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Blueprint Genetics Updates Technology as Expansion Continues

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NEW YORK (GenomeWeb) – Finnish molecular diagnostics company Blueprint Genetics continues to grow its business, which focuses on next-generation sequencing-based genetic tests for hereditary diseases, as it makes updates to its technology and prepares to open a laboratory in the US.

The company, based in Helsinki, started out with hereditary cardiology testing in 2012 and expanded into other disease areas two years ago. It now offers tests in 14 medical specialties that cover more than 2,500 genes in total. Cardiology accounts for the highest volume of tests, followed by ophthalmology, according to CEO Tommi Lehtonen. Though the firm does offer hereditary cancer testing, that is only a small part of its business, which focuses on complex hereditary diseases.

Last summer, Blueprint, which has grown to more than 100 employees, raised €14 million ($16 million) from investors to grow its business and further develop its sequencing and informatics platforms.

In 2017, the firm analyzed samples from more than 10,000 patients, a record for the company, and it plans to double or even triple that number in 2018. "There is very much space to grow," Lehtonen said.

Earlier this year, the firm migrated its disease gene panels to an exome-based platform, allowing it to run a single assay but only analyze those genes requested by a clinician.

Having just one workflow instead of many different assays is simpler and leads to economies of scale, Lehtonen said. It is also more flexible, as panels can easily be customized and genes can be added to the analysis. While the company did update its previous panels on a regular basis, that process was not as versatile, he said. 

The new exome sequencing assay runs on the Illumina NovaSeq platform and uses custom capture reagents from an undisclosed manufacturer. The capture design includes not only coding exons but also certain intronic regions that can be clinically relevant.

Moving from panels to more complex assays, such as exomes, has been a trend in the industry, Lehtonen said, though others have had problems with the quality of their exome tests.

Prior to its own switch, Blueprint validated the performance of its exome assay against its existing panels and was "extremely happy with the results," Lehtonen said. Specifically, the assay covers 99.4 percent of targets in coding regions with a minimum of 20x coverage and has high sensitivity and specificity for both single nucleotide variant and indel detection. In addition, it can detect indels up to 220 bases in size and has high sensitivity for detecting copy number variants.  

Validating CNV detection, in particular, involved almost 100 clinical samples, and for its new CNV pipeline, the company developed different algorithms to call small and large CNVs.

Blueprint is especially pleased with its ability to sequence certain difficult-to-sequence regions, Lehtonen said, which can result in increased diagnostic yield. For example, it is getting good coverage and mapping quality for the RPGR gene and its ORF15 isoform, which is mutated in retinitis pigmentosa, an important test in its ophthalmology portfolio. Improved results for difficult regions like this come from a combination of better assay design, bioinformatics, and clinical interpretation, he said.

The company has also invested heavily in its software, particularly the clinical interpretation of the results and test reports, which Lehtonen said distinguish Blueprint from its competitors. For example, it has structured the workflow of the clinical interpretation to make it very systematic, which he said "increases quality and diagnostic yield, as well as [reduces] human error." The platform also "takes care of the mechanics of the clinical interpretation and allows the geneticist to focus on the conclusions instead of going through a lot of manual steps," he said.

Customers particularly appreciate the transparency of the company's results, he added. "We're transparent about everything: how we get to the conclusions, what the validation results are, what the sequencing data is like," he said. "These are the factors that stand out from our reports."

Geographically, Blueprint's business is currently balanced between Europe – in particular the Nordic countries — the Middle East, and North America, Lehtonen said. All testing, which has a turnaround time of three to four weeks, is currently performed in its Helsinki laboratory. However, the firm is preparing to open a CLIA laboratory in San Francisco to process samples from the US and Canada. "It will take some time before we are sequencing there, but we are making progress," he said.

Pricing for its tests, which starts at $990 for institutions, has not changed a whole lot over the past year, he said, though there is price pressure in certain areas. Pricing pressure is also the reason why Lehtonen does not think Blueprint will move to whole-genome sequencing anytime soon, even though "that feels like a very natural step."

The company has contributed variants to sharing initiatives, such as ClinVar, but has had challenges keeping up as its testing volumes have increased. "We're doing the best we can, since it is a manual process," Lehtonen said, adding that the firm is working on software to automate the uploading process.

Blueprint has had limited exposure to reimbursement, since a large part of its business is based on institutional billing. However, where insurance billing is involved, in particular in the US, things have improved over time. "We see good results today, much better than two years ago," Lehtonen said. "There are new codes available, but also, the route for doing a custom claim is providing better results today."

In terms of future innovation, Lehtonen said, test requisition – the forms clinicians must fill out to order a test from a laboratory – is an area that could see improvements. A lot of orders today "are sent over fax, or land mail, or paper requisition forms," he said. "To make the whole process of genetic testing more efficient, it would be great to go into something that's more digital." More than half of Blueprint's orders are already digital, he said, but "there is still a lot of work to be done."

And while new testing methods, such as long-read sequencing, could further improve diagnostic yield in some areas, such as repeat disorders, "the bottleneck today is not technological," he said. "Of course, there is always more you can do with tech," he added, "but I think it's very important to advance the clinical adoption" of inherited disease testing.

Increasing clinical adoption is an ongoing process, he said, and Blueprint is working with key opinion leaders and clinicians on this, as well as distributing information on diseases that have been underdiagnosed. "There are great tests available for these disorders, and they are right there on our menu," he said. 

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