Roche NimbleGen has entered the SNP genotyping market with a new platform called AccuSNP for validating markers identified in next-generation sequencing-driven studies.
Additionally, the Madison, Wis.-based company has designed a focused AccuSNP array for pharmacogenomics research.
Lance Brown, Roche NimbleGen's director of international product management, told BioArray News this week that the company developed its SNP array platform to "complement and support" the adoption of next-gen sequencing. Roche NimbleGen already provides array and solution-phase products for sequence capture, and the company is interested in making new tools available to sequencing users, Brown said. He described the new platform introduction as an "obvious tie in" to this strategy.
Roche NimbleGen launched its AccuSNP arrays outside the US last month, and Brown said the chips will become available to US customers within the next few weeks.
The firm's AccuSNP-12 Custom Arrays consist of 12 arrays per slide, each containing 13,500 SNPs. According to the company, the chips are recommended for targeted genome-wide association follow-up studies or to screen variants identified by whole-genome sequencing or exome-sequencing projects.
Brown noted that Roche NimbleGen's arrays were not designed to compete against higher-density SNP chips sold by Affymetrix and Illumina, "but rather as a dedicated validation and screening tool." He also made clear that the firm was focusing on serving customers running sequencing-based studies.
"We expect customers will find many other uses for this technology, but currently we are focusing on expanding our strategy of supporting researchers that are using NGS for their discovery efforts," he said.
The company is marketing its custom SNP arrays by stressing the platform's flexibility and accuracy.
Brown pointed out that Roche NimbleGen AccuSNP-12 Custom Arrays can be ordered for as few as 12 samples, or one slide. This sets the firm apart from its competitors, which require clients to purchase a certain number of arrays to justify a custom-designed array. For instance, the minimum order for one of Illumina's iSelect custom BeadChips is for 1,152 samples. The minimum order for a custom Affymetrix genotyping array is for 480 samples. But, according to Brown, some customer projects do not involve enough samples to meet these requirements.
"More and more frequently, researchers do not have thousands of samples that require novel SNP validation," Brown said. "Researchers who have tens or hundreds of samples for novel SNP validation" can now order arrays to "move their studies forward."
One reason why Roche NimbleGen can offer custom SNP arrays for smaller-sized products is because it manufactures its arrays using photo-mediated synthesis chemistry. While Affy has to build a chromium mask for each array it makes, and Illumina has to generate a bead pool to fabricate its BeadChips — thus requiring a minimum number of orders to offset that development cost — Roche NimbleGen can program and build custom-designed arrays using its maskless array synthesizer.
Another platform attribute that Roche NimbleGen is keen to talk about is its accuracy. Brown said the firm's custom design process includes the use of algorithms that provide researchers with "significant insight into the likelihood of experimental success." Customers receive a "design report that indicates if each individual SNP will be successful experimentally," he said. He added that for those SNPs that Roche NimbleGen indicates as "good probe sets," the firm has a greater than 94 percent experimental success rate.
Still, the company has no shortage of competitors. In addition to Affy and Illumina SNP arrays, Illumina also offers the BeadXpress for lower-multiplex genotyping; and other firms, such as Fluidigm and Sequenom, also offer genotyping platforms for validation studies.
In addition to launching a custom SNP array offering, Roche NimbleGen has designed a catalog SNP chip for its customers. The firm claims that the AccuSNP-12 Pharmacogenomics Arrays allow users to generate genotyping information for more than 800 genes shown to have relevance in drug metabolism research.
Brown described the array as a "pharmacogenomics research tool that targets close to 13,000 SNPs." He said that the content for the design was selected from "a variety of databases" and the company "intends to provide the most comprehensive targeted pharmacogenomics microarray SNP design to date."
Again, Affy and Illumina also offer pharmacogenomics-themed arrays. Affy has for years offered its Drug Metabolism Enzyme and Transporter, or DMET array, a panel of 1,936 SNP, copy number, and indel markers across 231 genes; while Illumina sells its ADME VeraCode GoldenGate Panel for use on the BeadXpress. That panel covers 34 genes.
"While there are certainly other PGx designs from other vendors that focus on clinically relevant content, our design focuses on both the well-characterized and the not-so-well characterized pharmacogenomics SNPs," Brown said.
Though the firm is, in his words, a "new entrant" to the SNP microarray market, he said that the chip has performed well in test studies, the data from which "provides customers a nice example of the high accuracy and overall performance the AccuSNP platform."