Skip to main content
Premium Trial:

Request an Annual Quote

Rosalind, Formerly OnRamp Bio, Pushes Into Single-Cell Analysis, SARS-CoV-2 Variant Monitoring

Premium

CHICAGO – Rosalind, the company formerly known as OnRamp Bioinformatics, has been expanding its offering for researchers who need to interpret genomic data but don’t have extensive programming or bioinformatics expertise.

Last week, the firm introduced Rosalind Diagnostic Monitoring (DxM), a platform for monitoring new SARS-CoV-2 variants and evaluating how they may affect the ability of COVID-19 diagnostic tests to detect the virus.

The San Diego-based firm will offer Rosalind DxM both to manufacturers of diagnostic tests and to regulators. The US Food and Drug Administration warned in January about potential false negatives in certain SARS-CoV-2 tests due to mutations in the virus genome and advised test manufacturers to run occasional in silico assessments of their assays to monitor performance with variants.

Rosalind developed DxM with the help of a contract under the National Institutes of Health Rapid Acceleration of Diagnostics (RADx) program to support the development and commercialization of SARS-CoV-2 diagnostics. The company said that it received the contract in February, but waited until the product release last week to announce the federal funding. The contract value does not yet appear on the NIH website, and the firm said that it does not yet have approval to disclose that information.

Rosalind CEO and Founder Tim Wesselman cited the platform's scalability and the company's expertise in winning the RADx Tech contract.

March has turned out to be a landmark month for Rosalind. The company officially unveiled its rebranding at the virtual Advances in Genome Biology and Technology (AGBT) meeting at the beginning of the month and introduced a cloud-based single-cell data analysis module during the conference.

The new module, part of the company's third release of its core Rosalind platform, enables web-based collaboration and analysis and interpretation of single-cell data generated on 10x Genomics' Chromium platform. Users can generate and annotate single-cell clusters from FASTQ data files via a graphical user interface and perform downstream analyses.

Rosalind is now fully integrated with several 10x Genomics technologies, including the Cell Ranger pipeline and Loupe browser. Previously, Rosalind users had to import Cell Ranger data from the cloud onto local installations of Loupe. "Now it's a complete, end-to-end experience," Wesselman said.

Basic access to the technology is free for viewing and for nCounter analysis, and pricing starts at $49 per month plus per-unit charges for other Rosalind analyses for academic researchers. More comprehensive subscriptions are available.

As for the name change, Wesselman said that it had been in the works for a while.

OnRamp Bio, founded in 2013, introduced its Rosalind genomics analysis platform for life sciences researchers in 2017, which appears to compete with products from Congenica, DNAnexus, Illumina's BlueBee, and Genestack, particularly in  multiomics and single-cell data management.

Eventually, according to Wesselman, customers grew to know the Rosalind name more than the company's actual name and frequently referred to OnRamp as Rosalind, which was named for early DNA researcher Rosalind Franklin.

"Rosalind has really defined everything about what we've done," he said. "Furthermore, when it came back to our values and everything we stand for … that [name] really struck to just the core of who we are and what we stand for in empowering scientists."

Those values, Wesselman said, include simplifying some of the complexity in biology and bioinformatics to accelerate adoption of precision medicine.

"We believe it all starts with empowering the scientists at the beginning and enabling them with collaborative capabilities to bring their knowledge together with others in interactive and visual ways so they're not blocked by technology," he said.

He also said that the company wants to empower women and minorities in science, in the spirit of Franklin herself. "Core to that is making sure that we recognize the individual scientists much like Rosalind and making sure that those great contributions don't get swept to the side," Wesselman said.

The firm's new logo not only resembles rose petals as a nod to Franklin's name, it is meant to illustrate a cross-sectional view of DNA rather than the more common double-helix side view. "We take a whole new view that allows the big picture, combining multiomics, combining collaboration, and so we thought, why not get a top-down view of the genome?" Wesselman said.

