Fluidigm will later this year debut a 96-SNP panel for use in assessing the quality and identity of samples collected by biorepositories. Fluidigm is hoping that the panel, which was designed in collaboration with Rutgers University Cell and DNA Repository, will be adopted by biobanks seeking to establish the functional performance of their samples prior to analysis in larger, more expensive array- and sequencing-based studies.
"It's not just a proposal for a gold standard for large biobanks, but for anybody who is banking DNA samples and then anybody who is looking to qualify samples for clinical use, so that you know before that test that you have the right sample, and know the quality is going to give you a call you can trust," said Andy Brooks, RUCDR's chief operating officer.
Brooks discussed the new panel during the recent Human Genome Meeting and International Congress of Genetics, held last week in Singapore (see Q&A, this issue). He told BioArray News that the panel was created about four years ago to replace the older, gel-based methods that Rutgers had been using to QC its samples.
"The biggest limitation … is that you didn't know if it was the right sample," Brooks said of this older approach, which he claimed is still widely used in biorepositories. "You could have high-quality DNA, but there was nothing to say it was the right sample."
In comparison, Brooks said that the new assay, which he referred to as the RUID panel, provides for between $5 and $10 per sample the ability to assess a sample's quality and its identity via markers for ethnicity and parentage. For repositories like RUCDR, Brooks said it makes sense to obtain information about the functional performance of a sample at that price prior to further analyses.
"Before you go do an exome sequencing run for $1,000 or a microarray for a couple hundred dollars, or even quantitative PCR in thousands of samples, to know that you are going to get quality data from that sample, and that sample is banked to be used and distributed over and over again, $10 is a very small investment," said Brooks.
He noted that the RUCDR has seen a similar gene expression-based assay, which he called RUGX, licensed to be commercialized on Wafergen Biosystems's SmartChip platform.
Off The Shelf
Greg Fisher, director of product marketing at South San Francisco, Calif.-based Fluidigm, said that the new panel, should become available by midyear. Fisher told BioArray News this week that the complete offering will consist of an integrated fluidic circuit biochip and reagents run on the firm's BioMark HD system. Users will be able to genotype their samples using the firm's SNPtype assays, which are based on allele-specific PCR SNP detection chemistry.
According to Fisher, Fluidigm decided to make the product available to encourage standardization among the growing number of biorepositories.
"Over the past ten years there has been substantial growth in the number of laboratories that identify themselves as biobanks or biorepositories who serve the basic and clinical research markets, as well as
pharmaceutical companies and service providers that are creating their own sample repository labs," Fisher said. He said that the "broad majority" of these labs have not adopted standardized methods to identity or track samples coming into their banks or going out to their customers, and, as a result, there is a substantial error rate associated with misidentified samples.
Brooks said that about 98 percent of biorepository errors are attributable to misidentified samples and other errors in sample collection and reporting.
According to Fisher, a number of Fluidigm customers such as RUCDR have already created custom SNP panels for their labs' use, but a "far greater number" of the firm's clients have requested an off-the-shelf panel. He said that this "ongoing pull" from customers to help them improve their sample tracking processes, as well as the lack of standardized methods and industry requirements to do so, led Fluidigm to develop its product.
As RUCDR has been a "long-term" customer of Fluidigm and houses one of the world's largest collections, including 9 million nucleic acid samples, Fisher said the firm decided to "leverage this experience" to create the new product, ultimately selecting a panel of SNPs that can be used to "fingerprint a sample, identify gender and ethnicity, and confirm results through overlap with major microarrays on the market."
Fit with Biobank Arrays
Like Fluidigm, array vendors Affymetrix and Illumina have also taken note of the growing collection of biorepositories. Over the past six months, each has launched lower-cost genotyping arrays to meet the needs of such customers. Affymetrix sells its Axiom Biobank Array, while Illumina offers its HumanCore and HumanExomeCore BeadChips. Both products are partially customizable (BAN 10/16/2012).
The firms have seen interest in the products. Last month, Affymetrix announced an agreement with UK Biobank to genotype its 500,000-sample collection (BAN 3/26/2013). And Illumina has also reported demand: CEO Jay Flatley told investors during the firm's fourth-quarter earnings call in February that, since launching the arrays, it had received orders for enough HumanCore chips to process 325,000 samples (BAN 1/29/2013).
Brooks said that Fluidigm's new panel would complement rather than compete against the new microarrays.
"I think these arrays enhance the discovery process, and that they don't replace the RUID panel," Brooks said. "If the biobank arrays were $80 and the RUID panel was $80, I would say, 'Don't run both.' But for $5 you can make sure that the data you get with the biobank array is high quality," he said.
Brooks added that he thinks the concept of biobank arrays is "an excellent one" that "allows you to choose the samples for deeper investigation more sensibly."
Fisher said that customers running array-based genome-wide association studies had expressed demand for a tool such as the RUID panel. He also said that the same customers have been "demanding that the biobanks provide some type of analysis on samples before they are received."
According to Fisher, this demand is coming in part from researchers who are cognizant of the "obvious monetary return" on eliminating sample errors prior to their use as part of array-based association studies or next-generation sequencing.