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ViaGenetics Launches Genesis Platform to Offer Simplified Access to Data, Computation, Storage

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NEW YORK (GenomeWeb) – ViaGenetics launched a new version of Genesis last week, a proprietary platform that provides space and computational tools for searching, managing, sharing, and storing whole genome and exome information.

Besides storage and access to compute servers, Genesis 2.0 offers tools for processing and aligning raw sequences, as well as for calling and annotating genetic variants. It also offers tools for querying lists of variants across multiple genomes in seconds, according to the company. Customers' data is stored and analyzed on cloud infrastructure provided by Amazon Web Services. The platform can be used to identify variants associated with rare inherited disorders, as well as mutations linked to various cancers, cardiovascular disease, neurological disorders such as Alzheimer's disease, and other diseases.

Richard Postrel, ViaGenetics' CEO and chief innovation officer, told GenomeWeb that the company offers free use of its platform to nonprofit researchers and charges for-profit clients, such as clinical laboratories, a flexible fee based on case-by-case arrangements. ViaGenetics also offers a $2,000 service through which it helps customers sequence genomes or exomes, and uploads and stores their data in Genesis. As part of the deal, the company also provides optimized informatics pipelines for analyzing results, he said. ViaGenetics is currently self-funded and expects revenue from its sequencing and analysis service, as well as from the fruits of research partnerships, including intellectual property and other assets generated as part of these efforts, Postrel said.

Genesis started as a research project at the University of Miami in the laboratory of Stephan Züchner, ViaGenetics' president and a professor of human genetics and neurology at U of Miami's School of Medicine. Züchner started developing Genesis — then called Gem.app — in 2009 to provide an easy-to-use platform for analyzing exome data. This was in the early days of next-generation sequencing technologies, and at the time, there were no good tools available for researchers with little or no bioinformatics expertise to explore these datasets, he explained.

Initially, the Miami developers used the tool internally for their own research projects — Züchner's lab studies neurological diseases — but then, gradually, they began offering it more broadly to biologists in other institutions who were also new to NGS. Also, Züchner wanted to provide an environment where researchers could share information about inherited mutations, particularly in the context of rare diseases, that could benefit patients and families that are in similar situations, he told GenomeWeb. 

As part of their efforts to prep Genesis for launch, ViaGenetics spent the last roughly two years rebuilding and restructuring the system for commercial use and implementing it on  the cloud, to offer larger compute capacity than was previously possible and also to improve performance. The company also spent the intervening months improving the system's annotations — variants are now annotated with over 150 possible attributes — as well as automating processes to help speed up analyses tasks, according to Züchner.

When users log on to the system, they are greeted with an interactive linked network of member laboratories across the world and diseases that researchers in each lab are studying, which include conditions such as spastic ataxia, spastic paraplegia, dystonia, muscle atrophy, and others. It also shows the number of samples that each lab has in the system. A search toolbar lets users pare down this introductory image to show only labs and diseases that they are interested in. Users can search for potential disease variants using pre-set filters — such as inheritance pattern, genomic locus, and clinical significance — and they can select additional filters, such as evolutionary conservation, sequence quality, and variant class. Queries run quickly in Genesis as well.As an example, results to a query run on a 562-exome dataset took under six seconds using Genesis.

Sub-filters in the aforementioned categories let users further hone in on variants of interest to them. These sub-categories let users select loss-of-function and nonsynonymous variants, for example, variants reported in PubMed or ClinVar, and variants with known pharmacogenomics significance. Researchers can open lines of communication with existing member labs using the system, as well as set up closed or public projects, and they can invite other groups to contribute data and collaborate on common disease research interests.

A collaborative system like this that lets researchers pool and share data could help them more quickly identify variants linked to rare diseases in patients  than was previously possible. According to ViaGenetics, in addition to the discovery of 79 disease-linked genes during its beta phase from 2012 to2015, Genesis has led to the publication of 55 papers covering 21 diseases in 23 journals. Furthermore, Genesis' analysis capabilities free investigators to focus on research questions of interest to them and its speed lets them run multiple research queries quickly and at low cost, Postrel said.

