With the formal rollout of its CustomSeq chip last week, Affymetrix is going back to the future.
“We started out doing a lot of DNA analysis, then got into gene expression; now we are using the infrastructure we built for gene expression to create new products for analysis,” Greg Yap, Affymetrix senior director for DNA analysis marketing, told BioArray News. “This is our newest product in the DNA analysis area and a part of a new line of DNA analysis products coming out over the next several months, and on an ongoing basis.”
The chip is designed for comparative sequencing, or resequencing, at a cost savings over standard sequencing methods. It has a retail price of $600 per array.
Each CustomSeq array contains features of 20 by 25 microns, and will have a capacity of 30,000 double-stranded bases at a fragment length of 25mers. There will be eight features on the chip per base tested — four bases per strand, he said.
This technology derives from that used by Affymetrix spinoff Perlegen Sciences, which used most of $100 million in funding to buy the chips it needed to do 50 genomes in 15 months. Affymetrix slices whole wafers like the ones Perlegen ordered and sells them by the chip.
“Perlegen is pushing the limits of throughput,” said Yap. “We are building on that, and offering these chips to researchers to use in their own labs and their own resequences.”
Researchers will determine specific sequences they would like to resequence in order to detect specific SNPs, then the chip will be designed accordingly.
“So, for position 1,000 of a 30,000 kilobase length of contiguous [sequence], there will be a set of probes with the 25-base-pair region surrounding this specific region — 12 bases before it and the 12 after it. The change will occur in the center position of this length of oligonucleotide, interchanging the 13th base between A, C, T or G,” said Yap.
“You could read it off almost like you could read a sequencing gel,” he said.
The chips performed to 99.998 percent accuracy in a test against capillary resequencing, Yap said.
The company compared a 30 kilobase sequence resequenced 10 times on a chip against the same 30 kilobase sequence resequenced 10 times by a service provider on a sequencing machine repeated 1 to 4 times, he said. The chip had a call rate of 96 percent compared to 84 percent for the capillary, Yap said.
“So, out of 280,000 potential bases, we came up with 240,000 bases, and they came up with 180,000 bases. We took the overlap of only those bases which were called by the sequencer with a FRET score higher than 50. So, there were 120,000 bases of overlap and of those, there were two discordances. So, 2 of 120 is 99.998 percent.”
In conducting this test, the company also noted the considerable savings produced when compared with standard resequencing procedures, Yap said.
“It took us about four PCR reactions per sample for that 30,000 kilobases; the sequence provider needed over 100 PCR reactions per sample,” Yap said.
The chip took one technician to generate the data. “There was very little hand intervention there,” Yapp said.
The chip yields 10 data sets, each containing 30 kilobases of double-strand sequence for each hybridization experiment, he said. “With the provider, we got back about 984 sequence reads of about 500 to 700 bases each.”
The company will accept minimum orders of 80 chips, he said.
“We are looking for people interested in larger experiments,” he said.
The minimum order is created on two 49-chip wafers. Affymetrix keeps a number of chips for testing and for future reference. Customers usually receive the 80-plus black chips with white labels, shipped in boxes that contain from 5 to 20 chips each.
Affymetrix expects to sell its product to pharmaceutical companies, even those that already have sequencing equipment.
“It’s a labor question,” Yap said. “Many of them have sequencing and all of them have our instruments as well. We expect a pretty broad market. One of the things that we find interesting about the DNA analysis line is that we think there is a lot of integration with our existing RNA analysis customers.”
“Whole genome RNA analysis and whole genome DNA simply feeds people’s appetites for doing resequencing. We expect there will be a lot of customers who want to do both. By using resequencing arrays, we feel people can get much further into the problem and understand the root cause of expression variability in the context of sequence variability.”
Yap said the company expects some use of this in pharmacogenomics and for those who are doing bacterial or pathogenic typing.
“This is a key area for us,” he said. “We are hoping to establish our platform as the standard for DNA analysis.”
At a recent Wall Street conference in New York, Affymetrix CFO Greg Schiffman said the company is targeting the clinical genomics market.
The company has had its product available for its early access customers, but with a formal press release and a rollout at the American Society for Human Genetics in Baltimore last week, this chip is now available to anybody that wants it.
The company expects to sell the chip to pharmaceutical firms and academics who need to examine particular genes or regions identified through large-scale analysis. The company also sees a market in pharmacogenomics firms as well as researchers in clinical settings examining genomic variations that contribute to drug response, bacterial or pathogenic typing.
Yap said customers can expect delivery of their chips usually within eight weeks after the custom designs are finalized.