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With $50M in New Funding, Congenica Works on Platform Upgrades for Clinical Applications


CHICAGO – Fresh off a $50 million Series C round of funding, British bioinformatics firm Congenica is expanding into new markets.

The Cambridge, UK-based developer of genomic analysis and clinical decision support technology said that the money would enable the firm to explore new "strategic and geographic capabilities," particularly a push into clinical care from its historic focus on research and into disease states beyond its earlier focus on rare diseases and oncology. This strategy, which includes support for COVID-19 research and care, marks a change from the approach to expansion that Congenica took when it moved into the US and Chinese markets starting in 2017.

Congenica also expects to accelerate integration of its technology platform into electronic health records systems and to automate genomic interpretation.

"Part of the logic for raising the money was we felt we'd arrived at the scale-up position," beyond being a startup, CEO David Atkins said. "Once we got to a point where we had processes that could scale, we felt it would be reasonable to put some more resources against them."

Prior to this month, the firm most recently raised £23.3 million ($30.7 million) in a Series B round in 2019 and has banked more than $85 million in venture capital since its inception, including a Series A round in 2015 and seed funding a year before that.

Congenica makes a modular and scalable data analytics tool for annotating and clinically interpreting genomic sequence data to support clinical decision-making.

The firm claims that its system is as much as 20 times faster with tertiary analysis than standard off-the-shelf analytics tools. "The benefit our system provides is it takes a lot of the manual tertiary analysis out of the workflow," Atkins said.

According to Atkins, the company achieves the increased speed through algorithms, organization of reference databases for fast access, and an interface that is meant to reflect how clinicians make decisions. "Where there's manual intervention, we will lead our users through logical decision-making," he said of the latter.

But, he said that advanced technology by itself is insufficient. "You need to have powerful technology that can be delivered in a way that fits in with the current workflow and the current practices within your customer sites," Atkins explained.

He said that customers have given feedback saying that their need to have access to clinical scientists able to operate "semi-automated" informatics platforms has made some technology of limited utility.

Atkins said the platform will need a physician to sign off on decisions like with any other automated diagnostic system, but in the US, at least, clinical decision support systems are not regulated like medical devices.

Another element of ease of use is making sure that clinicians do not have to enter data twice. Thus, Congenica pulls in information from electronic health records and exports results back into the same systems.

Congenica also has been testing the core capabilities of its platform by looking beyond rare disease. A year ago, the company dropped the Sapientia branding for its platform. Atkins explained that customers often had trouble pronouncing Sapientia and just started calling the product "Congenica" on their own.

The firm is now turning its gaze to new areas, including disease risk assessment and pharmacogenomic testing.

"The capability we built with our core platform was not just being able to analyze variants, but to delivering that information in a relatively simple and easy-to-use way," said Atkins. "We have work to do on that, but we certainly see that the capability of our platform and the ease of use of it could work very nicely with some of those datasets, and we can deliver them to customers in the same way that we deliver the rare disease and oncology."

Atkins said that the platform that the firm started to commercialize in 2019 was the same technology that helped the company win a Genomics England bid.

In 2018, Congenica signed an exclusive deal with the UK National Health Service to provide diagnostic decision support services to the NHS Genomic Medicine Service.

Congenica was one of four companies tapped to provide genomic interpretation services for the first 8,000 patients in the 100,000 Genomes Project that ultimately morphed into the Genomic Medicine Service, and one of two working on rare diseases.

In 2018, Genomics England, which sponsored the 100,000 Genomes Project, ran a competition to choose a vendor to assist with routine clinical delivery of genomic data, and Congenica ultimately won the exclusive contract.

The full rollout of the broader clinical implementation has been delayed several times, including by the COVID-19 pandemic, but the firm continues to deliver technology services to the NHS and build on the work it did to win the contract.

Starting in early 2020, the vendor began releasing a series of disease-specific modules. Congenica Neuro helps characterize epilepsy and neurodevelopmental disorders, while Congenica Prenatal analyzes fetal exome and genome sequences to help detect causal variants of abnormalities in utero and generate actionable reports based on these analyses.

In July, the firm introduced Congenica Automation, which provides automated classification as well as evidence and reporting of recurrent "known" variants that customers observe in their rare disease cases. A COVID-19 module followed in September to support research into relationships between a patient's genome and COVID-19 infection risk, severity, and clinical outcomes.

When COVID-19 started hitting Europe and then North America late last winter, Congenica asked many of its customers how the company could help address the pandemic. Atkins said that the most common response was that users were struggling to understand the determinants that drive host response to SARS-CoV-2.

