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Biobase Throws its Hat in the NGS Ring with Genomic Variant Database


By Uduak Grace Thomas

With the release of its GenomeTrax database, Biobase joins the ranks of bioinformatics companies that have recently climbed aboard the next-generation sequence-analysis bandwagon.

GenomeTrax, which marks Biobase's first database that is geared directly to the NGS market, is a collection of manually curated datasets culled from peer-reviewed literature that helps researchers identify genomic variations that are important in health and disease. It does this by mapping variant sequences to known elements such as gene regulatory sites, drug target genes, and disease-linked mutations.

GenomeTrax, which was launched on Oct. 15, gives users access to 10 data tracks that include more than 37,000 regulatory sites from the company's Transfac database, and more than 80,000 disease mutations from HGMD professional, the company's human gene mutation database.

In addition, users can also compare their variants to SNPs from the National Center for Biotechnology Information's dbSNPs and the European Bioinformatics Institute's Ensembl, post translational and histone modifications, and more than 600,000 ChIP-seq fragments with binding site predictions, among other features.

Frank Schacherer, executive vice president of Biobase, told Bioinform that once users have sequenced and assembled their genomic data and identified the variants, the tool provides a "filtering effect" by highlighting which variants are important.

Users upload their list of variants into a web interface and GenomeTrax spits out all the variants in their data that map to known functional sites based on the information stored in the database.

Users can view their results in BED format, which works with the University of California, Santa Cruz, genome browser, and also in GFF format, which works well for tools like the CLC Genomics Workbench. GenomeTrax also supports Galaxy and the Broad Institute's Integrative Genomics Viewer, among visualization tools.

A New Market

Lately, several companies that have typically operated in other data-analysis markets have declared their intent to move into NGS analysis by releasing new products that target the space.

For example, Genedata, a company that has traditionally focused on microarray analysis, recently released a new NGS module for its enterprise Expressionist analysis platform. The so-called Refiner Genome module is designed to help users visualize their data and perform whole-genome transcriptome, methylome, gene regulation, copy number variation, and SNP analysis (BI 10/01/2010).

Likewise, Strand Life Sciences last week released a version of its Avadis software for NGS analysis (BI 10/8/2010); while Integromics, a software company that has also focused on microarrays as well as qPCR analysis, plans to release its first NGS-centered product later this quarter. The software will be used to analyze aligned and annotated sequences (BI 10/08/2010).

Now it's Biobase's turn. Founded more than a decade ago and headquartered in Germany with offices in Boston, India, and Japan, the company has to date developed databases that contain proteomic, gene regulation, and gene-expression data.

The company has also formed several partnerships with groups like CLC Bio, which integrated Transfac, Biobase's suite of protein databases, with its CLC Genomics Workbench.

In another partnership, with Strategic Medicine, Biobase identified a small molecule that the partners said may serve as an "adjunct" biomarker that could be used to resolve the “strong discrepancy” in outcomes of immunohistochemistry- and fluorescence in situ hybridization-based Her2 breast-cancer testing (BI 04/14/2008).

Two versions of GenomeTrax are available, Schacherer said. The web-based version of the database is hosted by Biobase and will let researchers load genome coordinates directly into an interface and export the results to whatever browsers they choose.

Users can also subscribe to a downloadable version of the database, which is geared toward researchers with more specialized applications in mind or who want to incorporate the data directly into their pipelines or platforms.

Potential customers can try out a free version of GenomeTrax using a sample dataset from chromosome 21 on the Biobase website. The company also offers several subscription models that are priced on a per-seat basis. For example, prices will differ for online users and those who install the tool at their sites, as well as for academic and commercial users.

A one-year subscription to the online version of the tool costs $1,800 per seat for a single named academic user and $450 for each year after that for continued access plus updates.

Concurrent users who plan to share a single seat, with the caveat that only one user at a time can access the database, will be charged a total of $3,600. Schacherer also said that pricing for academic users who download the database will be determined on a case-by-case basis.

Biobase also has subscription plans in place for commercial companies interested in either version of the tool but Schacherer declined to provide specific pricing information.

The company expects GenomeTrax to initially be adopted primarily by diagnostics laboratories, academic research groups, and core facilities in research institutes, and Schacherer said he expects pharmaceutical companies to also be interested in using GenomeTrax for their drug-discovery efforts.

Biobase is also holding discussions with several partners, including CLC Bio, who Schacherer said wants to integrate the datasets contained in GenomeTrax into its NGS tools. He could not name any other collaborators because he said so far there aren’t firm agreements in place.

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