Talkin’ ’bout my generation

Ingenuity Systems, Covance collaborate to support next-generation sequencing research

REDWOOD CITY, Calif.—With an eye on next-generationsequencing (NGS) analysis, Ingenuity Systems has entered into a research collaborationwith Covance.
The companies will work together to develop new and novelapproaches using Ingenuity's IPA software to obtain more actionable insightsfrom NGS data and to answer research questions in a relevant biologicalcontext.
"We're delighted that Covance has selected IPA for its NGSworkflows," says Doug Bassett, chief scientific and technology officer atIngenuity Systems. "We've been involved in several NGS collaborations recently,and our partnership with Covance, a leading drug development services company,represents another powerful validation of IPA's value in the NGS space. It isexciting to see IPA being used to accelerate and inform so much groundbreakingresearch."
Thomas Turi, vice president of science and technology forCovance Discovery and Translational Services, notes that this is the firstformal collaboration between the Covance Genomics Laboratory (CGL) andIngenuity Systems.
"Prior to its acquisition by Covance, CGL (formerly known asRosetta Inpharmatics) was a significant user of Ingenuity's IPA software," hesays. "Additionally, there had previously been significant interactions betweenkey scientific leaders at Covance and Ingenuity that facilitated thiscollaboration."
Ingenuity Systems is a provider of information solutions andcustom services for life-science researchers, computational biologists andbioinformaticists and life science industry suppliers.
According to Bassett, Covance proved to be a good fit forthis effort because of the company's standing as a provider of genomicssolutions for the drug discovery and development industry and the fact that thecompanies share many of the same customers. 
"Covance is also similarly forward-looking in how they arethinking about next-generation sequencing technologies," he says. "Both of ourcompanies recognize that without biological interpretation, the value andpotential in NGS technologies will not be unlocked for our mutual customers.Having Excel files of data or a list of variants or genes with associated statisticsis a first step, but it does not get researchers to their end goal of answeringa scientific question." 
The collaboration, Turi points out, is aimed at providingdeeper insights and interpretation of biological pathways and networks fromgenomic data.
"The key part of this collaboration is aimed specifically atmaking sense of large volumes of next-generation sequencing data to provide asystematic and multi-dimensional view of human genetics and cover various datatypes, e.g., gene expression, genotyping, splice variation and methylation," hesays. "Integrating these various data types into coherent biological stories iswhat constitutes the most challenging step."
In the collaboration, Ingenuity and Covance are workingtogether to develop new methodologies to help pharmaceutical clients maximizethe value of their NGS investments and obtain more actionable insights from NGSdata, including isoform-level biological interpretation for RNA-Seq studiesleveraging Ingenuity knowledgebase content, and helping customers usingresequencing technology to get from a list of 3 million-plus variants down tothe less than 50 most compelling for follow-up.
"Ingenuity's Knowledge Base of expert-curated, structuredbiomedical content provides the biological context necessary to move past longlists of genes, isoforms and variants, enabling researchers to more quicklyuncover those that are most critical to biology," Bassett notes. "Using thisapproach, Covance can more rapidly and confidently narrow in on what isinteresting or unique in a dataset and deliver more meaningful results to theircustomers."
Moreover, Bassett says the companies share a commonconviction that analyzing data in the context of known biology—like pathways,processes and diseases—is essential to uncovering novel insights and helpingresearchers quickly get to high-value outcomes like causal disease variants,biomarker identification, target ID and validation, understanding drugmechanism of action and safety assessment.
According to Bassett, success of this collaboration can bemeasured by the effectiveness and efficiency of their mutual customers.
"This partnership should enable scientists to invest theirvaluable time on the biological interpretation of their data—validating hypotheses,assessing safety, prioritizing biomarkers, identifying causal variants and soon—not dealing with data processing issues, manually iterating through largelists of variants or genes, or struggling to place their data into the contextof previously published mutations and findings," he points out.
Being digital in nature and due to its larger dynamic rangecompared to microarrays, this technology helps in the identification of novelgenetic alterations, non-coding RNAs and alternative splicing, in addition togene expression associated with various diseases.
"As more data becomes available, there is a growing need inthe industry to develop automated pipelines to integrate and mine complexdatasets for better understanding of biological processes that impact drugdevelopment," Turi explains. "Covance plans to use this collaboration tofurther develop its pipeline for analyzing complex datasets and aidpharmaceutical and biotech partners to identify targets or biomarkers for theirdrug discovery programs. Covance will test these capabilities using a pilotproject with Institute of Systems Biology (ISB) targeting glioblastoma."
Additionally, Turi says the collaboration will furtherenhance Covance's offerings in the genomics arena.
"As next-generation sequencing rapidly becomes the focus ofgenomics, Covance realizes that in the near future the platforms willsignificantly shift into the space of next-generation sequencing," he says.

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