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Diploid Expands Bioinformatics Business With Launch of First Software Product

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NEW YORK (GenomeWeb) – Hoping to secure a share of the commercial genome interpretation software market, Belgian firm Diploid has launched its first product for the space, a software solution called InHelix that is designed for analyzing copy number variants gleaned from next-generation sequencing-based tests focused on diagnosing rare diseases

The InHelix solution offers user-friendly tools for annotating and reporting on relevant CNVs from lists called by publically available solutions such as CNVnator, Pindel, Canvas, CNVkit, and Control-FREEC. The software includes tools for live filtering and paring down lists of CNVs and for integrating phenotype data from patients into analysis.

Diagnostic labs can also generate so-called Smart Panels, which are customized gene panels for patients that clinical researchers can create based on terms from Human-Phenotype Ontology — InHelix mines the literature weekly and automatically adds new gene-phenotype correlations to the system. The final output of the analysis is a pdf report with a list of relevant CNVs ranked according to their relevance to disease. InHelix also offers a flexible application programming interface for accessing data from high-throughput sequencing projects.

InHelix's launch adds a new dimension to Diploid's business. Initially, the company launched under a bioinformatics services model seeking to cater to diagnostic laboratories that prefer to outsource their genome data interpretation needs. Diploid offered services based on an internally built pipeline comprised of proprietary and open-source tools, which it used to identify and annotate both known and potentially pathogenic variants associated with rare diseases. It could also screen for known markers associated with about 1,800 inherited diseases and conditions. That initial focus on services set it apart from competing firms that chose to license their interpretation solutions such as Tute Genomics and Euformatics

However, the company always planned to eventually move into the commercial software space, according Diploid CEO Peter Schols. In fact, the company expects that its software revenues will surpass service revenues within the next two years, even accounting for growth in the software services department.

"The fact that we provide interpretation services ourselves [to] diagnos[e] rare diseases every day helps us create better software, because we have a lot of medical and genetics expertise in house," he told GenomeWeb. "In addition, the fact that we develop our own software greatly benefits our service, as we can apply cutting-edge techniques and algorithms to solve cases for our customers."

There was also a push from current and potential Diploid services customers to make some of its code available as a commercial software product that they could run independently. They chose to launch software for CNVs first because that market is not as well served as the market for SNP-based analysis, Schols said. Also, labs are increasingly moving away from array-based CNV testing to NGS-based testing, which provides better resolution. 

"Over 80 percent of all CNVs in the human genome are actually smaller than what arrays can detect," Schols said, so, technologies like arrayCGH could miss more than 80 percent of all the CNVs in the human genome. "We think there are going to be a lot of platforms switching from arrayCGH to NGS-based CNV detection, and we think that InHelix is the perfect tool to make this switch possible."

Diploid first introduced InHelix as part of its services offering earlier this year. In the intervening months it has tested and refined the software with collaborators in UK institutions. The company has also used the software in a number of customer projects involving real patient data and it has also tested the software on data from cases previously described in the literature. This includes one published in Nature Genetics that was done by researchers at the Radboud University Medical Center. It focused on identifying variants associated with severe intellectual disabilities. "The Nijmegen lab solved this case without InHelix, [but] we just used the data from the literature to show how simple it is to solve this kind of cases with InHelix," Schols said.

Repeated testing has helped the company's geneticists pre-build and curate more than 80 gene panels that they make available to InHelix users. This is one of the distinguishing features that sets the InHelix solution apart from software from companies like Cartagenia, now owned by Agilent. Cartagenia's software portfolio includes Bench Lab CNV, a solution that helps small and medium-sized cytogenetics labs analyze CNVs from microarrays and sequencing instruments. 

"Because we [use] this internally, we keep track of the literature, and we have this great set of built-in panels that InHelix [customers] can use free of charge," Schols said. Like InHelix, Cartagenia's solutions let users build their own panels, but the company's offering does not include pre-built panels, he claimed. Also, customers can't use phenotype data to construct bespoke panels in Cartagenia's solutions, but they can do so in InHelix. Finally, InHelix enables trio-based analysis for CNVs, a feature not included in competing offerings, according to Schols.

Cartagenia does have the benefit of a much broader pool of solutions sold by Agilent that could be bundled with its software. "Over time, however, we anticipate that our customers will prefer to use the best possible solution, regardless of whether it 'comes standard' with reagents or not," Schols said, because "efficient, user-friendly software can make a big difference in the productivity of diagnostic labs and researchers."

According to internal benchmarks, compared to some competing solutions, InHelix allows geneticists to identify causal CNVs and generate reports two to three times faster than the competition. "We are confident that if labs discover that InHelix can lead them to a causal CNV significantly quicker than competing software, because they can easily run CNV family analyses or because we deeply integrate with phenotype information, it will be an easy choice."

InHelix is available on the cloud, but Diploid also offers an onsite deployment option for larger hospitals and laboratories as well as for nationwide genome projects. As an introductory offer, Diploid is offering potential customers a chance to analyze five samples for free. Afterwards, customers will have to upgrade to a paid option. For the cloud-based option, Diploid charges $29 per sample for CNV annotation and interpretation. The company offers a discounted rate for customers who have a large number of samples that they would like to analyze. Customers who prefer an onsite deployment are charged an annual license fee.

Moving forward, Diploid plans to expand its commercial software portfolio. The company already plans to launch separate software later this summer for calling CNVs that will be integrated with InHelix, allowing users to move seamlessly from one solution to the next. However, users will still be able to upload CNV files from existing callers to the software if they chose to, Schols said.

Diploid will also expand the features available in InHelix over the coming months. "Integration with widely used CNV callers will be a top priority," Schols said, as well as adding new visualization capabilities. There are additional features planned for future releases of the software, but Schols declined to disclose what these will be.

Meanwhile, Diploid plans to continue offering its genome interpretation services. The company has lowered the starting price for its services. Previously, its services started at around €550 ($740) per whole exome or genome with significant discounts offered for bulk interpretation projects. However, because of lower sequencing costs and high sample volumes from customers, the company has reduced its prices and now charges €490 (around $552) per whole exome or genome, Schols said.

It has also expanded the breadth of its services. In February, Diploid launched Diagnosed, an interpretation service for interpreting and reporting on both SNPs and CNVs found in whole-genome sequencing data. The company has a rather unique pricing model for this particular service. It only charges customers if it is able to find the causative variants in their samples. "The idea is that clients have nothing to lose by sending us their WGS data for undiagnosed patients," Schols explained. "We either find a plausible causal variant, or the analysis is free."

The company provides genome interpretation services to over 40 hospitals and commercial sequencing labs worldwide. "Some of these customers distribute our interpretation to several of their customers, too, so the actual number of hospitals that we work for is even higher," Schols said.

One of its US-based clients is Otogenetics, a private next-generation sequencing-based lab located near Atlanta, which offers testing to hospitals and universities. Otogenetics offers whole-genome and whole-exome sequencing, RNA-sequencing, as well as disease panels for genes associated with deafness and various cancers among other NGS services.

The lab has its own internal bioinformatics team but uses Diploid's interpretation services when it receives orders from international clients who require that their clinical reports be reviewed by international medical geneticists, according to Adrian Costa, Otogenetics' director of sales and business development. Some of the benefits of Diploid's service include access to a "one-stop shop" for clinical NGS interpretations, access to medical geneticists to meet clinical testing requirements, and access to the most current annotation information for variants, he told GenomeWeb in an email. 

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