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BigOmics Analytics Building 'End-to-End' Omics Pipelines via DNAnexus Integration


NEW YORK – By virtue of a recent tie-up with DNAnexus, Swiss biomedical data analysis startup BigOmics Analytics can now provide a more complete pipeline for end-to-end analysis of transcriptomics and proteomics data.

BigOmics CTO and Cofounder Ivo Kwee said that the integration of the company's Omics Playground visualization and interpretation system into the DNAnexus precision health data platform gives the startup important access to the latter's library of workflows. It also facilitates collaboration in the secure DNAnexus cloud environment.

"Partnering up with well-established players in the market like DNAnexus [is] crucial for us to provide end-to-end analysis and value," added BigOmics CEO and Cofounder Murodzhon Akhmedov.

The integration, announced earlier this month, was completed in a matter of days through a standard application programming interface, according to Matt Newman, senior VP of solutions and services at Mountain View, California-based DNAnexus.

Akhmedov described BigOmics as a data visualization and exploration company that currently specializes in proteomics and transcriptomics data. Omics Playground can only process one type of data at a time, but the firm has a forthcoming product called Multi-Omics Playground currently in beta testing.

Integrated multiomics was the company's original intent. "We started with tackling multiomics, but then we realized that most of the labs had challenges already with the analysis of single omics," Akhmedov said. Only now is BigOmics ready to expand its scope.

Newman called Omics Playground an example of an RNA-seq visualization tool that can sit on top of the DNAnexus platform, allowing the data to live in its secure and collaborative environment.

BigOmics, a spinout from the Università della Svizzera italiana's Institute of Oncology Research and the Dalle Molle Institute for Artificial Intelligence, in Lugano, Switzerland, was founded in 2018.

For more than two years, the founders bootstrapped the company while still working part-time at the university. "It helped us [in] this bootstrapping period to get immediate feedback from end users" in the Institute of Oncology Research, Akhmedov said.

The company has raised CHF 2.7 million ($3.1 million) in venture capital to date, none since early 2022. Akhmedov said that funding is sufficient for now because BigOmics has revenue from paying clients including Remix Therapeutics, ProFound Therapeutics, the University of Antwerp, University College Dublin, and South Korea's National Cancer Center.

Akhmedov said that BigOmics currently has 10 employees, half software developers and half on the commercial side. The Korean customer notwithstanding, the firm's target markets are the US and Europe.

Like so many other software developers, BigOmics seeks to ease the burden of "repetitive and standardized bioinformatics tasks" on bioinformaticians so frontline biologists can receive accurate reports more quickly, according to Akhmedov.

Kwee noted that biologists and informaticians tend to operate in different worlds. "The technology of high-throughput genomics [advanced] so fast and the amount of data in that field [grew] so fast that biologists were not properly trained … in data sciences like programing and also statistics," he said.

A long line of vendors promise to "democratize" bioinformatics, including Sophia GeneticsRosalind, Velsera and Almaden Genomics. BigOmics does in fact use that language on its website, but right now it sees an opening in RNA sequencing data, including with fast-emerging fields like single-cell analysis and spatial transcriptomics, Akhmedov said.

Drug discovery with the help of transcriptomics and proteomics data is a key focus for the company because that is what many customers are involved in, but BigOmics also supports biomarker identification and target identification for academic users. "In some cases, it's just for understanding a disease," Akhmedov said.

Omics Playground is capable of crunching patient datasets as well as both long- and short-read sequencing data because BigOmics takes preprocessed data rather than raw sequences, according to Kwee.

Because of what clients are involved in — and because the firm spun out of a cancer institute — BigOmics currently deals with a small set of disease areas, namely oncology, neurodegenerative disease, aging, and regenerative medicine. 

Currently, BigOmics only supports analysis of human and mouse data. More organisms and more omics are in the plans, Kwee said.

"There is a huge amount of data we would like to help scientists to understand" for tasks including shortening time to market for new therapies, Akhmedov added. "With our platforms, we would like to empower this visualization and interpretation aspect in this long value chain."

DNAnexus' Newman previously worked in business development for Qiagen and, before that, OmicSoft, a company acquired by Qiagen in 2017. OmicSoft specialized in omics analysis and visualization.

Newman said that he was "personally struck" by the web-based visualization tool that BigOmics has built. "I think they've done a very good job of coming up with a platform that makes it easy for biologists to answer questions and not rely on building their own R notebooks or Shiny apps or things like that," he said.

"This expands the potential for biologists to stay on [our] platform, which helps our customers," Newman said. "It's a feedback loop, the security and collaboration."