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With $20M Cash Infusion, Genomenon Seeks to Curate Entire Human Genome


This story has been updated.

CHICAGO – Following the closing of a $20 million Series B funding round this week, Genomenon plans to advance its goal of curating the entire human genome through its artificial intelligence-based Mastermind Genomic Search Engine.

"Think about what's needed to do newborn screening with next-generation sequencing for rare diseases or when you get into the world of liquid biopsy," said CEO Mike Klein. "What we really need is a lookup table" to cover every variant involved in thousands of rare diseases.

Ann Arbor, Michigan-based Genomenon expects to achieve this in the next three years, thanks to the new investment as well as to a recent $1.7 million grant from the US National Institutes of Health's Small Business Innovation Research program to accelerate development of the firm's variant interpretation engine.

The firm has now raised $35 million from venture capital and grants since its inception in 2015.

While he did not divulge sales figures, Klein said that Genomenon has more than doubled its revenue and customer base each year since 2019. He said that the company has about 40 employees right now and expects that number to double in the next 12 months.

Curating the entire human genome will be a tall task, though. Genomenon has curated a little more than 250 genes for rare diseases and cancer to date, Klein said, and even the largest manually curated databases such as ClinGen only cover about 2.5 percent of variants listed in the medical literature. Instead, researchers and clinicians still have to do their own literature searches for the vast majority of variants.

Genomenon wants to close that gap by curating more variants to inform automated searches. "We take 60 minutes or 90 minutes of research down to five minutes because you can plug in protein nomenclature or chromosome position, any one of the standard nomenclatures," Klein said. "We normalize everything that's been found in the research, and we present it and put it right at the clinician's fingertips."

The company does this through Mastermind, which allows clinicians to search for genomic variants from scientific publications to help diagnose patients suffering from rare and genetic diseases. Another product, Prodigy Genomic Landscapes, helps pharmaceutical and biopharma companies understand genetic drivers and clinical attributes of genetic diseases, which allows them to accelerate target discovery, identify genetic biomarkers for better clinical stratification, and develop companion diagnostics for regulatory approval.

"Our whole thing has been about making genomic information actionable, which we see as being the biggest bottleneck in really leveraging next-generation sequencing across the market," Klein said.

The company's flagship Mastermind product uses AI to index medical literature. To date, Genomenon has scanned 8.5 million full-text articles and 3 million supplemental datasets to create a database of associations between diseases, genes, phenotypes, and therapies.

About two and a half years ago, according to Klein, pharma customers began asking about how Genomenon could help them understand the molecular drivers behind specific diseases, so they didn't have to search one variant at a time. Thus, Prodigy Genomic Landscapes was born.

For Prodigy, Genomenon has a team of human curators to perform quality assurance and quality control on the back end of its database. The firm is building disease-specific datasets to help drug companies target their research and stratify patients for clinical trials.

Competitors in variant curation include Qiagen and Deep Genomics.

Klein said that Genomenon partners with about 75 percent of tertiary analysis companies out there today, including OmniTier, Nostos Genomics, BC Platforms, Sophia GeneticsCongenica, and Fabric Genomics. The firm also has a partnership with Illumina for identifying genomic biomarkers for companion diagnostics.

Those partnerships differ in terms of the depth of integration. Some have chosen to integrate Mastermind into their platforms through an application programming interface, while others simply link out to Genomenon's Mastermind.

Genomenon also counts nearly 20,000 Mastermind users in more than 1,000 labs in 140 countries. The company is now looking to expand its pharma customer base as well as its disease scope.

"Our beachhead market has been rare diseases, but we've done a number of datasets in the oncology space as well," Klein said. The firm will be looking to cover more indications in oncology, regarding both germline and somatic variants, since cancer is simply a bigger market.

Klein sees the company entering its third phase now. Mastermind represented what he called "Genomenon 1.0," while Prodigy Genomic Landscapes is Genomenon 2.0. "Genomenon 3.0 is taking what we've done in these [genomic] landscapes and expanding it across the entire genome," he said, making the results available both to clinical users and pharma customers.