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Qiagen Launches Collaborative Community around Ingenuity Variant Analysis Software


This article has been updated to correct the previously reported number of myopia genes identified by Qiagen's analysis from 46 to 26, and to note that only 12 of these genes were implicated in eye phenotypes not 17

Qiagen is offering free use of its Ingenuity Variant Analysis software as part of a new effort it launched this week called the Empowered Genome Community, which is intended to provide individuals who've had their genomes sequenced with a secure collaborative environment within which to share data with one another and access tools to interpret it.

Through the community, Qiagen hopes to contribute to the body of knowledge around the genetic underpinnings of diseases, and also to provide a pool of potential case and control data that researchers could tap into for current and future genetic disease studies, Nathaniel Pearson, Qiagen's principal genome scientist told BioInform.

It's also an opportunity, he said, for the company to expose the genomic analysis capabilities of the Ingenuity platform to a much broader range of individuals who could eventually become its customers. Qiagen acquired the platform when it bought Ingenuity Systems — renamed Qiagen Redwood City — for $105 million this summer (BI 5/3/2013).

It’s a chance to "increase the number of minds who understand how useful our platform can be for helping people get more out of comparing many genomes to each other … [using] the statistical comparison methods we have," he said. "In the long run … we want Variant Analysis to be the [tool of choice for] anyone who sequences a new genome."

The arrangement is also intended to benefit individuals who have recently had their genomes sequenced, because they can use the community to, for instance, connect with expert researchers who may be studying rare phenotypes that are of interest to them. It could also be a boon for cash-strapped researchers who may not have sufficient funds to sequence enough individuals for their studies, Pearson said.

As part of efforts to drum up interest in the EGC and to jumpstart the community's activities, Qiagen has released early results of an internally run analysis of myopia genes in 111 people whose genomes were sequenced through Harvard University's Personal Genomes Project. When the data was analyzed initially, researchers identified 26 genes that were enriched with rare, potentially functionally relevant variants in people with myopia. Further filtering using Variant Analysis and the Ingenuity Knowledgebase revealed that 12 of these genes were implicated in eye phenotypes in people or mice.

Hoping to further refine these findings by taking advantage of community-wide expertise in areas such as myopia physiology, epidemiology, and filtering strategies, Qiagen is making the PGP dataset available for open analysis through the end of January 2014. Its plan is to jointly publish any useful results along with individuals in the community who make substantive contributions to interpretation process — the deadline will not affect the broader EGC, which will be able to continue sharing and analyzing data beyond that date.

To join the genome interpretation community, interested contributors are invited to sign up for Variant Analysis accounts and then upload their genomic data. Historically, customers were charged yearly fees to "activate" genomes for analysis in the Ingenuity Variant Analysis tool once they'd created accounts and uploaded data. However for the purposes of its EGC program, Qiagen is footing the bill for year-long access to its analysis capabilities, Pearson said. The goal of EGC isn't to generate revenue for company, he told BioInform. "The idea here is to let people make their data more scientifically useful by pooling it and then [be] actively involved in understanding it."

Participation in the EGC is open to researchers including existing customers of the Ingenuity platform, subjects in large-scale sequencing studies such as Illumina's Understand Your Genome program, as well as citizen scientists looking to try their hands at genomic data analysis. People who decide to share their data with the community will have full ownership and control of their data and will decide with whom and how much of that information is shared.

Also, data sharing isn't a prerequisite for registration or participation in the EGC. Members don't have to upload their data if they don't want to but they can still help with ongoing interpretation efforts around the PGP data and they can use Variant Analysis' tools to analyze data that others in the community choose to share with them.

However, Qiagen believes that most people who sign up will be willing to play nicely with each other. "I think … they recognize the value of pooling their data together and actively talking about it and sharing the analysis process," Pearson said. So far, early participants in the program have been "excited to share [data] with each other … [and] with full-time researchers," he said.

Its also possible for members to bring in additional information such as linkage mapping data and incorporate it into their analysis. They can also export results — in the VCF file format — into other tools that they want to use to further explore their data.

Currently, members can only upload and analyze whole genomes, but Qiagen is contemplating whether or not to begin accepting whole exomes as well, according to Pearson. He explained that the company is evaluating the community's level of interest in whole-exome analysis but that it hasn’t yet made a decision about whether or not to expand its scope to include it and the appropriate time to do so.