The petals also represent the scientists, corporate partners, insights, and even base pairs that Rosalind hopes to bring together in a multiomic environment.

Wesselman likened the Rosalind product to a productivity suite like Microsoft Office or Google Docs for scientists. "[We enable] them to bring all of their omics [data] together in a collaborative way," he said.

"We've sought to make single-cell analysis as easy as doing just a regular bulk gene expression analysis," said Jay Gerlach, Rosalind's VP of strategic marketing for partnerships. "The idea is really to take these … increasingly complex and large datasets and reducing that so that it's accessible to a broader base."

Maximiliano D'Angelo, associate professor in the development, aging, and regeneration program at the Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California, adopted Rosalind last year and is starting to work with the new single-cell analysis technology.

Historically, D'Angelo's research laboratory had performed genetic analysis on the institution's bioinformatics core. As he started incorporating more single-cell analysis in his work, the core proved to be poorly suited for his research needs, in particular because results would come back as emails that did not fit into the lab workflow, he said.

In addition, his lab had no experience with computer programming, and the computer scientists who run the computing core were not well-versed in biology, so making adjustments was a cumbersome process.

"We've got all the data from the core. What do we do with this? How do we analyze this thing?" D'Angelo said. He eventually started asking researchers involved in single-cell genomics about other options. Contacts at 10x Genomics, which supplies Sanford Burnham Prebys with reagents and other wet-lab products, led him to Rosalind.

"We liked the interface. It was easy to use. With no experience, we can really get on going with this," D'Angelo said.

Before the single-cell module launched, D'Angelo performed secondary analysis in Rosalind, then had to export the results to Loupe for clustering before reimporting the information to Rosalind for further analysis. Now, it is all integrated.

"It is the first [system] I have used in RNA sequencing analysis that really allows you to easily get the results and analyze data without knowing anything about how to program or to change the specific details of the analysis," D'Angelo said.

The visualization functions of Rosalind also are helpful for preparing graphs for grant applications, he suggested. "Getting those sometimes was kind of a pain. You had to go to different software or the core," he said. "In Rosalind, that's all integrated."

Since 2018, the technology has supported RNA-seq, assays for transposase-accessible chromatin by sequencing (ATAC-seq), and chromatin immunoprecipitation sequencing (ChIP-seq). Rosalind now draws from about 50 knowledgebases, covering pathways, transcription and regulation, virology, pharmacology, cell and tissue types, gene ontologies, and several disease states.

The software also incorporates the open-source Seurat platform for single-cell RNA-seq analysis and is compatible with NanoString's nCounter, by virtue of a deal struck with NanoString last year

Wesselman said that these collaborations are part of Rosalind's goal of breaking down data silos.

The company has numerous other partnerships, including with Active Motif for epigenetics research, Science Exchange for interactive genomic analysis services, and a tripartite agreement with ScaleMatrix and Cloudian for efficiency improvements.

However, a 2018 partnership with Advaita to combine data analysis technologies has dissolved. "We had good adoption on the platform and customers really enjoyed the solution and saw strong value from it," Wesselman said. But the two companies had what he described as an amiable split over "a difference of opinion on business model and economics."

Rosalind has customers in nearly two dozen countries through sales and marketing partnerships. The firm does not have any offices outside the US, but Wesselman said that he is "actively working on" establishing an overseas presence, though he offered no details.

The firm employs about two dozen people in the US. Wesselman said that he expects the workforce to grow to about 30 by year's end.

Since it was founded, Rosalind has raised an undisclosed amount of early-stage venture capital, but none since 2019. Wesselman said that the company is now cash flow-positive and fully funded through revenues. "While we are well funded for current operations, we may consider additional growth financing to accelerate our growth initiatives and international expansion," he said.

Wesselman added that he is committed to maintaining the company's independence for at least the next four to five years. 

The Scan

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge is weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.