NEW YORK (GenomeWeb) – Molecular diagnostic firm Bioarray has begun offering a next-generation sequencing-based preimplantation genetic screening and diagnostic test, following the completion of a clinical trial in which it compared its test to array CGH in more than 100 embryos, company officials told GenomeWeb.
The firm, which is based in Elche, Spain, was founded in 2008 with a focus on medical genetics, developing microarray-based genetic tests. Later on, it began converting some of its genetic tests to NGS, running gene panels for epilepsy, mitochondrial diseases, congenital deafness, and hereditary spastic paraparesis on Thermo Fisher's Ion Torrent PGM.
Now, the firm has moved into reproductive genetics, developing a way to do both preimplantation genetic screening for couples undergoing in vitro fertilization as well as preimplantation genetic diagnosis and informativity testing in one assay.
At the European Society of Human Reproduction and Embryology meeting in Helsinski, Finland earlier this month, the firm presented an abstract on its combined method, which uses low-coverage whole-genome sequencing to detect chromosomal aneuploidies, higher-coverage targeted sequencing of a known mutation carried by either the mother or father, and a tag-SNP method that determines the haplotype of the gene of interest in case allele dropout occurs in the targeted sequencing protocol.
"We did in the same NGS run at the same time PGS as well as PGD for monogenic disease," Luis Alcarez, laboratory director of Bioarray, told GenomeWeb.
Typically, PGD is performed through what is known as informativity testing using STRs to determine the haplotype of the region of interest. Prior to IVF, a couple undergoes STR haplotyping to identify informative STRs that identify the presence of the defective gene. But the Bioarray team uses a set of of SNPs rather than STRs, to enable the method to be performed in the same sequencing reaction as PGS and PGD.
The team performs whole-genome sequencing to 0.1x coverage using Thermo Fisher's Ion ReproSeq kit. For couples who are carriers of known monogenic disease-causing variants, the firm does PGD by adding sequence coverage of the gene region of interest. The SNP-based informativity test provides extra validation in case of allele dropout, which is known to occur in PGD.
The firm has carried out a validation study and found that its NGS-based PGS method was 100 percent concordant with array CGH in 100 embryos. In total, it has analyzed nearly 5,000 embryos using low-coverage whole-genome sequencing to screen for chromosomal aneuploidy.
In addition, the firm said that it has agreements with the fertility clinics IVF-Spain and iGLS in Alicante, Spain to offer PGS/PGD testing. Those partnerships, which have been in place for two years, have thus far resulted in 64 healthy babies and 53 ongoing pregnancies.
Twelve couples have undergone the combined PGS, PGD, and informativity testing, Luis Valiño, international area manager of Bioarray, told GenomeWeb. The company also plans to submit its tag-SNP informativity method to a peer-reviewed publication, Valiño said.
Of the seven couples presented in the ESHRE abstract, two females were carriers of PKD1 mutations, one female had a RET mutation, and one female had a L1CAM mutation. In addition, in one couple, both partners had a LAMB3 mutation and in another couple, both partners had UNC13D mutations.
To perform informativity testing, the researchers used a panel of 130 SNP markers selected to be within a 200-kilobase flanking region of each of the affected genes. The tag-SNP informativity test is designed specifically for each patient.
For the couple with the PKD1 mutation, combined PGS/PGD testing found that of 12 embryos generated from IVF, four were euploid, four were aneuploid, and four described as "chaotic." Of the four euploid embryos, PGD and informativity testing identified two that were free of the PKD1 mutation.
Being able to combine PGS and PGD in one test based on NGS has a number of advantages, Alacarez said. Conventional methods for PGS, PGD, and informativity testing involve multiple technologies — array CGH for aneuploidy screening, plus Sanger sequencing for STR analysis and single-gene diagnosis — which requires clinical labs "to manage a lot of different techniques and to invest in a lot of resources and personnel," he said. By moving the whole process to one NGS test "we were able to simplify the protocols and one person can do the entire thing," he said.
Alcarez said that the firm's next steps are to continue to work on its protocol to be able to detect smaller aberrations and to be able to diagnose more diseases. Although the company has entered the reproductive health field, Alcarez said that it does not have plans to develop an NGS-based noninvasive prenatal test. That market is already mature, he said, and developing and validating a test would require a large volume of samples, which would not make sense for Bioarray as a small clinical lab.
Instead, said Valino, the firm will focus on the niche PGS/PGD market as well as the inherited disease market. The firm's main customers for PGS/PGD testing are IVF clinics, including IVF-Spain. It markets its gene panel tests to hospitals.
Valino said that the main competition for PGS/PGD testing are other clinical laboratories that are developing such tests. Although Illumina has developed its own PGS test, VeriSeq, Valino said that Illumina is not really a direct competitor since it does not market VeriSeq directly to IVF centers. In addition, VeriSeq is a PGS test only and does not include PGD and informativity testing.
A number of other firms have entered into the NGS-based PGS field, however. Good Start Genetics launched its EmbryVu test last year based on technology it licensed from Johns Hopkins University. Researchers at Peking University have been conducting a clinical trial of a combined PGS/PGD test using technology developed by Harvard University's Sunney Xie.
Valino said that reproductive genetics is becoming more of a focus for Bioarray and that aside from PGS/PGD testing, the firm is moving into carrier screening as well as screening gamete donors for IVF clinics.