NEW YORK – In acquiring longtime partner Boston Genomics this week, Genomenon is stepping up its efforts to become the first entity to curate the entire human genome, though it may be the only one to have declared such an intention.
By adding Cambridge, Massachusetts-based Boston Genetics’ team of about 75 genetic scientists — and doubling its total headcount — Genomenon now claims to have an inside track toward its goal, which CEO Mike Klein said is intended to combine artificial intelligence and next-generation sequencing to accelerate diagnosis of rare diseases and inform drug discovery.
“We’ll organize all the disease-gene relationships, we’ll organize all the variant landscapes across every disease, to really provide the insight for precision medicine,” Klein said.
While nobody else has publicly declared a similar intention, Klein has been talking about a “race” to curate the complete human genome, and the firm has been on this mission for several years on the back of its flagship product, the AI-powered Mastermind Genomic Search Engine.
Genomenon’s focus has evolved from building an AI-enabled genomic search engine to curating the human genome. The firm has added AI curation tools, augmented by human expertise as necessary, as it has grown in the pharma marketplace.
The company has now indexed 22 million variants by combing entries from the medical literature, a number that is growing because Mastermind’s AI is “ingesting” and reviewing about 750,000 new scientific articles per year, according to Klein. “No human can fully do that,” he said.
Genomenon has been focusing its curation efforts on the clinical exome of late. “That’s the most actionable area of the genome,” Klein said, with “low-hanging fruit” to pick off early in the process to curate the entire genome.
The company’s goal is to curate the clinical exome by the end of 2024, then complete the entire genome a year later. Current market conditions call for innovation on the clinical side, particularly understanding and managing genomic data, according to Klein. “Ultimately, we think this market is turning from a [sequencing] platform play into a content play,” not unlike the evolution Netflix has gone through in the last decade, he said.
To Klein, success would reduce costs and turnaround times for molecular diagnostics and drug discovery he said. A fully curated genome would also create opportunities in newborn screening and in liquid biopsy, the latter because access to interpretations of every known onco-variant would speed the diagnostic process. “It opens up a realm of new applications that were otherwise hard to get to if you didn’t know what you’re looking at,” he said.
Genomenon is a founding member of BeginNGS, a consortium led by Rady Children’s Hospital-San Diego that aims to make rapid whole-genome sequencing a standard of care for newborns.
Klein likened the curation quest to the race to sequence the first genome in the 1990s and early 2000s. Since then, he noted that the cost of sequencing has dropped dramatically as technology has improved.
Still, it is not clear what it means to curate the entire genome, as there may always be variants to discover and interpret. The Human Genome Project declared the first sequence complete in 2003, but the first telomere-to-telomere sequence was not fully assembled for 18 more years. Even then, Telomereto-Telomere Consortium Cochair Adam Phillippy called that assembly “the last base camp before the summit,” so work has continued.
Some other wide-scale genomic curation efforts do exist, though none is identical to what Genomenon is pursuing. The ClinVar and ClinGen projects employ a combination of manual and automated curation, while the Qiagen-owned Human Somatic Mutation Database and Catalogue of Somatic Mutations in Cancer (COSMIC) are smaller, manually curated repositories.
The acquisition of Boston Genetics also allows Ann Arbor, Michigan-based Genomenon to create a genomic data services division to help genetic testing laboratories reduce turnaround times. Boston Genetics Cofounder and CEO Arslan Berbic has been named VP of business development at Genomenon and will be in charge of the new services platform.
The Boston Genetics technology platform has already been integrated into Mastermind since 2019 through a partnership between the companies, and Genomenon was the first customer of Boston Genetics.
Berbic described Boston Genetic as a contract genomics organization. The firm was founded by a team that was laid off by Samplify Bio, a commercial genomics firm that spun out George Church’s laboratory at Harvard Medical School, then decided to get together and work on genome curation. All of the company’s employees were offered positions at Genomenon, Berbic said.
“Our main focus has been variant curation, according to our customers’ [standard operating procedures],” particularly in clinical applications, he said.
Acquisition talks came “naturally” as the result of “synergies” between the two companies, he said. “We knew that Genomenon tools were superior to everything else that we use, and we decided to place this bet and work together.”
“It just became a natural to … bring the two companies together because you cannot just use AI to do this curation,” said Klein .
“If you’re doing patient diagnosis, you need to make sure you’re presenting accurate, scientifically reviewed material. You can leverage the AI to organize the data. You can leverage it to cue it up and make sure it’s organized in a way that the … genetic scientists can look at the data, but on the back end, you need to have scientific review,” he explained.
It will be “business as usual” for the contract genetics services and interpretation services that Boston Genetics provides, according to Klein, but the tie-up with Genomenon allows the combined company to add AI to those services.
Other than operational pieces like payroll and finance services, there does not need to be much integration with Boston Genetics because the technology has already been integrated, he said.
Genomenon expects to hire additional staff as the curation service is rolled out to a growing customer base, he added.
Genomenon has about two dozen pharma companies among its customers, including Flagship Biosciences, Alexion Pharmaceuticals, and Rhythm Pharmaceuticals.
The company raised a $20 million Series B funding round in early 2022, a year after closing a $5.3 million Series A.
Klein said that the Series B has put the company in a good financial position. “In the short term, through this year and the middle of next year, we’re not looking to do additional fundraising,” he said.