This story originally appeared in Biocommerce Week, a newsletter that has been discontinued.
Applied Biosystems last week struck a deal to integrate its genotyping tools with BioTrove’s OpenArray platform in a collaboration that it hopes will reach more customers doing downstream applications.
ABI’s genotyping assays currently run on any real-time platform, usually in a 384-well format, but running the assays on BioTrove’s system will enable a far greater number of samples to be screened. The pact also gives ABI an option to collaborate with BioTrove to develop and market OpenArray for high-throughput gene-expression applications.
Under the agreement, ABI will develop and market custom arrays of TaqMan SNP genotyping assays pre-loaded on BioTrove’s OpenArray, which is a flexible array format that allows researchers to perform over 3,000 different high-throughput genotyping assays in different configurations. This integrated platform will enable researchers to conduct high-throughput genotyping studies at a “lower total cost compared to commercially available methods,” ABI said.
ABI said the integrated Taqman and OpenArray platform will enable an end-to-end genotyping workflow of less than four hours, thus allowing researchers to analyze thousands of samples for large-scale genotyping projects in days rather than weeks.
Whether customers choose to use the BioTrove OpenArray system or a standard 384-well instrument will depend on what they want to do, according to Phoebe White, senior director of ABI’s genotyping product line. “For example, if you look at 15 SNPs against 200 samples, that kind of a study — small sample size, small number of SNPs — is still going to be much better suited to running on the standard platform with 384-well plates,” she told BioCommerce Week.
However, if a customer wants to look at 50 SNPs and has 10,000 samples they want to screen, “that customer is going to be significantly enabled by the OpenArray platform,” she said. The platform would be ideal for customers who want to run tens to a couple of hundred of SNPs, but have very high-sample throughput, White added.
She said trying to do that many samples on a 384-well system would require a lot of robotics, a lot of plates, and a lot of work. “What we want to enable customers to do is use the TaqMan assays that they’re using today … and use them in a much more high-sample throughput application,” said White.
She said the OpenArray system is “not going to replace [current 384-well systems], but it’s going to enable many more customers who are doing these high-sample throughput studies and give them a quick, easy, TaqMan-based platform to work on. There are no really good technologies out there that can provide the sample throughput that that kind of platform can,” she said.
The OpenArray technology is at the opposite end of the spectrum from the high-density SNP microarrays offered by firms such as Affymetrix and Illumina, and is ultimately a complementary technology, White suggested.
“The microarray platform will give you anywhere from 10,000 SNPs … to 1 million SNPs, and customers will typically run those across tens of samples, maybe hundreds of samples,” she said, noting that researchers tend to use these high-density microarrays to discover SNPs.
However, once customers want to validate those SNPs across thousands of samples, “that is where an array platform becomes cost prohibitive, and also you don’t need the volume of data you’ll get off of an array platform,” she said.
White said ABI sees customers taking these results into commercial studies and a variety of testing environments. She cited agricultural genotyping as a prime example, in which crop manufacturers are trying to identify SNPs associated with specific traits in crops and are then doing high-throughput breeding to try and introduce those traits into the crops.
“There’s a huge amount of work in agriculture,” said White. “We see it emerging in animal testing, QC testing, we see it emerging in fisheries management. Also, we’re seeing many more high-sample throughput of genotyping disease-association studies taking place.
“All of the microarray studies that are being done are yielding all of these different sets of SNPs or groups of SNPs that people want to validate and then start to use in clinical studies, disease studies, or on the agbio side,” said White.
As part of the agreement, ABI will hold the rights to sell all genotyping applications, including some not based on its TaqMan technology, for OpenArray. The company expects to begin selling these tools in the second half of 2008.
“There are no really good technologies out there that can provide the sample throughput that that kind of platform can.”
Because ABI classifies its TaqMan arrays as consumables, the agreement also is expected to drive consumables sales, which has been a key focus for ABI over the past couple of years.
Gene Expression Option
ABI also holds an option to collaborate with BioTrove to develop and market OpenArray for high-throughput gene-expression applications. While ABI is not certain yet that it will exercise this option, such a move would likely interest customers and investors alike.
Just last month, ABI announced that it would discontinue its 1700 microarray platform for gene expression applications and would instead market its newly launched SOLiD next-generation sequencing platform for expression analysis. ABI first launched its 1700 Chemiluminescent Expression Analysis System in 2003 and now sells whole-genome microarrays for expression studies for human, mouse, and rat.
An ABI spokesperson told BioCommerce Week sister publication BioArray News that the company plans to phase out the array system over the next two years while seeking to fulfill its customers’ expression analysis needs with the SOLiD System, which ABI maintains is a better platform for expression studies.
ABI’s decision to discontinue the array platform coincides with Nanogen’s decision to shut down its array business (see Briefs), and comes nearly a year after GE Healthcare decided to end its involvement in the array market. Over the past 12 months CombiMatrix also decided to ditch the research market for chips, and began focusing solely on growing a diagnostics business.
“The 1700 system was a niche product for Applied Biosystems, and we've concluded that the SOLiD System with its proprietary stepwise ligation technology will be very good for counting applications including gene expression,” the spokesperson said at the time.
However, the option agreement with BioTrove opens up the possibility of ABI being involved in the gene expression market at the high-sample throughput end of the market.
“We don’t necessarily see the gene expression market unfolding as quickly as the genotyping market with respect to these very high-sample throughput studies,” said White. “We really wanted to wait and see a little bit how the gene expression market unfolds.”
As part of last week’s agreements, ABI granted BioTrove a worldwide license to its patents covering real-time thermal cyclers, microfluidics, and data analysis. This contract will allow BioTrove to make and sell real-time thermal cyclers and array sample loaders for life science research purposes and to develop more real-time PCR applications, including gene expression, for OpenArray.
“We have given BioTrove a real-time license, and we are working with and encouraging BioTrove to continue development of the gene expression platform themselves, so we can partner up with them at the right time for AB,” said White.
She noted that ABI also plans to address the digital gene expression market with the SOLiD System.
“We are trying to work very hard to define how that platform will play both in future gene expression and in genotyping [applications] and how we’re going to position the technologies off of each other,” she said. “A little bit of time is needed to really figure out what’s going to work and what isn’t.”