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Omixon Will Develop NGS Kit Based on CHOP's HLA Typing Service


NEW YORK (GenomeWeb) – Next-generation sequencing interpretation firm Omixon plans to launch its first kit, a research-use HLA kit based on the clinical service offering at the Children's Hospital of Philadelphia.

Omixon has licensed the rights to develop CHOP's service offering into a commercial kit, which it will eventually market to HLA typing laboratories and other customers for research-use only purposes.

CHOP began offering a clinical HLA typing service internally earlier this year. The test is run on the Illumina MiSeq and interrogates polymorphisms in the HLA-A, HLA-B, HLA-C, HLA-DQA, HLA-DQB, and HLA-DRB1 genes. With the exception of HLA-DRB1, the genes are amplified in full using long-range PCR.

The test will evaluate more than 10,000 known alleles, but can also identify novel SNPs, since it looks at entire genes. CHOP validated the test with 100 percent sensitivity and 85 percent specificity. Omixon's research kit will be equivalent to the test run by CHOP.

Omixon Founder and CEO Attila Berces told Clinical Sequencing News that the kit marks the firm's expansion from solely a bioinformatics company to one that also develops NGS-based assays.

He said that adding an assay component to the firm's offerings will enable it to deliver a more complete solution to customers. "We are also convinced that a very close collaboration between the software development and the assay development is absolutely crucial to have outstanding results," Berces said.

He declined to elaborate on the company's plans to expand into other areas, saying that for now it would focus on the HLA market and related industries.

Berces said that the company is still evaluating its options for bringing the HLA assay through US Food and Drug Administration clearance.

Next-generation sequencing has only recently begun to be used for HLA typing, but interest has rapidly picked up. Aside from the services being offered internally by CHOP, HLA-typing firm HistoGenetics now uses the more than 30 Illumina MiSeqs it has purchased over the last year as its main workhorses for HLA typing for donor registries.

HistoGenetics runs a targeted sequencing HLA typing panel that includes exons 2 and 3 for HLA-A, -B, and -C genes and exon 2 for DRB1, DRB3/4/5, DQB1, DQA1, DPA1, and DPB1 genes. It processes between 80,000 and 100,000 samples per month, primarily from donor registries, and has the capacity to process 150,000 samples per month. In addition, the firm recently purchased two of Pacific Biosciences' RS II systems that it is currently validating for clinical HLA typing.

Illumina has also said that it plans to market an HLA typing assay on either the MiSeqDx or MiSeq system by the middle of the year to tap into the nearly $300 million HLA typing market. The assay will be based on Illumina's TruSight chemistry and consist of eight HLA genes that will be sequenced completely and fully phased, and will include analysis software from an unnamed provider.

Pacific Biosciences' CEO Mike Hunkapiller has also noted that HLA typing is a growing opportunity for the company, and said during a conference call discussing the firm's 2014 first quarter results that it would eventually seek to bring an HLA typing assay that used PacBio single-molecule sequencing through the FDA clearance process.

Berces said that Omixon's assay will differ from competing offerings. Compared to HistoGenetics, he said the Omixon assay will be more complete since it will include full-gene sequencing, rather than focusing on just exons 2 and 3.

He added that Omixon doesn't consider HistoGenetics to be a competitor because it is a service company doing HLA typing on a large scale for donor registries. Rather, he said, Omixon will target the 1,200 or so HLA typing laboratories that have a smaller number of samples but want to evaluate them at a higher resolution.

With regards to Illumina's potential clinical HLA assay, he said Omixon's could be complementary. "This is a large market," he said. "And it's not the type of market where one particular solution will fit everyone."

Roche and RainDance Technologies have also developed research kits for HLA typing. Roche's GS GType HLA medium- and high-resolution kits evaluate the HLA-A, -B, and –C genes, as well as the DQB1, DRB1, DRB3, DRB4, and DRB5 genes. But even the high-resolution offering does not sequence the entire genes, Berces noted.

RainDance Technologies' HLASeq panel uses an amplicon-based approach to target all of the exons and introns for both HLA Class I and Class II genes, and the company says that its assay can phase the alleles.

Berces said Omixon's next steps include publishing a peer-reviewed study on its assay and bringing the kit to market. He did not provide a timeline as to when the assay would launch.

In addition, he said that there are "logical connections" for adding genes or developing related assays. For instance, the KIR genes are also involved in transplantation, and there are also other genes of interest involved in immunology, he said.