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Ingenuity Rolls out iReport Software for Array Analysis, Plans to Add NGS, qPCR Capabilities


By Justin Petrone

Ingenuity Systems last week introduced iReport, an analysis tool for microarray-based gene-expression profiling data.

Ingenuity plans to add analysis capabilities for expression data generated by other technologies, such as next-generation sequencing and quantitative PCR, though it has not disclosed a timeline for these capabilities.

The offering builds upon the company's flagship Ingenuity Pathway Analysis platform by enabling rapid data analysis for specific instrument platforms and experimental goals.

The new product is intended to appeal to researchers who may not have the same bioinformatics expertise as an IPA user. It uses the same knowledge base as IPA, "but it is a simpler interface and gets you quickly to genes you want to look at," said Amy Palmer, Ingenuity's senior marketing programs manager, who discussed the product with BioArray News at Select Biosciences' Microarray World Congress in South San Francisco, Calif., last week.

The software provides a "standalone report" for statistical and biological interpretation of data "without the need for training, software, statistics, or informatics expertise," according to the company. Researchers upload their array data and receive an interactive report with a list of significantly differentially expressed genes. The report then allows researchers to explore genes "by function, biological process, role in pathway and disease, and cellular location," the company said.

Ingenuity is making iReport available for free to up to 5,000 early-access customers, but Palmer declined to say when it would offer it as a catalog product.

"We will wait and see; we want feedback," Palmer said of iReport's undecided launch date. "We want to make sure it is really useful, that it is delivering value, and our goal is to get that right."

While most would consider the market for expression arrays to be a mature one, there is no shortage of new analysis tools for the technology. For instance, Qlucore, a Lund, Sweden-based software developer, has announced two deals related to its new Omics Explorer software in recent weeks (see story, this issue).

Palmer said that there is a clear need for tools like iReport. "There is a big hurdle right now in data analysis," she said. "A lot of people don't have in-house resources to make sense of expression data, so they get a giant spreadsheet of genes, but they don't have statistical know-how, they don't have bioinformatics resources."

Even if researchers do have access to analysis tools, she said the analysis process "takes too long" and users are often unsure how to interpret their results.

She said that iReport has an integrated statistical pipeline. "If you have a data set, it runs statistics against that, and you get a list of differentially expressed genes," she said. "You will very quickly see the most relevant diseases, cell processes, and pathways to that set of differentially expressed genes."

Beyond that initial report, Palmer said that Ingenuity offers users tools to help them "drill down" to relevant gene sets. "There might be a list of 30 diseases that are known to be related to your, say, 280 expressed genes," she said. "We offer tools to see what genes are relevant to, say, lung cancer."

Another component of the offering is a visually interactive tool the firm calls "the wheel" — a circular representation of the information provided in the report. During a conference presentation, Senior Scientist Megan Laurance said the wheel "serves as guide to the entire report – what pathways, what diseases, what molecular interactions are related to these genes."

"It is a way to filter genes and group genes very quickly so that you start to understand how they work together," said Palmer.

She said that the firm's visualization tools could give it a leg up in the market, where it competes not only against other commercial offerings, but bioinformatics tools developed in house. "It is very hard to look at a whole spreadsheet and grasp what is going on, and the wheel is a way to intuitively and visually organize results in a way that is important to the way that you are thinking about your experiment," said Palmer.

Founded in 1998, Ingenuity's flagship platform to date has been IPA, which takes a pathway-centric approach to analyzing data from gene expression and SNP microarrays, as well as RNA-seq, microRNA, and proteomics experiments. IPA includes capabilities for toxicology and metabolomics studies, as well as biomarker analysis.

Palmer said that IPA has a "strong presence in pharmaceutical companies, academic and research institutions," but described it as a "more robust tool" in terms of the types of experiments and data it can accommodate.

"If you are trying to integrate multiple experiments with more complex types of data, IPA is a great tool," said Palmer. "But if you don't have bioinformatics training or just want a quick answer," iReport may be a better option.

Unlike IPA, which the company markets to groups with established bioinformatics resources, Ingenuity is marketing iReport to "bench biologists who don't have the statistical resources for data analysis," as well as "core labs and service providers that … want to return something [to researchers] that is understandable and enhances their value as a provider," Palmer said.

Daryl Michalik, a senior product manager at Ingenuity, told BioArray News that the company is looking into bundling iReport with kits sold by platform providers, though he didn't elaborate. Ingenuity is also interested in expanding iReport's capabilities to include RNA-seq and qPCR data analysis. In time, the firm may also add other types of data, such as SNP and copy number variation analysis, to its iReport menu, said Michalik, who also attended the conference.

Still, for the time being, he said the company is "most interested" in seeing the tool adopted by early-access users.

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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