By Monica Heger
This article was originally published Aug. 2.
Life Technologies has submitted its 3500 Dx Genetic Analyzer capillary electrophoresis sequencer and its SeCore HLA typing kit for US Food and Drug Administration 510(k) clearance.
If approved, the assay would be the first sequencing-based HLA typing test to get the FDA green light, and could pave the way for FDA clearance of a next-generation sequencing-based HLA assay as well as other approved diagnostics on the 3500, Todd Laird, Life Technologies' vice president and general manager of the Fragment and Sequence Genomics Division, told Clinical Sequencing News.
The HLA test covers six genes within the major histocompatibility complex, including the Class I genes HLA-A, HLA-B, and HLA-C, as well as the Class II genes DRB1, DQB1, and DPB1. The company is designing separate kits for each gene, which will cost between $30 and $50 each, depending on the gene and the number of kits ordered. Kits will either come in a small size, with the primers and reagents to run around 500 tests, or in a large size, with materials to run 25,000 tests.
Life Tech has completed its clinical trial of the test and is "comfortable that the trial itself, the outcomes, and the data are satisfactory for submitting our application to the FDA for review," said Laird.
"It is the most unambiguous assay that's available out there for resolving these variants in the HLA complex."
If approved, the company will market its test to donor registry organizations, as well as clinics and physicians.
Laird said that the Sanger-based kit would not preclude the development of a next-gen sequencing-based kit, and the approval of the Sanger-based kit could even "be the predicate for generating a solution on a next-gen sequencing system."
FDA approval of the 3500 could also spur development of other diagnostic tests on the CE system. The company is considering tests in the areas of "inherited disease and infectious disease" and is currently in discussions with a number of companies "to grow a menu of assays that would use the 3500," Laird said.
The company has already taken steps in this direction. In May, it announced a partnership with Gen-Probe to develop and market diagnostic tests for the 3500 (CSN 5/24/2011). The agreement covers Gen-Probe's Elucigene genetic disease tests as well as other assays.
Laird said that Life Tech began its clinical trial of the HLA test this spring at an undisclosed clinical research organization but declined to provide details of the trial or the outcome until the company has heard from the FDA.
While the Life Tech test would mark the first FDA-approved sequencing-based HLA typing test, other companies are looking to use next-gen sequencing for HLA typing. RainDance Technologies and Roche 454 Life Sciences, for example, have already launched HLA typing kits for research purposes on next-gen systems (CSN 4/5/2011).
454's assays target one to three exons of up to 10 HLA genes and can be run on its GS FLX or GS Junior. The company has said it would eventually like to launch an assay for clinical use.
RainDance has also launched its HLASeq kit for research purposes, which covers the entire 3.8-megabase HLA superlocus, including all Class I and Class II genes as well as several minor HLA antigen genes. The kit works with any next-gen sequencing platform, according to the company.
Other labs have also designed protocols for HLA typing on next-gen systems — also for research purposes — such as Paul de Bakker's group from the Broad Institute, who designed a protocol to sequence the HLA regions of up to 96 individuals on the 454 platform (IS 1/25/2011).
Laird said that Sanger sequencing offers a number of advantages over next-gen sequencing, particularly for HLA typing. The MHC locus has the "most variability across the genome," and Sanger sequencing "provides the longest read lengths and the highest accuracy," he said.
By contrast, though, next-gen sequencing offers higher throughput and less ambiguity, said Henry Erlich, director of human genetics at Roche Molecular Systems, who spoke this week at the Next-Generation Sequencing and Genomic Medicine Summit in San Francisco.
Because 454 and other next-gen systems are based on clonal sequencing, researchers can distinguish heterozygous variants without additional analysis. "In the first pass, you have higher resolution because it's clonal sequencing," Erlich told Clinical Sequencing News.
For example, in a collaboration with the Children's Hospital of Oakland Research Institute, researchers found that using 454 for HLA typing resulted in 92 percent of the alleles being assigned one possible genotype. After a round of Sanger sequencing, though, only 5 percent of alleles could be assigned a genotype, with the remainder having two or more possible genotypes and requiring further analysis.
Additionally, next-gen sequencing offers much higher throughput, particularly when paired with improved sample-prep methods. For instance, Roche/454 has begun using a Fluidigm microfluidics chip for the sample prep, which has reduced hands-on time and allowed it to sequence up to 480 samples in one run, Erlich said.
While 454 has said it plans to develop its HLA assays for clinical purposes, Erlich said the company hasn't yet decided whether it will launch the assay as a laboratory-developed test or apply for FDA clearance.
A company spokesperson told Clinical Sequencing News via e-mail that 454 plans to begin selling its HLA assays in the transplantation registry market some time in 2012, but did not comment on the company's regulatory strategy.
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