"We felt the most valuable thing we could do would be to curate the genes that are thought to be involved in differences in COVID response, and then build a module within our platform that could be used to very quickly start looking at those genes and their involvement in the datasets that are starting to appear," he said.

Congenica initially turned to the set of SARS-CoV-2 genomic sequences collected by Genomics England and lately has begun incorporating data from its customers.

According to Atkins, current users of the COVID-19 module are mostly researchers who are trying to understand what in the viral genome might cause different host responses.

Customer feedback also led the company to diversify into several types of deployments, from on-premises installations to both public and private clouds. For those who want the highest level of security, Congenica has introduced an appliance-type version as well.

"I think over time we're going to see probably a migration toward more cloud-ready customers, but there still is a discomfort with using public cloud or the commercial cloud providers," Atkins said.

The on-premises option is the result of a partnership with Hong Kong's Digital China Health Technologies, which joined with Congenica two years ago to adapt the genome analysis platform because Chinese hospitals have been wary of sending patient data to public clouds. Atkins said that customers elsewhere need to have local installations because genetic information is not allowed to leave certain countries, particularly in the Middle East and Southeast Asia.

"There's another driver there for having an instance locally, and it's around clinical sites all around the world really appreciating the value of data," Atkins said. He added that the old model of sending a sample to a lab and then getting a report back hinders the accumulation of valuable data for analysis and reanalysis.

"What I think the clinical community is seeing with rare disease is that reanalysis is a really important capability," Atkins said.

While part of the demand for local hosting is data sovereignty, much of it is a desire to have samples and data readily available.

Since the diversification of deployment options, the company has been able to win customers in more than a dozen countries, including academic medical centers and relatively small reference laboratories. "That gave us the confidence that we had market fits for our rare disease platform," Atkins said.

One such customer is preventive genomics medicine company Veritas Intercontinental. That independently run, Madrid, Spain-based subsidiary of Veritas Genomics that serves Europe, Latin America, East Asia, and the Middle East, has been using Congenica for about a year and a half, according to CTO Vincenzo Cirigliano.

Veritas Intercontinental offers patients access to advanced preventive medicine via whole-genome sequencing. Its signature myGenome test provides information on more than 650 diseases and conditions. The company also offers tests for maternal-fetal medicine, oncology, and cardiovascular health, and is one of just a few companies that offers whole-genome sequencing for healthy individuals. It also provides diagnostic services through whole-exome sequencing.

That company developed its own bioinformatics platform to manage data in the wet lab as well as in analysis of WGS, but it turned to Congenica to help with analyzing the diagnostic panels. Cirigliano said that the Congenica technology is vital to linking phenotypes to exome sequences so that clinicians can make proper diagnoses.

"Having a platform that allows you to have these graded charts based on the phenotype of your patients is a huge advantage for the person that actually has to analyze one by one all the genetic variants," Cirigliano said. "It's much faster for you to actually find the disease-causing variants in the great majority of cases."

He said that he likes that the Congenica platform integrates the widely used, open-source Exomiser software, which was developed by the computational biology and bioinformatics group of the Institute for Medical Genetics and Human Genetics at Charité Berlin for identifying, annotating, filtering, and prioritizing likely disease-causing variants in coding regions. Cirigliano also praised the user interface, which he said makes it easy to customize panels, workflow processes, and reports.

Congenica said that it would put some of its new funding toward integration with electronic health records and laboratory information management systems.

"It all comes along [with] the need to make our systems relatively easy to use and to operate seamlessly with the existing infrastructure," Atkins said.

He said that it starts by building a series of application programming interfaces to major EHR and LIMS products, but it goes beyond simply moving data from one point to another. The flow needs to be bidirectional, but the data also has to fit seamlessly with records that exist on other platforms. "It is difficult for an informatics system of any nature [to have] the success that it desires if it's not integrated within what already exists," Atkins said.

That kind of integration would move Congenica toward Atkins' goal of supporting true precision medicine.

"Our vision is that the role of genomic data in providing information is going to move away from being sort of an individual analysis," he said, explaining that there will be many points in a person's life where it would be helpful for clinicians to be able to re-access genomic data.

"We see a day where an individual's electronic patient record will be appended with their genomic sequence, and we want to be the platform that allows that relatively rapid and routine analysis of that genomic data so it's not a major episode to generate that data and do the analysis," Atkins said.

Atkins would like Congenica's software to be more friendly for clinicians as well as researchers because practitioners have been clamoring for information at the point of care to help them make clinical decisions.

"Wherever you are in the world, the continual refrain from physicians is there's insufficient time, there's insufficient information. They don't have the capability to go off and do a complex analysis," Atkins said.