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Dante Labs Taps BC Platforms for Informatics Support as NGS Testing Ramps Up


CHICAGO – As it builds what it hopes to become Europe's largest private next-generation sequencing laboratory, Italian genetic testing firm Dante Labs has enlisted BC Platforms to automate the facility's informatics pipeline and workflows.

For the recently announced partnership, BC Platforms will provide its technology platform to automate and expedite whole-genome sequencing throughput at the Dante Labs testing site in L'Aquila, Italy that opened last summer. The software vendor also will integrate existing sequencing systems at the lab to support data interoperability.

Dante Labs CEO Andrea Riposati said that the company in 2018 had been experiencing delays with tests send to third-party sequencing laboratories. "And we realized that in Europe that there is not a lab for whole-genome sequencing that can sequence genomes at scale," he said.

The firm opened its sequencing laboratory in the central Italian city in mid-2019, with the goal of sequencing 10,000 whole genomes before the end of last year. That goal was hit. The 10,000-square-foot facility, which features both Illumina NovaSeq and Oxford Nanopore Promethlon sequencing systems, is now processing 600 to 700 whole genomes per week, according to Riposati.

But the three-year-old company is quickly diversifying from its initial plan of offering a handful of direct-to-consumer sequencing tests, including for hereditary cancer and cardiovascular disease, for customers in Europe. Since then, it has revised its business model from disease-specific tests to whole-genome sequencing and now ships its saliva collection kits globally.

"We started Dante Labs about three years ago with the mission of making advanced genomics and specifically whole-genome sequencing accessible to everyone," Riposati said.

With the debut of the sequencing lab last summer, the firm has broadened its focus from the DTC market to offer sequencing services to hospitals and medical clinics in Europe and beyond. It has opened a US office in New York.

Dante is looking at moving into the research space as well. It started an epilepsy study last year to find new drug targets via genome sequencing and has been planning on opening an office in Finland to concentrate on data analytics for drug discovery for specific diseases.

The lab also is ramping up for a massive effort called the Ulysses Genome Project to sequence 100,000 whole genomes in the Mediterranean region — Europe, Africa, and the Middle East — in the next three years.

Large population genomics projects like this often lack the technology infrastructure to manage workflows and deliver reports, particularly when dealing with multiple countries that might have different regulations, Riposati said.

The infrastructure that Zurich, Switzerland-based BC Platforms is providing will allow lab workers to know exactly where each sample and each sequence is, as well as to help ensure that they perform the proper test on a given sample, according to Riposati.

"We know well how to build this workflow, but it's a different challenge with the plans that they have, so it's a very interesting project," said Nino da Silva, executive vice president for Europe and the Asia-Pacific regions at BC Platforms.

Dante Labs offers several different tests, including 30x and 50x WGS. "Some whole genomes are in a region with an exome, so there is a whole genome plus a whole exome. Some of them are long reads. Some of them are long reads plus short reads, which require a completely different bioinformatics pipeline," Riposati noted. The company recently began receiving some tumor samples as well.

"We optimize the sequencing, both in terms of timing and in terms of data generation," Riposati said. "It's a lot of moving parts and we have different types of requirements for each set."

Riposati said that the Italian facility will feature technology modules from both Dante Labs and BC Platforms, including some that they will codevelop in the future.

Dante Labs initially created its own software to analyze WGS test and generate reports. But workflow has proven to be an issue for DTC testing in a market like Western Europe.

"Each genome is an individual with different needs," Riposati noted. Some customers might be searching for answers on rare diseases, while others could be interested in pharmacogenomics. Similarly, some need one-week turnaround, while others are fine with waiting two weeks. Plus, Dante Labs serves people all across Europe, so reports need to be generated in different languages.

With DTC testing, volume can vary widely from week to week, while labs at academic medical centers operate best when there is more certainty such as with hospitals. "They know how to manage projects where the volumes are known in advance," Riposati said.

"The bioinformatics is complex for primary, secondary, and tertiary analysis and then for the generation of the report," Riposati said.

Enter BC Platforms to help Dante Labs manage multiple pipelines and to support population genomics.

"Multiple really means French people with rare diseases and then German people who are healthy, but then also population genomics in this country or population genomics in another country," Riposati explained.

"Instead of developing that part internally, we're really looking forward now to working with BC Platforms so that we can automate all the bioinformatics up to the report delivery to the customer, to the patients, to the individuals, starting really from the FASTQ file," he said.

BC Platforms will integrate this analysis with Dante Labs' own report-generation software, as well as with laboratory information management systems.

Da Silva said that Dante Labs also wanted his company's workflow management modules for the security and interoperability features as well as the automation.

The BC Platforms interoperability connects genomics data with hospital and lab information systems via application programming interfaces or Health Level Seven International (HL7) communications standards.

"What Dante is trying to do is to ensure that as they grow, we help them maintain the best possible customer service for them," Da Silva said. "Because of their plans and their ambitions and the fact that they are realizing them quite rapidly, they're the type of customer that challenges [us]."

Da Silva said that BC Platforms' technology allows users to create custom sets of standard operating procedures for workflows to suit different use cases.

"Those can then be packaged in a sense that you build ... a condensed workflow so you don't have to have bioinformaticians to run every step. The bioinformaticians can instead focus on building and developing new features and pipelines," Da Silva said. He noted that this feature is particularly suited for high-volume labs.

Dante Labs and BC Platforms will collaborate on developing new features for the latter's software platform, according to Da Silva. BC Platforms is doing similar work for several large labs, including Helsinki University Hospital's HUSLAB.

Before the end of 2020, Riposati wants to be able to boast that the partners have completed integration with at least one healthcare delivery system, at least one population genomics project, and one pharma company. He also hopes this year to add new reports and analytics capabilities to the lab.

"We'll definitely keep investing on the software side, on the reporting capabilities, on the analytics, and in bioinformatics, as well as on the lab," he said.

Da Silva stressed the need to be transparent with Dante Labs customers. "We need to install our platform and we need to integrate their workflows, and build the SOPs, but more than that, I think also we need to be quite open about how to customize for the specific customers that Dante has, the workflows that they need," he said.

Da Silva described the BC Platforms technology as about 80 percent ready out-of-the-box, with just a small amount of customization necessary for each client like Dante Labs. The platform supports the three major cloud providers, namely Amazon Web Services, Microsoft's Azure, and Google Cloud.

"I think the principal rollout is easy and it works well," Da Silva said. "The 20 percent that is left that we will focus on is the customization of the workflows of the SOPs for the pipelines."

He noted that BC Platforms installs about 20 projects a year around the world, and is growing its team. The company closed a $15 million Series C investment round in December, led by health analytics giant IQvia.