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Ingenuity Preps New NGS Variant Analysis Tool, Signs Translational Oncology Group as Beta Tester


By Uduak Grace Thomas

Ingenuity will soon launch a standalone product for selecting clinically relevant genomic variants from next-generation sequencing data, BioInform learned this week.

The software, dubbed Ingenuity Variant Analysis, is currently in beta and will be released this quarter, Dan Richards, Ingenuity's co-founder and director of its computational biology arm, told BioInform in an e-mail.

The company disclosed this week that the Translational Oncology arm of the University Medical Center Mainz, dubbed TRON for short, is a beta tester for the software. The group is using Ingenuity Variant Analysis to identify cancer variants to support the development of personalized drugs.

John Castle, who co-heads TRON's Biomarker Development Center, explained to BioInform that the institute is analyzing mutations in patient tumor samples and prioritizing those that are immunogenic. After selecting the most useful markers, it designs personalized RNA therapeutics.

He said in a statement that Ingenuity's software helped TRON investigators "identify 30 compelling tumor-specific variants in record time that we then used to inform our first experimental therapeutic RNA cocktail."

Ingenuity Variant Analysis is a web application that uses Ingenuity's databases of curated biological data and mutation information to help researchers sift through millions of variants in resequencing data to identify causal variants based on known relationships with pathways, genes, biological processes, and diseases.

The database includes known and predicted deleterious variants and also allows researchers to use genetic criteria such as haploinsufficiency and hemizygosity to identify candidate markers, Richards said.

The tool also lets users integrate their own data such as RNA-seq isoform expression data or epigenetic genome coordinate data to further refine their analysis.

He explained that the company chose to develop a variant analysis tool to help clinical researchers with the task of "sifting' through large quantities of candidate variants to find those that play a role in disease progression or drug response.

"By leveraging Ingenuity’s Knowledgebase of ... curated literature findings and computational pathway models, together with our collaborators and customers, we found [variant identification] could be done in a fast, interactive, systematic way," he said.

TRON's Castle told BioInform that the institute explored several commercial software and open source options for its variant analysis needs and selected Ingenuity's package because it combines necessary features, including open source algorithms like SIFT, with an interface that’s easy for immunologists, clinicians, molecular biologists, and other non-bioinformatics experts to use.

For example, the software provides variant filters that allow users to upload expression values and locate those that are nonsynonymous and occur in genes that are highly expressed and are known to have a pharmacogenetic impact, he explained. If users then decide to filter variants based on genes that have a different expression, they can modify the filters themselves without requiring assistance from bioinformaticists, he said.

In addition to its ease of use, TRON opted to use Ingenuity's tool because of the depth of the curated content that the company provides in its databases, Castle said.

Although it is moving into a new market with the variant analysis module, Ingenuity isn't abandoning its pathway analysis roots.

Richards said the company has continued to improve its flagship product, Ingenuity Pathway Analysis, by adding more content and support for integrated biological analysis that spans multiple omics data types.

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