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Era7 to Integrate 16S Analysis Software With EHRs to Support Clinical Use of Microbiomes

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NEW YORK (GenomeWeb) – Era7 Bioinformatics is using a $430,000 grant from the Spanish Ministry of Economy and Competitiveness to extend its cloud-based platform for analyzing 16S metagenomics data to support clinical use of microbiome data.

The funds are part of a larger roughly $1 million grant awarded to the CardioBiome consortium — a group of four companies working on a platform for studying patients' microbiomes — by the Centre for the Development of Industrial Technology (CDTI), a public corporation under the Ministry of Economy and Competitiveness.

The consortium members are Ayesa, a company that offers, among other products, information and communication technology systems for use in healthcare; Health in Code, which provides sequencing-based genetic testing services for inherited cardiovascular diseases; Lorgen, a genetic testing laboratory established by researchers at the University of Granda; and Era7 Bioinformatics.

Initially, the partners plan to analyze data from patients with acute myocardial infarction as a proof-of-concept project — previous studies have shown a connection between the oral microbiome and the cardiovascular condition. They'll sequence 4,000 samples from four local hospitals in Granada, Spain. 

Era7 already offers a 16S sequencing service that covers sample prep and DNA extraction through results interpretation; however, it is working with partners to fulfil the funding requirements for the CDTI grant. Lorgen will handle DNA extraction while Health in Code will be responsible for sequencing the samples. Era7, for its part, will be responsible for handling the 16S amplification using a mix of old and newly developed approaches — the company received a $100,000 grant last year to design and test new 16S amplicon and sequencing approaches for exploring microbiome data. The company will also be responsible for handling the bioinformatics component of the consortium including developing functionality for integration with EHRs. Finally Ayesa will be involved in the systems integration aspects of the project. The company will work with the Andalusian Health Service to integrate the Era7 software with the healthcare system's EHR. 

Although the initial focus of the project is on myocardial infarction, "the ultimate goal of this project is to have a service to local hospitals that attempts to solve all the needs of the hospital from sequencing, to bioinformatics analysis, to integration of the result with visualization of the results with electronic health records," Era7 CEO Eduardo Pareja told GenomeWeb.

On one hand, the company will use the funds to generally improve its existing metagenomics infrastructure; for example, it will update the knowledgebase that underlies the service. But it will also develop specific capabilities that target clinical use. That includes developing interactive visualization tools that make it easier for clinicians to explore metagenomics results as well as a more user-friendly interface to the software, Pareja told GenomeWeb.

The company will also develop functionality that facilitates the integration of its software with EHR systems from different vendors. "We will build layers with standards [such as HL7] to be able to interact with different EHR providers," Pareja explained. Clinicians will be able to view their patients' metagenomics results alongside the rest of their clinical data and they'll also be able to compare data from groups of patients. The company also plans to integrate its software with mobile devices such as smartphones and tablets so that clinicians can explore data on these devices as well.

Enabling clinical use of the microbiome is a task that Era7 believes it is well positioned to tackle because of its expertise in metagenomics, microbiology, and genomics, Pareja said. The company offers sequencing and software services for bacterial genomics and metagenomics analysis primarily in the context of research projects, but also has experience with clinics and stays up to speed with standards such as Health Level Seven and Fast Healthcare Interoperability Resources, and resources such as the Substitutable Medical Apps and Reusable Technologies platform, he said.

"A lot of people are working [on] human genomics and transcriptomics, and other kinds of omics and the integration of that data with EHR ... for clinicians. But we think that microbiomes could be a very important part of precision medicine based on genomics," Pareja said. The results of analyzing human microbial communities such as those of the mouth, gut, blood, skin, and other sources could provide useful biomarkers for disease prevention, diagnosis, and follow-up. As such, "we are really convinced that there is an opportunity in integrating with EHRs," he said.

Era7 plans to roll out the new visualization capabilities and updated web interface soon, Pareja said. Like its existing software products, these updates will be made available to the research community under an open source license — the company's revenue comes from sales of services, not software. However, the integration with EHRs will take more time. Pareja said the company hopes to begin testing the first iteration of the integrated software in about a year but a fully mature solution is still some years away, he said. 

The CardioBiome project is expected to wrap at the end of next year.