sequencing kit to identify aneuploidy across all chromosomes. It’s looking for whole-chromosome aneuploidies, segmental aneuploidies or mosaicism.” The latest release, the Ion ReproSeq PGT-A Kit marks an expansion of the technology, which was previously only available on Thermo Fisher’s Ion GeneStudio S5 NGS System to the Ion Torrent Genexus Integrated Sequencer. A turnkey system, the Ion Torrent Genexus automates NGS library preparation (including cDNA synthesis), template preparation, sequencing, primary data analysis and variant reporting.
However, Ms. Davy emphasized, Thermo Fisher is not seeking to replace the use of Ion GeneStudio S5 within the pre-implantation genetic screening market with the Ion Torrent Genexus. “It’s really just an offering on our Genexus system that allows a little bit greater ease of use for those customers that may not be as familiar with NGS, as well as it allows for a menu addition on our Genexus platform,” she noted. “So for customers that are working across multiple areas. they can run reproductive health; they can run inherited disease [and] they can run oncology assays.”
Together, the Ion ReproSeq PGT-A Kit and the Ion AmpliSeq Polyploidy Kit address a gap in the market. Many labs now send out their samples to larger labs to do PGT-A testing. But, as Ms. Davy explained, “For labs who want to perform PGT-A themselves, this new combined assay are the only solutions that deliver PGT-A testing with quality controls,” She added, “Our [test] is a distributed version that allows those that want to take it in house to do it themselves. It really allows them to have a more competitive advantage to offer premium testing with in-house NGS rather than sending their samples out.” The kits are unique to Thermo Fisher. “It is my understanding that we are the only ones that offer this on a distributed basis,” noted Ms. Davy. “It is a first time that we are offering this, with this specific kit.”
Potential customers include IVF centers and fertility clinics. “I think this allows a greater portion of labs to do this with ease of use, which is good because some of them don’t necessarily have all the staff and the skill sets that would be needed,” stated Ms. Davy.
The new Kits are available now worldwide. The offering is part of Thermo Fisher’s comprehensive solutions for the reproductive health cycle, which encompass preconception carrier screening, pre-implantation testing, prenatal testing, newborn testing, and post-natal genetic testing.
Reproseq + Polyploidy throughput (if run together on every sample):
- Genexus can run up to 96 ReproSeq samples and 96 Polyploidy samples in the same run
- GeneStudio can run up to 48 ReproSeq samples and 48 Polyploidy samples in the same run
Gene Studio turnaround time (TAT):
- TAT for 96 samples (on 530 chip) on GeneStudio for ReproSeq is 13 hours
- TAT for 60 samples (on 530 chip) on GeneStudio for Polyploidy is 18 hours
Genexus turnaround time:
- TAT for 48 samples (one lane of GX5 chip) on Genexus for ReproSeq is 10.5 hours
- TAT for 48 samples (one lane of GX5 chip) on Genexus for Polyploidy is 18 hours
- TAT for 48 samples ReproSeq samples (one lane of GX5 chip) and 48 Polyploidy samples (separate lane in GX5 chip) simultaneously is 21 hours