If one whole genome on a single microarray is good, are six better?
Illumina last week launched two BeadChip products that mark the company’s continued attack on the gene-expression marketplace and present researchers with an interesting alternative — the opportunity to interrogate six separate samples against six whole-human genome probes on one slide.
Illumina, based in San Diego, entered the gene expression market in September (see BAN 9/17/2003) with the launch of its Sentrix Array Matrix and Sentrix BeadChip product lines.
“This is an exciting time for Illumina,” Jay Flatley, the company’s chief executive officer and president, told attendees at the JPMorgan Healthcare conference in San Francisco, while at the same time, company representatives worked the show floor at the International Plant and Animal Genome conference in San Diego.
The company’s newest offerings are two slides for use in the BeadChip product line, and are only readable on the company’s scanner technology. The products are to undergo beta-testing with customers and are targeted for commercial launch in the middle of the year. The company declined to provide pricing information.
The new products are designed to enable whole-genome expression profiling of multiple samples on a single chip.
One BeadChip product is set up to analyze six discrete whole-human-genome samples on one 1x3 chip. The second product is set up to analyze eight samples in parallel against the approximately 22,000 genes represented in the RefSeq database, also on one chip.
The six-sample and eight-sample Sentrix BeadChip products each contain millions of beads. On the six-sample chip, the beads are arrayed into 12 lines visible across the short side of a 1x3 format slide. The eight-sample chip has eight lines arrayed across the width of the slides.
Each of the lines contain thousands of wells, with each well holding a 3-micron bead coated with DNA probes 50 base pairs long. The wells are situated six microns (center to center) from their neighbors and are designed to interrogate approximately 48,000 transcripts from the estimated 30,000 genes in the human genome.
The company’s BeadArray technology is built around beads that self-assemble into microwells etched into an array substrate. To form an array, a pool of the coated beads is flooded onto the array surface where they are drawn into the wells. A subsequent decoding process enables the company to determine which bead type or sensor occupies each microwell, which results in a map that is used in downstream analysis and operates as a quality-control metric for each bead in each array. If a bead doesn’t exhibit sufficient intensity, it is excluded from the map, the company said.
The new products require Illumina hybridization reagents, sample preparation and labeling protocols, and, because of their format, are only readable on the company’s BeadArray Reader. The company provides software for analysis and the ability to export data to other commercial expression programs.
The products illustrate the flexibility of Illumina’s manufacturing process, and allow the company to conduct its own market tests.
“We are looking forward to seeing which one is more interesting to more people,” said Bill Craumer, Illumina’s director of marketing communications. “We are not sure which one is going to sell more.”
The 8-sample chip is designed for researchers who aren’t interested in any more content than the genes available from the RefSeq database, he said.
The six-sample chip takes that same RefSeq information and adds additional probes based on data from the Unigene database.
As for pricing, Craumer said that the company is determined to explore the boundaries of the low-pricing envelope.
“I can guarantee you that these will be significantly below anything on a per sample basis,” Craumer said.
Response to the announcement of the new products has been positive, he said.
“We have been delighted with response,” he said. “We have way too many lining up at the gates.”
Beta testing will be conducted in two phases. Customers will conduct validation tests that Illumina uses internally, and then will conduct their own research, while meeting regu-larly with Illumina representatives.
The products were made possible as the company improved its methods for decoding what beads were where on the arrays, Craumer said.
The processes used can apply to other whole-genome data, and the company will expand its product lines to include those, he added.