Golden Helix has been bitten by the NGS bug. The company this week launched a Sequence Analysis Module for its SNP and Variation Suite software, joining the ranks of bioinformatics firms that are adding next-generation sequence data analysis tools to their existing offerings.
Joshua Forsythe, vice president of Golden Helix's sales and marketing department, told BioInform that the firm, which has traditionally focused on software for analyzing genome-wide association studies and copy number variation, is moving into NGS data analysis because its customers are "dipping their toes in as well."
Christophe Lambert, founder and CEO of Golden Helix, said in a statement that while most tools in the DNA analysis space focus on aligning or assembling raw reads and generating variant calls, there haven’t been any "comprehensive, integrated solutions created for tertiary analysis," which he described as "the ‘sense-making’ part of the process."
Sequence data analysis generally falls into three areas: primary analysis, which comprises base-calling and computing quality scores; secondary analysis, in which raw reads are aligned or assembled and variant calls are made; and tertiary analysis, which is focused on study-specific investigations based on the differences between sequenced samples and the reference genome.
The company said that the new module will provide an integrated desktop tool for tertiary analysis of next-generation DNA sequencing data. The module will enable researchers to import, manage, and manipulate hundreds to millions of common and rare variants to assess their impact on diseases and other traits; find genes or regions with an abundance of variants in samples; assess the rare variant burden; and understand the contributions of rare variants using functional predictions.
Forsythe described tertiary analysis as the company's "core competence," adding that the firm has received requests from scientists that are using NGS to, for example, resequence candidate genes or to perform whole-exome studies to identify rare variants, and don't have the adequate data analysis tools.
Although the Sequence Analysis Module is part of Golden Helix's SNP and Variation Suite, customers can purchase and deploy it without installing the entire suite, Forsythe said, adding that the tool is targeted at biologists and geneticists who have a "little bit of a statistics background."
Evolving and Competing Markets
As a newcomer to an already congested market, Golden Helix is in good company, as last year several vendors that have traditionally peddled tools in other sectors reached for their slice of the NGS cake.
Some examples include Spanish bioinformatics firm Integromics, which rolled out a tertiary NGS sequence analysis tool while holding onto the reins of its microarray, qPCR, and proteomics businesses (BI 10/08/2010).
Meanwhile, Genedata, a microarray-based company, launched the Genedata Expressionist Refiner Genome module to process and analyze NGS data in addition to the mass spectrometry, genomic profiling, and microarray modules in its Expressionist analysis platform (BI 10/01/2010).
On the commercial front, Golden Helix believes it has no competitors. Although Integromics recently launched SeqSolve, a tool for tertiary analysis of NGS data, Forsythe pointed out that Integromics — along with other tertiary analysis tool vendors — focuses on analyzing RNA-seq data and not DNA variants, which distinguishes Golden Helix's tool from similar offerings.
Forsythe described the NGS portion of Golden Helix's business as "complementary" to its microarray analysis arm, explaining that the firm believes that both technologies can be compatible because the cost for large-scale studies on NGS platforms is still quite high.
While open source tools remain his firm's largest competitor, Forsythe said that the new module offers an integrated solution whereas most free tools are designed to perform specific tasks and offer users point solutions.
Speaking more generally, Forsythe observed that as sequencing prices drop, he expects more researchers to begin using the technology for their studies thus increasing the need for data analysis tools. On the other hand, he said, RNA sequencing "has taken off a lot faster" and will soon — if it hasn’t already — supplant microarrays.
In spite of evolving markets, Golden Helix will continue to "fine tune" its microarray data analysis tools to handle next-generation data from new custom arrays and rare variant arrays produced by companies like Affymetrix, Forsythe said.
He also said that Golden Helix has plans to develop more NGS-based tools but declined to comment on what those are or when they will be available.
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