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Reprogenetics to Adopt NGS for Pre-implantation Genetic Dx to Partially Replace 'Workhorse' CMA

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NEW YORK (GenomeWeb) – One of the world's premier pre-implantation genetic diagnosis laboratories is inching closer to offering a next-generation sequencing-based aneuploidy screening service.

Livingston, NJ-based Reprogenetics has developed an accurate, low-cost sequencing protocol for the diagnosis of aneuploidy in cells from human embryos prior to implantation as part of an in vitro fertilization cycle, according to its Founder and President Santiago Munné. Scientists from Reprogenetics described the protocol in the most recent issue of the Journal of Medical Genetics, and the company is making plans to transition from chromosomal microarray analysis to using next-generation sequencing for PGD.

"We foresee that within the year to next we are going to move to NGS," Munné told BioArray News.

Founded in 2000, Reprogenetics has prided itself on being ahead of the curve when it comes to new technologies. The company's decision to move to sequencing for PGD also seems to jibe with Illumina's position that the reproductive health market will eventually migrate to NGS from arrays, in part because of the "richness and completeness of the data," as CEO Jay Flatley said recently. To encourage this transition, Illumina earlier this year rolled out VeriSeq, a sequencing-based application for PGD.

According to Munné though, Reprogenetics' move to next-generation sequencing-based PGD is not necessarily based on the superiority of the technology, but on customer demand.

"It's really the customers and patients who are asking for NGS," Munné said. "There is not an advantage price wise or in the amount of sequencing information you get," he said. The reason for this difference is that Reprogenetics has to run 98 samples at a time using low-pass sequencing to equal the cost per sample of chromosomal microarray. In its case, Reprogenetics uses 24sure bacterial artificial chromosome arrays supplied by BlueGnome, an Illumina company.

Given the lower coverage, Reprogenetics is able to count chromosomes using the sequencing-based approach, but is unable to obtain information about genetic defects. In fact, for the same price, Munné maintained that more information can actually be obtained by CMA. That has not cooled clients' enthusiasm for the newer technology, though, with many of them excited by news last year of the birth of the first IVF baby whose embryo had been selected using next-generation sequencing.

"IVF doctors are not conservative," Munné said. "Whenever there is something new, they immediately want it."

Giving them next-generation sequencing-based PGD, however, is not easy and the company has now embarked on several studies to compare sequencing results with CMA. "It's one thing to show something works, it's another thing to offer it clinically," Munné said. "But that's what they want and so we are running randomized clinical trials."

CMA is currently Reprogenetics' "workhorse," and 95 percent of the 7,000 samples the company runs each year are analyzed using the technology. It also uses fluorescence in situ hybridization and conventional molecular karyotyping to look at specific gene defects, Munné said. In addition to using CMA for PGD, the company also has adopted Illumina's CytoSNP Karyomapping array for pre-implantation genetic diagnosis of single-gene defects. Investigators from the company and colleagues detailed their use of the new array in the journal Genetics in Medicine in May.

Looking ahead, Munné said that Reprogenetics will likely use sequencing to screen banked frozen embryos, as it will take time to collect the 98 samples needed for one low-pass sequencing run. The company will continue to use CMA for couples who want results more quickly, he said. He also said it was likely that only the busiest labs could afford to introduce next-generation sequencing for PGD at this point, given the volume requirements to make it economically feasible.

"There are probably three or four labs that could have volume in the world, but the rest I wouldn't recommend for them to buy the equipment, they should stick with array CGH because NGS will be more expensive for the time being," Munné said. "I think most customers are confusing NGS with whole-genome sequencing, but right now the only thing we can offer them is aneuploidy screening," he said. "We won't be able to offer whole-genome sequencing for several years."

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