According to ViaGenetics, Genesis makes genomic data accessible in a way that appeals to less bioinformatics-savvy researchers compared to existing products from companies like DNAnexus. Züchner described Genesis as complementary to the DNAnexus platform in that it provides simpler, more user-friendly access to annotated variants and lets users search results in much the same way they perform internet searches. 

Postrel told GenomeWeb that ViaGenetics is currently a DNAnexus partner and that his firm hopes to keep partnering with the more established player in the future. ViaGenetics showcased its technology alongside DNAnexus' at the annual meeting of the American Society of Human Genetics in Baltimore last week. Furthermore, compared to existing bioinformatics companies, ViaGenetics believes that because it offers a complete pipeline that covers raw sequence through annotation along with compute and storage, it has an advantage over vendors that offer solutions tailored to address different aspects of the analysis process but do not cover the whole process, Postrel said.

In addition to offering its platform on a commercial basis, ViaGenetics has also set up a separate nonprofit organization around the Genesis platform that will offer collaborative research opportunities to members of academia and industry. The so-called Genesis Project is intended to bridge the gap between academic researchers on the one hand, who struggle with finding adequate resources and funding, and for-profit groups like pharmaceutical companies interested in low cost, efficient methodologies for running projects of interest to them, according to Postrel. It gives these stakeholders opportunities to access potential projects and offers opportunities to collaborate on areas of shared interest on the ViaGenetics platform, he said. Partnerships are structured in a way that the majority of any returns from collaborative projects funnel back into the Genesis Project and support additional research projects, he added.

One of the benefits of the Genesis Project, Züchner said, is that it provides an outlet for following up on potential research avenues that might otherwise be dropped. Züchner's lab, for instance, has helped identify and published genes associated with a number of rare diseases, but quite often no additional work is done to explore potential therapies, he said. The Genesis Project is an attempt to encourage and enable researchers to move beyond just discovery.

The Genesis platform is currently being used by researchers such as Ray Hershberger, a professor of medicine and human genetics at Ohio State University. Initially a faculty member at the University of Miami, Hershberger, like Züchner, was one of the early users of exome sequencing to explore disease-specific cohorts and similarly needed tools to explore the exome datasets. He told GenomeWeb that he began using Genesis because it was the only tool available at the time that best fit their research needs and continues to do so, which is why the lab has stuck to the platform.

A cardiologist by training, Hershberger researches dilated cardiomyopathy, a condition that adversely affects the heart muscle and is the leading cause of heart transplants, accounting for potentially half of heart failure cases in the US. He is the principal investigator of the Dilated Cardiomyopathy Research Project, an ongoing effort to combine clinical and genetic information from DCM families to better understand the genetic basis for the condition. 

The DCM project includes the DCM discovery study, which aimed to discover the genetic basis of DCM. To date, the project has gathered some 450 exomes from individuals with the condition and that data is currently stored in Genesis. The platform has also been used to explore that data as part of efforts to discover genes associated with the disease. Hershberger also told GenomeWeb that the consortium recently secured a National Institutes of Health grant to add another 1,500 to 2,000 exomes to its existing cohort as part of a precision medicine study that will build on the consortium's previous research into DCM.

Michael Shy, a professor of neurology at the University of Iowa, told GenomeWeb that he was introduced to Genesis because of his participation in a collaborative research effort that also included the University of Miami. Shy is the principal investigator of a consortium that studies patients with inherited peripheral neuropathies. He said that with the help of Gem.app, the predecessor of the Genesis platform, the consortium was able to identify more than half of all the known causes of inherited neuropathies. He highlighted the ease of use of both Gem.app and its successor, and also the filtering capabilities of the platforms, as key advantages of ViaGenetics' technology. He also highlighted the ease with which researchers can share data across sites as an important benefit of the system.

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