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Illumina Upgrades Custom Genotyping Offering to Suit Human Health, Ag-bio Market Needs

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By Justin Petrone

Illumina this week launched the next generation of its iSelect custom genotyping product line, hoping to attract human health and agricultural biotechnology researchers by offering higher-density arrays and expanded multi-sample formats.

The San Diego firm's customers can now design custom arrays containing between 3,000 and a million markers in multiplex formats that will allow them to run up to 24 samples per chip. With the previous generation of the iSelect offering, customers could design arrays with up to 250,000 markers and run up to 12 samples per chip.

More specifically, using Illumina's online Array Design Tool, customers can create arrays containing between 3,000 and 60,000 markers that can be run in the 24-sample-per-chip format; arrays containing between 60,000 and 250,000 markers in a 12-sample-per-chip format; and arrays containing between 250,000 and a million markers in a four-sample-per-chip format.

Illumina also allows clients to add supplemental content to their arrays after the fabrication of an initial design, an option that was not available before, according to a company official.

Tristan Orpin, Illumina's chief commercial officer, told BioArray News this week that the added flexibility of the iSelect custom genotyping offering will allow the firm to reach more customers doing human health and ag-bio research.

"The advantage is one of cost and one of sample throughput, so that customers can process more samples more rapidly," Orpin said. "You are going to find a lot of use [for this new offering] in two main streams: human health research and agriculture," he said.

Orpin predicted that human health research consortia will take advantage of the higher-density and increased multiplex offering to design chips for their studies. "Instead of using the [whole-genome] Omni2.5 BeadChip, people might do an all-exon or something for psychiatric disorders," Orpin said. "Or they might do an Omni2.5 first to find hits of interest, and then run targeted [assays] against whatever disease it might be," he added.

In ag-bio and aligned markets, such as crop science and animal husbandry, Orpin cited the "amazing content" becoming generated by next-generation sequencing projects that have identified "hundreds of thousands, if not millions, of SNP variants across species of interest." Ag researchers will be able to use the iSelect arrays to "make high-quality screening and genome-wide association tools for agricultural applications in plant and in animal research," Orpin said.

Illumina anticipates that new custom arrays will also lead to new catalog products for its menu of genotyping chips. Orpin noted that Illumina has launched three catalog arrays in the past year based on custom arrays designed for different research consortia. Specifically, the firm now sells a SNP panel for oncology studies, a SNP panel for studying metabolic diseases, and a SNP panel for immunology research.

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While custom arrays lend themselves to variant confirmation, fine mapping, and target validation, Orpin said it is feasible that some groups will wish to use the higher-density and multiplex formats to design custom whole-genome arrays for genome-wide association studies. Earlier association studies were based on arrays containing similar densities, such as the HumanHap550 BeadChip, which contains more than 550,000 markers, or the Human1M DNA Analysis BeadChip, which contains more than a million markers.

"Some people will use this as a first-pass genome-wide association product, others will use it as a secondary" [platform]," Orpin acknowledged.

Orpin said the company has also revised its cost structure to offer a broader range of low-priced options, but declined to provide pricing details on the new offering because it is "so varied" and "depends on number of samples, number of loci, and is a very complex analysis." He did say that researchers in applied markets, like ag-bio, will benefit from the new cost structure.

"We are extending some of the pricing we offered largely for human research into all applied markets, including agricultural applications, and anything that aligns with it," Orpin said. "We are basically providing more attractive pricing on a larger range of markers."

Ultimately, the new iSelect will "open up the market from the top end in that people want to do much higher-complexity products that we previously could not support for custom" [arrays]," Orpin said. He added that the company is "making it more financially attractive for those for whom we did not have special pricing programs."

The extension of iSelect will allow Illumina to compete against other vendors. Most array firms big and small allow their clients to design custom arrays. Agilent Technologies, for instance, has built a custom array business around its inkjet array printing process and eArray online design tool.

Illumina's main competitor in the array-based genotyping space, though, will be Affymetrix, which allows customers to design their own genotyping arrays through its MyGeneChip Custom Array Services. The ability to design custom whole-genome genotyping arrays using its Axiom Genomic Database is also a tenet of the GeneChip maker's approach to the genotyping market.

While the genomics research market is hungry for next-generation sequencing platforms, some of which are sold by Illumina, Orpin said that next-gen tools do not compete against genotyping arrays, as opposed to gene- expression arrays, which he said are being "replaced" by NGS.

"Genotyping on arrays and sequencing play much better together than expression and sequencing," Orpin said. "With genotyping, you get higher- quality data on an array, the cost is still lower, so these play much better," he said. "Sequencing is discovering the broad variation in the genome that is put on the arrays for screening."

The constant discovery process supported by NGS has prompted Illumina to enable customers to add content onto arrays that have already been designed. When Illumina makes a BeadChip, it first synthesizes thousands of oligonucleotides that are complementary to different target sequences. The oligos are then immobilized to beads that are then pooled together and loaded onto microwells that have been etched on the surface of a BeadChip.

In the past, custom arrays were designed by creating custom bead pools, which could not be altered after being generated. Now, Illumina allows customers to design new content for existing arrays using markers identified from association studies and sequencing efforts.

"Before, you developed your product once, and based on what you had, that's what you got," Orpin said. "Now, if you find new markers that you can use, you can add those onto the array later on."

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