NEW YORK (GenomeWeb News) – Having recently secured a license to data generated by the Deciphering Developmental Disorders (DDD) study, Oxford Gene Technology is preparing to launch a new line of genome-wide arrays incorporating the study results next month.
Called Constitutional v3, the upcoming arrays represent the next generation of OGT's constitutional arrays, featuring the addition of newly identified genomic regions linked to learning difficulties/developmental delay, as well as the removal of ones found to have no pathogenic significance, James Clough, OGT's executive vice president commercial, told GenomeWeb this week.
The company's current constitutional arrays, sold under the CytoSure ISCA v2 brand, are based on data collected by the International Standards for Cytogenomic Arrays (ISCA) consortium and were designed around five years ago, Clough said. But the availability of new genomics technologies in recent years has led to an improved understanding of which genetic variations are implicated in learning and developmental disorders, prompting OGT to begin work on an update to its constitutional arrays.
For instance, the DDD initiative, which began in 2011 with the goal of analyzing the genomes of up to 12,000 children with physical and mental developmental problems and birth malformations, employed Agilent arrays with 2 million probes to identify genomic copy-number changes, deletions, and duplications.
According to Clough, this enabled the identification of smaller changes than those that would be picked up with standard arrays. "The DDD project has used 10 times the number of probes that other labs would routinely use," he said.
Seeing value in the DDD study findings, earlier this month OGT secured a license to access and use those data in its Constitutional v3 arrays, which the firm said will be able to accurately identify copy number variations that are implicated in genetic syndromes, as well as amplifications and deletions and loss of heterozygosity regions.
In developing the new arrays, OGT also referenced ClinVar, a universal centralized database of human sequence variation and phenotypes hosted by the National Center for Biotechnology Information, which led to the removal of genes targeted in the version 2 arrays but are now classified as having "no pathogenic significance whatsoever," Clough said.
Doing so, he added, eliminates uninformative content that researchers would have to flag as benign in the course of their experiments. More importantly, it frees up room on array slides for probes directed to key genomic regions.
"There's been a gradual but continuous move over the last few years to look at smaller changes in specific exons," he explained. "Therefore it's important … [to] have enough probes in the important exons to be able to detect a copy-number change."
Clough also said that the Constitutional v3 arrays will feature prioritized backbone coverage of the genome, with a greater number of probes in high-priority regions versus lower-priority ones.
"We want to get the most informative probe coverage in the most informative regions," he said.
The new arrays are currently being evaluated by a number of labs, which are providing feedback to OGT so that it can refine the arrays before their official introduction. The company, however, remains on track for a May market launch, Clough said.
The Constitutional v3 arrays will be marked for research use only in the US, he noted, but OGT has been looking into the possibility of their diagnostic use and has already had discussions with the US Food and Drug Administration on the matter.
To date, only one vendor, Affymetrix, has obtained FDA clearance for a microarray-based assay with its CytoScan Dx Assay chromosomal microarray analysis product that was approved in January 2014.
Clough did not provide a specific timeline for when OGT hopes to get the FDA greenlight for its Constitutional v3 arrays, but referred to the "complexity" of such a process and the importance of having an array design "that is likely to be current for a good length of time" before seeking regulatory clearance.
"It's something we're working through," he said, adding that the approval of the Affymetrix array does provide some guidance on how OGT might proceed.