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Seer Aims to Streamline Proteogenomics With New Software Suite


NEW YORK – Proteomics firm Seer is looking to tackle the proteogenomics market with a new software suite the company claims will offer a more streamlined approach to integrating genomic and proteomic data.

Launched last week, the company's Proteograph Analysis Suite 2.0 includes tools for mapping peptide-level variants back to their genetic sources in sample-specific databases and for visualizing relationships between peptides and gene structure, protein domains, and functional regions, simplifying what Margaret Donovan, product marketing manager of bioinformatics at Seer, said has been a cumbersome, complicated process.

As the name suggests, proteogenomics involves combining genomic and proteomic data from a single sample, typically by using next-generation sequencing to generate a sample-specific reference database that can be used for identifying proteins and peptides measured in that same sample by mass spectrometry. The approach allows researchers to analyze protein variants specific to that sample as well as to better understand the relationship between genetic variation and its expression at the protein level.

Researchers have been performing mass spec-based proteogenomic analyses for more than a decade and the approach has featured heavily in major projects like the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the APOLLO (Applied Proteogenomics OrganizationaL Learning and Outcomes) initiative, but the technique has by and large remained the province of highly expert labs.

Redwood City, California-based Seer is hoping through its new software package to make the technique more accessible, much as it has marketed its Proteograph Product Suite as a tool for making mass spec proteomics in general more user-friendly and easily scalable.

"There are no commercially available tools that at the click of a button will integrate your genomic data and begin to find variant peptides to get down to this high-resolution perspective on your proteomic data," Donovan said.

In January, Seer formed a Proteogenomics Consortium with Discovery Life Sciences, one of the company's early-access users, and Sciex. Omid Farokhzad, Seer's chairman and CEO, said upon announcing the formation of the consortium that it looked to build the capacity to run 100,000 samples per year. It combines the Proteograph system and Sciex's ZenoTOF 7600 mass spec and will begin offering analysis services in the second half of 2022.

Sciex launched one of the earliest commercial efforts aimed at enabling proteogenomics when it partnered with Illumina in 2014 on what the companies called the OneOmics project, a partnership to integrate proteomic and genomic data by placing informatics for proteomics and genomics — including tools for integrating sample-specific RNA-seq reference databases with mass spec proteomic data — in a single cloud computing environment. The OneOmics resource never found a large user base for these tools, however.

In an email to GenomeWeb, Michael Pisano, executive VP of proteomics at Discovery Life Sciences, said that the company sees the Seer system as filling several important gaps in existing commercial proteogenomic solutions.

"Typically, researchers need to develop their own in-house pipelines, which can be time-consuming and makes standardization of analysis methods challenging," he said. "Another major issue is having a workflow that is scalable and high-performing to even enable the storage and analysis of large numbers of genomic and proteomic samples. Additionally, if you are new to either field [proteomics or genomics], it’s unclear where to even start to integrate your data together, as it requires domain expertise to process new molecular data types."

"Seer’s workflow automates the analysis process — raw LCMS data to high-resolution, sample-specific proteome results," Pisano said. "This means we can spend less time developing in-house pipelines, can use state-of-the-field and standardized analysis protocols, and have all this data ready to be shared with collaborators."

The software's data visualization tools are also key, he said, noting that while "great tools exist in the genomic space to view data … there are no commercially available, easy-to-use, scalable viewers for the proteogenomic space."

During a conference call following the release of Seer's Q2 2022 financial results on Tuesday, Farokhzad said that Discovery Life Sciences is in the process of installing and validating the ZenoTOF 7600 and the Proteograph Suite with 500 internal samples on which it is performing proteogenomic analyses.

Pisano said Discovery Life Sciences expects to have its proteogenomic platform operational and running client samples in Q4 of this year.

Seer President Omead Ostadan said during the call that the company does not anticipate the Proteograph Analysis Suite 2.0 will directly affect its revenue this year but said that it expects the software's offering of a more streamlined workflow will "have a positive impact on adoption and the rate at which customers can not only execute experiments but extract useful information."

Seer reported Q2 revenues of $3.6 million, up nearly threefold from $1.3 million in Q2 2021 and beating the consensus Wall Street estimate of $3.3 million.

Product revenue was $2.4 million, up roughly threefold from $837,000 in the year-ago period. Related party revenue was $1.1 million, up nearly threefold from $380,000 in Q2 2021. Related party revenue consisted of sales to diagnostics firm PrognomiQ, in which Seer owns a roughly 15 percent stake. Grant revenue was $50,000, down 57 percent from $117,000 in the year-ago period. The firm also reported service revenue of $57,000 versus no service revenue in Q2 2021.

Seer's net loss in the second quarter was $22.8 million, or $.37 per share, compared to $16.6 million, or $.27 per share, in Q2 2021, beating the average Wall Street estimate of a loss per share of $.39. Seer used approximately 62.4 million weighted-average shares to calculate per-share loss in the recently completed quarter compared to about 60.8 million shares in the year-ago period.

The company's R&D expenses in Q2 2022 were $10.9 million, up 57 percent from $6.9 million in Q2 2021. General and administrative costs were $14.2 million, up 35 percent from $10.5 million in the year-ago period.

It said it expects full-year 2022 revenues to be in the range of $14.0 million to $16.0 million.

Seer ended the quarter with $79.0 million in cash and cash equivalents and $372.2 million in short-term investments.