Reproductive Medicine Associates of New Jersey is currently enrolling patients in a clinical validation trial of targeted next-generation sequencing-based preimplantation genetic testing to aid in the selection of embryos for transfer as part of in vitro fertilization.
According to Marie Werner, a reproductive endocrinology and infertility fellow at the lab and a primary investigator in the new trial, RMA of NJ currently offers testing using both SNP microarrays and quantitative PCR, as part of what it calls "comprehensive chromosome screening."
If the trial — which is comparing the success rates of IVF using NGS to select embryos versus selection based purely on embryo morphology — is successful, the lab plans to integrate NGS into its comprehensive screening strategy along with the other tools it currently uses.
"We've already done initial validation studies against current screening platforms to show that NGS works on single cells and aneuploid embryos that have been discarded with the same results, so now we want to see if it makes a difference in clinical outcomes, the same way our previous SNP microarray and qPCR-based methods have," Werner told Clinical Sequencing News.
RMA of NJ's sequencing method is a targeted strategy using the Ion Torrent PGM and a set of sequence-specific primers, Werner explained.
The center previously published a study in Fertility and Sterility describing the method and its performance compared to both reference laboratory and internally developed qPCR-based analyses. In that study, the group's method showed 100 percent equivalent diagnoses of compound point mutations and small deletions and insertions with reference and qPCR results.
In the new trial, Werner and her colleagues plan to divide participants into a selection group and a non-selection control group. In the selection group, the team will sequence DNA from embryos that have been cryopreserved after reaching the blastocyst stage using the group's targeted NGS method to identify chromosomal aneuploidies that indicate embryos that will not survive. The group will then choose the two morphologically best embryos that make it through this NGS-based screening process to implant.
In the control group, the two morphologically best embryos will be transferred without any additional screening.
According to RMA of NJ, extensive data has shown that embryonic aneuploidy is one of the largest contributing factors in IVF failure or miscarriage across all age groups. Fittingly, numerous clinics have adopted array-based strategies, such as array-CGH and SNP arrays, as well as qPCR, for chromosomal screening in IVF embryos over the last several years.
"SNP microarrays and qPCR are accurate and precise, but we hope NGS will be even more accurate and precise, because it gives us additional genotyping data which can be used as a second assessment of copy number for each assay," Werner said. "Although current techniques are already 99 percent accurate, we are looking at any small improvement to be a step forward."
However, Werner explained, NGS currently can't replace the rapid screening capabilities of qPCR, so regardless of how the sequencing strategy does in the trial, the lab will still continue to use a variety of technologies in its clinical practice moving forward.
According to Werner, RMA of NJ has already recruited 50 of a planned 200 patients for the study and aims to complete the trial by the end of the year. If the method improves IVF outcomes, it will be offered clinically by the center as part of its comprehensive chromosomal screening service.
Werner said that by RMA of NJ's calculations the cost of the NGS-based screening method has the potential to be lower than its currently used array and PCR protocols, but how this actually shakes out in clinical practice is something the group will investigate more fully in the ongoing trial.
The NJ center is not the only fertility clinic or company to investigate NGS for preimplantation screening.
Illumina recently said it plans to launch an NGS-based test for preimplantation genetic screening called VeriSeq in the second quarter of this year, which will initially run on the MiSeq platform, with plans to offer it on the NextSeq 500 later on.
Illumina currently offers array-based preimplantation screening, using technology it acquired when it bought BlueGnome in late 2012, which it has said represents 90 percent of all PGS currently performed.
Dagan Wells from the University of Oxford's Nuffield department of obstetrics and Xiaoliang Sunney Xie from Harvard University have also reported that they are developing single-cell sequencing techniques to improve IVF success rates and have demonstrated in proof-of-concept studies that the tests can accurately detect chromosomal aneuploidy in clinically relevant time frames.
In addition, BGI said last year that it has been testing a method, published in PLoS One, for detecting copy number variants from single-cell, low-pass, whole-genome sequencing on couples undergoing in vitro fertilization.
China's Berry Genomics also offers a single-cell sequencing test for preimplantation genetic diagnosis called Chrosure.