A version of this story previously ran in BioInform's sister publication BioArray News.
Seeking to broaden its customer base beyond researchers conducting genome-wide association studies, Golden Helix last week launched an upgrade of its SNP & Variation Suite 7 software that includes features expected to appeal to cytogeneticists and researchers in the agricultural biotech market.
Bozeman, Mt.-based Golden Helix initially launched SVS 7 last year to support the analysis of large data sets generated by genome-wide association studies and next-generation sequencing instruments. While the firm's main customer group to date has been researchers conducting GWAS, the company is targeting the latest installment to those using arrays in cytogenetics and agricultural biotechnology studies.
With an eye on these markets, SVS 7 now includes an interactive genome browser that enables customers to directly compare their results with data from several resources such as the Centre for Applied Genomics’ Database of Genomic Variants or the University of California at Santa Cruz's Genome Browser. SVS 7 also supports the direct import of data from Roche NimbleGen's menu of comparative genomic hybridization arrays and Affymetrix's Cytogenetics Whole-Genome 2.7M and Molecular Inversion Probe arrays. Finally, Golden Helix also added the capability to analyze non-human genomes, such as mouse, rat, chicken, cattle, horse, rice, soy, and others.
Andy Ferrin, executive vice president of business development at Golden Helix, told BioInform's sister publication BioArray News that the company added the new genome browser to "aid anyone trying to find and understand relationships in genetic data," but noted that the browser should "certainly be of interest to cytogenetic researchers" who are "trying to correlate phenotypic anomalies with genetic variation and understand if and how those variations contribute to the issue at hand."
"Watching how our customers worked, and also evaluating how molecular cytogenetic labs analyzed samples, it became clear that a consolidation of the various genome tracks in such a way that they could be viewed side-by-side with a researcher's own data would save a significant amount of work and time," Ferrin said.
Ferrin noted that the existence of multiple resources with the same information has posed a challenge for cytogeneticists. Researchers are typically forced to bounce from site to site or browser to browser to explore their data, because only pieces of the information reside in any one place. SVS 7's Genome Browser was designed to simplify this process.
In terms of SVS 7's added import capabilities, Ferrin said that the software currently supports all of Affy and Illumina's SNP arrays, as well as Agilent Technologies' CGH arrays. By adding support for NimbleGen arrays, Golden Helix now offers specialized tools for the four major array platforms used in molecular cytogenetics, a relatively new market for the decade-old firm, given its background in GWAS.
Josh Forsythe, vice president of sales and marketing, noted in a statement that the consistent generation of data by cyto labs represents a "virtual treasure trove of data and represents tremendous opportunities for understanding more about the role of genetics in constitutional disorders."
Cytogenetics presents a growth opportunity for the microarray market, and subsequently, the array analysis market. Over the last several years, many cytogeneticists have adopted array-based chromosomal analysis over traditional methods such as karyotyping.
In May, the International Standard Cytogenomic Array Consortium recommended that chromosomal microarrays replace G-banded karyotypes as the first-tier technology to test individuals with unexplained developmental delay and intellectual disability, autism spectrum disorders, or multiple congenital anomalies.
In its recommendations, published in the American Journal of Human Genetics, ISCA noted that chromosomal microarrays have a higher diagnostic yield than karyotypes and are technically superior to other cytogenetic testing methods.
Likewise, in June, the Association for Molecular Pathology issued a statement in support of array-based cytogenetic testing as part of a meeting hosted by the Food and Drug Administration to discuss a possible regulatory framework for these tests.
AMP noted that "array-based cytogenetic tests provide much higher resolution than traditional karyotyping, with expansive capabilities to diagnose and identify causes of genetic syndromes due to chromosome abnormalities," and argued that "the standard of care in molecular and cytogenetic laboratories as well as genetics clinics is shifting from traditional karyotyping to array-based cytogenomic analysis."
According to a market research report published by Frost & Sullivan last year, the US array-based molecular cytogenetics market was approximately $41.7 million in 2008, which comprised around one-third of the total US molecular cytogenetics market. The firm projects that arrays will comprise approximately 60 percent of the total market by 2015.
Like the molecular cytogenetics market, most array vendors also see agbio as a growth opportunity, and Ferrin said that Golden Helix views the market similarly.
"We are seeing an increase in interest from those in the agbio sector — they are getting more sophisticated, getting larger data, and realize that fighting with difficult tools, or creating their own difficult-to-use tools, is simply not an efficient use of their time," Ferrin said.
According to Ferrin, due to more limited budgets, agbio researchers have long had to make do with makeshift analysis tools. "In many ways, the agbio space has always played second fiddle to human research," he said. "Billions of dollars are spent on human research each year, and there is a number of robust software tools, [both] commercial and academic, which help researchers tease out important information from vast amounts of data," he said.
The agbio market is smaller and has less funding, Ferrin noted, and researchers are "often forced to make do with whatever tools they can get their hands on — typically difficult to use, command-line freeware, or they write their own tools in R." Ferrin said that in recent years, the increased density of arrays and their declining costs have fostered increased adoption of the technology among agbio researchers, resulting in an "explosion in data size, making the tools they have been getting by with more and more difficult to use – impossible in some cases."
Golden Helix's Forsythe noted that the firm has "experienced significant growth" in the number of its customers performing advanced statistical analysis on non-human genetic data. "Until now, there really haven't been any integrated, easy-to-use tools for this market," Forsythe said.
'No Longer Bleeding Edge'
It is freely available and homemade software solutions that Golden Helix counts among its main competitors. To win new clients, the company must convince researchers that they should pay for better analysis tools rather than continue to do it by themselves.
While such free tools "often do a good job for a specific function or two, we find that researchers spend an inordinate amount of time formatting data so they can pass it back and forth between tools, and even more time learning how to use them," Ferrin said. "There are a large number of genetic researchers out there who have been forced to become programmers just so they can get their analysis work done," he said. "Just think what they could have accomplished if they had easy to use, comprehensive tools and were able to focus entirely on their research instead."
Still, Golden Helix has seen an uptick in customer interest as studies, particularly GWAS, become larger, and new researchers opt to buy into SVS 7 rather than invest in building their own tools from freeware. "More and more people see the academic freeware alternatives; realize the massive investment of time that goes along with 'free,' and come directly to us," he said.
From Golden Helix's perspective, this new generation of customers is a boon to its business, as it expects "solid, straightforward" tools. "Genetic research is no longer considered bleeding edge, and more and more researchers are interested in exploring the relationships between genotype and disease," Ferrin said.
"People on the bleeding edge, the early adopters, expect to struggle with tools and standards — they make them as they go," he said. "As research modalities become more mature, expectations around tools and standards rise," he added. Customers are therefore "less willing to struggle with difficult tools or confusing workflows."