How Protean BioDiagnostics utilizes SOPHiA GENETICS for more comprehensive genomic analysis and research

Published on 03/14/2022

5 min read

Larger panels may cast wider nets, but optimization with patented algorithms through our universal platform gives more actionable insights without sacrificing data quality.

As an early adopter of our innovative technology, Protean BioDiagnostics’ President/CEO explains how his lab has already benefited from analyzing complex datasets with SOPHiA DDM™ for TSO500.

“Precision medicine is changing quickly. It’s getting more complicated. But it’s amazing to see how far we’ve come in a short time working with SOPHiA GENETICS,” explained Dr. Anthony Magliocco, President and CEO of Protean BioDiagnostics during a virtual discussion. “Our expertise is in tissues management and integration of data. We have to work with other experts and collaborate with them to fill gaps in our ability.” For this reason and others, Protean has worked with SOPHiA GENETICS to fill those gaps and further enable research possibilities for the clinical research experts they serve.

Protean BioDiagnostic’s vision is to bring precision medicine to all patients, regardless of where they live. That includes empowering community cancer centers and smaller labs (sometimes in very remote areas) that traditionally lag behind in developing digital workflows. Their patients could greatly benefit from the latest and greatest technologies. This is where the two companies have common goals, to evolve the landscape of medical research through Data Driven Medicine.

“SOPHiA DDM™ is a knowledge management system. It’s able to help us curate the data and is continuously updated with connections to world databases. It’s a very important tool for us and our partners to simplify the analysis of complicated data. It allows our customers to better analyze the results from genomic profiles as well as clinical trial matches, which I feel is an often-unmet need in research,” said Dr. Magliocco.

Not every hospital system or regional lab has the storage capabilities for large sets of data that are generated with more comprehensive panels and testing. For this reason, the two companies’ shared goal of providing smaller labs advanced tools comes with options for cloud storage that are highly protected. Data storage security is a major priority for SOPHiA GENETICS users. We ensure that they are getting HIPAA and GDPR compliant storage capabilities no matter how large or small their lab may be.

“I’ve known SOPHiA GENETICS for a long time,” said Dr. Magliocco. Protean BioDiagnostics had an existing bioinformatics partnership with the SOPHiA GENETICS team and they signed on as an early adopter of SOPHiA DDM™ for TSO500 within the past year. “I became more interested recently with the work they’re doing with large panels. You’re dealing with DNA and RNA and now you also have to deal with other markers in the DNA like tumor mutational burden and micro satellite instability. To be able to visualize it and report it back quickly and accurately makes this a very powerful tool. I’m also impressed by the experience of their bioinformaticians and their approach. They’re always trying to move forward. You know that the product will not be the same in a year or two, that it will improve. It’s a true partnership. I’ve been privileged to make suggestions from a user’s experience, and they actually make those new features available.”

The aim of improving technologies for SOPHiA GENETICS partners is to offer deeper, more accurate analysis. Larger panels may cast wider nets, but optimization with patented algorithms through our universal platform gives more actionable insights without sacrificing data quality.

“The real problem is integrating the data, putting it together, and giving it back to them in a way that’s manageable so that it can actually guide treatment,” said Dr. Magliocco. “With the Bioinformatics provided by SOPHiA GENETICS, you’re able to pull together tens of thousands of variants, sift through them all, and get the ones that are meaningful. They highlight the significant data with reporting in a way that makes sense, while still allowing you to ‘open up the hood’ and look further, to see where this reporting comes from. They simplify the reporting, but I know that the complex data is still there if I have to go back and look for more answers. This is a great tool for further research.”

SOPHiA DDM™ for TSO500 is a fully integrated bioinformatic workflow (FASTQ to Report) for Illumina TruSight™ Oncology 500 panel. The SOPHiA DDM platform combines analytical performance with streamlined interpretation of complex genomic variants in the context of comprehensive genomic profiling.

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