NEW YORK (GenomeWeb) – Belgian data interpretation firm Diploid is seeking to build a business based on providing genome interpretation services to hospitals, commercial and academic clinical laboratories, and the research and development arms of pharmaceutical companies that are trying to identify the genetic bases of rare genetic conditions.
Unlike Qiagen Redwood City (formerly Ingenuity), Tute Genomics, NextCode, and other companies that provide the interpretation software directly to consumers and let them run their analyses themselves, Diploid intends to cater to that segment of the clinical genetics market that outsources data interpretation needs in order to cut down on the cost of parsing and making sense of sequence data internally, among other reasons, Peter Schols, Diploid's CEO, told BioInform this week. Moreover, the service frees clinical geneticists to focus on their research rather than spend time worrying about the logistics of implementing and maintaining bioinformatics pipelines. Diploid estimates that firms that outsource their interpretation needs spend 50 percent to 65 percent less than they would have setting up an internal pipeline and hiring staff to run it.
The company has 10 employees with expertise in clinical and molecular genetics and informatics who develop and run the internal built infrastructure that powers its interpretation service. The company uses a secure pipeline comprised of bespoke and open-source tools and algorithms to analyze the contents of VCF and/or BAM files along with phenotypic data and annotate both known and potentially pathogenic variants in the data. The company's system can also screen for known markers that are associated with about 1,800 inherited disorders and conditions.
Clients get a post-analysis report that contains the list of variants relevant to their case along with background information, links to reference resources and repositories such as dbSNP, ClinVar, and the Online Mendelian Inheritance in Man, and a description of the company's filtering and annotation procedure. If clients don’t have their sequence data generated already, Diploid can put them in touch with CLIA- and CAP-certified labs located near them that can handle the customer's sequencing needs and send the resulting files directly to Diploid for analysis, Schols said.
Diploid officially began offering its interpretation services earlier this month. The service has been used by Oxford University Hospitals, King Faisal Specialist Hospital in Saudi Arabia, and Verona University in Italy, as well as other unnamed laboratories. The company was also selected as one of the winners of Genomics England's annotation assessment competition, an effort to evaluate and select potential service providers for the UK's 100,000 Genomes project. Other winners were Congenica, Nantomics, Genomics Ltd., Illumina, Qiagen, Lockheed Martin, NextCode Health, Omicia, and Personalis.
Among other benefits, Diploid has a quick turnaround time, completing its analysis and returning results in two weeks, Schols said — there's also a fast-track option, which enables customers to get their results back in seven days. Furthermore, the data is perused by experienced clinical geneticists on Diploid's staff, who review the variants shortlisted by the company's system and check references before the results are returned to the client. Another benefit of using the service is that Diploid will re-analyze at no additional charge previously generated reports if new data relevant to the sample in question becomes available. It can also include incidental findings in reports if customers request it, Schols said.
Pricing for the service starts at €550 ($740) per whole exome or genome with significant discounts offered for bulk interpretation needs. Diploid also interprets the first genome or exome submitted by prospective clients for free to give them a chance to become familiar with the service. Furthermore, they will analyze familial data associated with a particular genome or exome — data from the parents of a child being tested, for example — at no extra cost, Schols said.
Diploid opened its doors early this year backed by $500,000 in private investments. The company will likely run another financing round by the end of this year, Schols said. It will also focus on improving the diagnostic yield of its informatics applications. Right now, the company is able to identify pertinent variants in exome sequence data in 30 percent to 40 percent of the cases it analyzes, but it intends to improve those numbers. The company is also looking to add tools that can identify more complex variants, Schols said.