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Congenica Announces First Clinical Customer for Sapientia Platform


NEW YORK (GenomeWeb) – Congenica has sold the first license to its Sapientia platform to Central Manchester University Hospitals NHS Foundation Trust's (CMFT) Manchester Centre for Genomic Medicine (MCGM).

Sapientia, according to the company, is a modular and scalable data analytics tool for annotating and clinically interpreting genomic sequence data. MCGM researchers will use the system in clinical practice to identify genetic mutations associated with a range of diseases including various types of cancers as well as developmental disorders and disabilities. Adding the system to MCGM's portfolio will have an immediate benefit for patients and further improve the existing services offered by the lab, according to Graeme Black, a professor of genetics and ophthalmology at CMFT.

"With Sapientia you can look at the whole genome and see more quickly which single genes are associated with disease, this offers the opportunity to offer a diagnosis to more people, more quickly," he said in a statement. "Until now much of the analysis has been manual and done on a step-by-step basis [so] being able to automate the process so that it is easier for clinicians to reach a diagnosis is really exciting."

The genomic medicine department at MCGM sees roughly 15,000 patients a year, a number of whom have rare inherited conditions that lack a diagnosis, Bill Newman, a clinician at MCGM, told GenomeWeb. To help diagnose these conditions, he said, the center has deployed a number of gene sequencing panels and whole-exome sequencing capabilities and developed a number of in-house tools that it uses to process and interpret data from patient samples. However, it continued to search for ways to improve the speed and efficiency of its process to get to answers more quickly.

Attempting to deliver services quickly to patients in today's evolving research climate leaves little time for the innovation and development of needed software solutions, according to Newman. "Certainly, we've been very happy with what we've developed in-house, but there's always the possibility that you get a little bit left behind," he said. This arrangement with Congenica offers an opportunity to combine efforts and develop a solution that actually delivers the functionality that the center needs on a daily basis.

In fact, Congenica has embedded two members of its team at MCGM to work with researchers there to not only tailor the solution to their needs but to also learn what sorts of capabilities to include in future iterations of the product that would be more broadly useful to other similar centers. That ambition to grow the tool and improve its clinical utility over time was one of the factors that made Sapientia attractive to MCGM, Newman said. MCGM researchers were also familiar with the efforts of some Congenica employees on the Deciphering Developmental Disorders (DDD) study and the UK 10K project and that made the company's offering standout among other similar solutions up for consideration, he said. 

Congenica, a spinout from the Wellcome Trust Sanger Institute, officially set up shop in October 2013. The company was formed by six geneticists and was established to develop solutions that bridged a perceived need at the time for tools that would enable clinical researchers to make use of burgeoning next-generation sequencing technologies in clinical contexts, Philip Beales, a Congenica co-founder and the company's clinical director, told GenomeWeb. 

In developing Sapientia, the company's goal was to offer tools that would make it possible to not only analyze NGS data and identify variants, but also to interpret their results and bring their findings to bear on patient care and treatment. That's especially pertinent as whole-genome sequencing becomes more affordable and the quantity of data that can be generated from a single patient sample grows. Sapientia makes it possible to look at these larger datasets and do things like identify copy number variations within whole-genome sequence as well as compare multiple genomes as part of trio analysis, he said.

Sapientia "overcome[s] a major bottleneck experienced by many genetics labs that have invested in next-generation sequencing platforms, and now they've found that they have inadequate bioinformatics or computational support [and] lack a clinical support tool such as the one I've described," he said. That ultimately benefits patients by helping to shorten the time to a correct diagnosis and, by extension, access to appropriate treatments, he added.

Developed by a team of bioinformatics experts and computer scientists, Sapientia is based on informatics infrastructure that was initially developed and used for the Sanger Institute-led DDD study, a project that aimed to use genomic technologies to improve the diagnosis of developmental disorders in children. Thus far, more than 12,000 patients with developmental disorders from 23 regional genetics centers have contributed data to the study. The DDD initiative, for its part, grew out of the DECIPHER consortium, a global partnership of clinical genetics centers that established a database for sharing clinical and genomic data from patients worldwide.

Beales, who is also a professor of medical and molecular genetics at University College London, said that Congenica took over the DDD pipeline and expanded it to offer more than just sequence analysis. In addition to code, Sapientia benefits from lessons learned and experience gained during the DDD study on setting up and running clinical bioinformatics pipelines, Anthony Rogers, Congenica's operations manager, told GenomeWeb. The software features basic bioinformatics capabilities for tasks such as read alignment, variant calling and annotation, and also includes a clinical support tool, not available in its predecessor, which provides users with information about the pathogenicity of the variants.

That tool lets users drill down into variants of interest and access supporting information about those variants drawn from publicly available repositories and databases, Eugene Bragin, Congenica's head of product development, explained to GenomeWeb. There are also visualization tools that let users explore patient data and assess the validity of the variant calls. As a final check, clinical specialists internal and external to the company are on hand to review Sapientia's results and sign off on reports before they are returned to a requesting lab.

Sapientia is currently offered under a software-as-a-service model. The firm charges an upfront annual license fee and then a volume-dependent per-sample price thereafter, Craig Taylor, the company's head of finance and business development, told GenomeWeb via email.

There are also two service options available to customers. They can choose to access and run the Sapientia system and generate and issue the clinical report themselves, or, they can send the patient's DNA to Congenica, which will provide a full end-to-end service that covers sequencing through to issuing the final clinical report, he said. The exact pricing for licenses is not being disclosed at this time. Also, Congenica is mulling making its system available for local installations, but at the moment is not offering that as an option, Bragin told GenomeWeb. 

Last December, Congenica received £1 million ($1.6 million) in seed funding from Cambridge Innovation Capital to use for Sapientia's development. Congenica also received a number of grants from Genomics England to develop its software, including a £200,000 Small Business Research Initiative award last summer. Sapientia also is one of four platforms selected by Genomics England from a pool of 10 to be used to interpret data from the first 8,000 persons participating in the UK's 100,000 Genomes Project. Sapientia will be used to interpret variants associated with rare disease variants as part of the effort. Other companies selected for this phase of the project include Omicia, NantHealth, and WuXi Nextcode. 

Those companies are potential competitors for Sapientia as it seeks to push its product deeper into the genomics market, Beales said. However, he noted, that much of the competition appears to be based in the US market with some other competitors in Europe and Asia. In contrast, there are fewer players in the UK market, so there is room for the company's offering to be more broadly adopted and used. Furthermore, members of the Congenica team have worked with the NHS for many years and have deep knowledge and insights into how the UK health system works and are able to use those experiences to develop solutions that best suit emerging needs, Beales added.

Congenica currently has other customer agreements in place and plans to disclose who those clients are in the coming weeks and months, Beales said.