NEW YORK (GenomeWeb) – Golden Helix has launched an early adopters program for VSWarehouse, a database infrastructure for its VarSeq software suite that's designed to help clinical research labs better manage and query next-generation sequencing variant call sets, clinical reports, and variant assessment catalogs.
The company already conducted a beta program in the fourth quarter of last year to test drive the newly minted solution with some existing VarSeq customers including the University of Iowa's College of Medicine. For this next round of testing, the company hopes to work with a broader range of customers to do more in-depth testing in the context of a broader range of clinical use cases and provide feedback ahead of a full commercial launch planned for the end of March, Andreas Scherer, Golden Helix's CEO and president, told GenomeWeb.
Scherer declined to disclose pricing details but did say that the solution will be available at a much lower price point that existing database systems, which is one of the ways the company hopes to compete in the market. GoldenHelix will also publish a free ebook next week that will provide additional information about the new product.
Golden Helix developed VSWarehouse to address a need for tailored data-management infrastructure within the genomics space, Scherer said. Unlike standard SQL databases, which are not optimized for genomic searches, with VSWarehouse, "we've made a number of architectural decisions that allow us to scale and allow for the performance that is required to operate in a clinical setting." That includes versioning capabilities that let users keep track of changes in their datasets. For example, labs could create custom annotation sources that are pertinent to particular diseases or a subset of the population that they are interested in studying, and those labs could track changes in annotations as they update them over time, Scherer said. The warehouse also provides manually curated information the company has culled from repositories such as ClinVar.
Moreover, the solution comes pre-integrated with the VarSeq suite, saving customers time and effort that would otherwise have been spent on integrating and setting up a more general purpose database. The company also offers an application programming interface that can be used to connect the warehouse to existing systems in the lab, Scherer added. VSWarehouse can be installed on servers of different sizes and customers could potentially have more than one system in place. For example, specialized labs in large research institutions could set up individual warehouse instances with a centralized warehouse to aggregate from each system. Similarly, multi-institution consortia could have warehouse instances at each participating institution that operate independently but communicate with each other. Golden Helix is open to supporting both kinds of arrangements and others, Scherer said.
For researchers in University of Iowa's cytogenetics and molecular laboratory, VSWarehouse is a useful addition to the VarSeq clinical suite, helping them more easily manage and search the large quantities of data that their next-generation sequencing projects generate.
"We've been doing research-grade sequencing and interpretation for several years now and we were looking for a solution that could tie together, into one large sort of central knowledge repository, both our research data as well as our clinical data" but would also provide "appropriate tags and compartmentalization so that those two would remain separate, but information from one could inform the other," Benjamin Darbro, the lab's director and an associate professor of pediatrics in the college of medicine, told GenomeWeb.
Equally important, the system needed to be easy enough to use for a wide range of lab technologists with varying levels of computer expertise. "One of the big hurdles for a lot of labs of our size [is] we don't have a large number of people who can write their own code or use other people's code but we have the need for just as sophisticated tools and methodologies as anyone," he said.
Prior to adopting Golden Helix's products, Darbro's lab cobbled together its own bespoke pipeline for processing data from FASTQ files through to clinical reports that included well-established programs like Annovar and SNP-Eff. The homegrown pipeline worked well "but it did require a level of expertise to be able to run it, monitor it, troubleshoot it or quality control it. We don't have that depth of bioinformatics expertise," he said. To hold their variant information, the researchers simply stored calls in a vcf file that they updated along the way as they generated information from new cases. "We could use that very easily to annotate each new case but obviously that is not a very good long-term sustainable solution."
VSWarehouse, in Darbro's estimation, meets all the aforementioned needs. "All of the reports that we generate go into the warehouse, all of the variants and how we've classified and interpreted them, that information and metadata goes into the warehouse," he said. It's also a straightforward task to import and export information between the VarSeq suite and the VSWarehouse and to query existing datasets for information on variants that show up in multiple clinical cases, for instance.
VSWarehouse features a slightly different user interface for querying the warehouse than the one customers see with the broader VarSeq suite, but it shares many of the same filtering mechanics and conceptualizations and things are organized in much the same way, according to Darbro. "The other thing about the warehouse that I like is that when you log in, it has this current status graphic that shows you how many cases are in there, how many variants are in there — it's a nice snapshot of what your repository is at that moment," he added.
In the coming months, Golden Helix plans to expand its clinical software suite including developing capabilities that target a number of new areas. "It's a little bit too early to talk about but you will see a lot of more capabilities that will be developed on top of VSWarehouse where we already know that there is a demand," Scherer said. The company also continues to grow its research software business and to pursue new business opportunities in that area, he added.