NEW YORK (GenomeWeb) – Stanford Genome Technology Center spin-out Sirona Genomics plans to start alpha testing its next-generation sequencing-based human leukocyte antigen typing technology in collaboration with transplant testing labs by the end of this year, Clinical Sequencing News has learned.
Last week, the company said it received funding from Immucor, a transfusion and transplantation diagnostics company headquartered in Norcross, Ga., to develop its HLA-typing technology commercially. As part of the agreement, Immucor has the right of first refusal to acquire Sirona.
According to Michael Mindrinos, Sirona's president and CEO, Immucor is contributing several million dollars in funding for research and development and will provide its expertise in kit manufacturing and other aspects of commercialization to Sirona.
At present, Immucor, which is owned by TPG Capital and had $348 million in revenue in fiscal year 2013, offers several HLA genotyping kits that use sequence-specific oligonucleotide, sequence-specific primer, and other established technologies, among other products.
Mindrinos, until recently associate director of the Stanford Genome Technology Center, founded Sirona with Marcelo Fernández-Viña, co-director of the Histocompatibility, Immunogenetics, and Disease Profiling Laboratory at Stanford; Ron Davis, director of the Stanford Genome Technology Center; Mark Davis, director of the Stanford Institute for Immunity, Transplantation, and Infection; Sujatha Krishnakumar, a former research associate at SGTC; and Chunlin Wang, a former senior research scientist at SGTC. Mindrinos is taking a leave of absence from Stanford to run the company.
Over the next few months, Sirona plans to hire a total of about 15 employees, including laboratory scientists and software developers, to get the technology into early access testing.
Mindrinos and his colleagues developed the HLA typing technology at the SGTC during the last few years with grant funding from the National Institutes of Health and the Defense Threat Reduction Agency, and published the method two years ago in the Proceedings of the National Academy of Sciences. Sirona exclusively licenses intellectual property covering the technology from Stanford.
In all, the Stanford researchers have typed more than 10,000 samples, including for several disease-association studies, which has allowed them to fine-tune the technology. "It is pretty much ready to be tested in the outside world," Mindrinos said, and only minor adjustments will likely be needed during the alpha-testing phase.
The method relies on long-range PCR of HLA genes, spanning most coding regions and known polymorphic sites for each gene. PCR products from several genes are then ligated, randomly sheared, and sequenced.
In their publication, the scientists demonstrated the approach for four HLA genes using 40 reference cell lines and achieved 99 percent concordance with previous results. They also tested the method on 59 clinical samples, where they found three previously undescribed alleles, and they were able to type five clinical samples on an Illumina MiSeq with a five-day turnaround time.
Since then, they have improved the technology in several ways. For example, they have developed proprietary PCR conditions to minimize differences in allele amplification, which is important for being able to call heterozygous alleles. In addition, they have developed a database and strategy that build on existing public databases of HLA alleles for analyzing the data.
The assay, which is automated, uses a library preparation protocol that reduces the risk for cross-contamination and enhances sample quality. It now covers all major HLA gene regions, including HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, and -DRB1/3/4/5.
Stanford currently runs the assay on Illumina sequencing platforms, both the MiSeq and the HiSeq, but could potentially adapt it to other platforms, like Thermo Fisher Scientific's Ion Torrent platforms, Mindrinos said.
He and his colleagues have already applied the assay in several disease-association studies, for example, for schizophrenia and multiple sclerosis, and are planning to publish results from some of these studies in the near future.
The main clinical application of the typing technology will be in transplant medicine, he said, where the current gold standard is the analysis of just a few exons for a small number of HLA genes. "People believe these are the important ones, but the question is, how do you know these are the only important ones?" he said.
Whether high-resolution sequencing of more HLA genes will make a difference in clinical outcome remains to be demonstrated, Mindrinos said, and will not be Sirona's goal initially. "But down the road, I think this is a very important experiment that someone needs to do," he said.
Sirona's first objective is to test the technology outside the SGTC. By the end of the year, the company plans to start an alpha-testing program with a number of laboratories in the US and in Europe that perform HLA typing for transplant centers, including academic medical centers and nonprofit organizations.
This will be followed by beta testing and a clinical trial that will enable Sirona to apply for CE marking, which is required for an HLA kit to be sold in Europe. In the US, approval from the Food and Drug Administration is currently not required for HLA typing kits, Mindrinos said.
Sirona will face competition from several other players. "We're not the only ones, that's for sure," Mindrinos said. "But I think our advantage is the wealth of information we have in our hands, because we've been working on this for quite some time," and because of the company's unique PCR amplification conditions.
Illumina, for example, said earlier this year that it is working on an HLA typing system, consisting of a TruSight sequencing panel for eight HLA loci, the MiSeq or MiSeqDx instrument, and integrated analysis software.
Also, this summer, GenDx of the Netherlands said it received CE-IVD marking for an HLA typing kit that can be used with the MiSeq, Thermo Fisher Scientific's Ion PGM, or the Pacific Biosciences RS. In addition, the firm struck a co-marketing agreement for the kit with PacBio, which has seen increasing demand for its platform for HLA typing.
Overall, interest in more complete and high-resolution HLA typing for transplant medicine appears to be high. "In every meeting you go, next-generation sequencing is at the top of the agenda," Mindrinos said.