Russian bioinformatics firm iBinom has released a beta version of a data interpretation solution that bears the company name and is designed for analyzing whole-genome, whole-exome, and targeted sequencing data in clinical contexts.
The company designed the software-as-a-service solution, it said, to provide clinical researchers who are studying inherited diseases in medical centers, academia, and so on, with a tool to rapidly identify known pathogenic mutations in their data and was simple enough for users without informatics expertise to operate.
The software accepts raw sequence in the fq.gz or fastq.gz file formats, analyzes and processes it — a step that takes about 40 minutes for a panel, about 80 minutes for large exomes, and around three hours for whole genomes — and returns a ranked list of variants that have each been assigned a so-called iBinom score. That score is a value between zero and one where variants with scores closer to one are more pathogenic, and is based on about 50 genomic features. A subset of the variants that it identifies are selected and reported to the requesting physician. The rest of the variants can be accessed in the variant call files, which are generated as part of the system's final output.
The software provides clinical researchers with "precise" algorithms for making sense of the large quantities of genomic data that are currently available to them and which will continue to grow as the number of sequenced genomes increases, company Co-founder Valery Ilinsky, said in a statement. In addition to being easier to use than some current solutions that require technical know-how and do not return reports, the company's use of infrastructure from Amazon and Yandex — an internet company that operates the largest search engine in Russia and other countries — gives the iBinom product an edge in terms of time to results compared to some competing products, according to the company. Ilinsky told BioInform that the company plans to publish a paper in BioMed Central that will offer details about its product's performance.
Speed and ease of use are among the factors that iBinom believes set its software apart from competing products such as Tute Genomics' cloud-based interpretation engine for annotating and prioritizing genetic variants, which is based on the Annotate Variation (ANNOVAR) software, according to company Co-founder and CEO Andrey Afanasyev. The aforementioned iBinom paper planned for publication will include the results of a comparison between the iBinom software and the open-source version of ANNOVAR.
Another factor in iBinom's favor, Afanasyev told BioInform, is that its workflow covers the entire analysis process — activated by a single click — from raw sequence through to the ranked list of variants, so that customers don't have to combine multiple solutions to run separate parts of their analysis or need to put together their own internal pipelines.
The initial target market for iBinom is the clinical researchers who are trying to diagnose the genetic basis of inherited disease in their patients. As such, its system currently identifies pathogenic mutations associated with conditions that are recorded in the Online Mendelian Inheritance in Man database, Afanasyev said. However, the company has plans to extend the list of conditions that it can help clinical researchers diagnose to include non-Mendelian diseases and tumor profiling and to support drug response biomarker discovery studies.
There are also plans in place to incorporate additional capabilities that will allow customers to select which variants they want to see in their reports based on the patients' phenotypes, he said. At present, the system reports on all pathogenic variants it finds whether or not these are related to the patient being studied. The new capability, he explained, will make it possible for physicians to receive reports that contain only variants associated with muscular dystrophy and exclude variants that are tied to eye diseases, for example. It should be added to the system within a month, Ilinsky said.
The company has not set a launch date for its product and it doesn’t intend to, according to Afanasyev. He said that the company will continue running the beta until it is satisfied that it has incorporated all of the features that customers require, at which point it will officially launch the software.
It has, however, begun charging customers to use its solution. Each customer can analyze five exomes and five targeted sequencing panels for free. After that, they are charged per analysis run, and pricing varies depending on the sort of data being analyzed. For targeted sequencing, customers pay $199 per sample; whole-exome sequencing costs $499 per sample; and whole-genome sequencing costs $999 per sample. The company also offers 250 gigabytes of free storage space to each user, although it can make additional room available for those who need it at no cost, Afanasyev said.
iBinom opened its doors officially about a year ago, and it currently has 10 employees, offices in Moscow and St. Petersburg, and a US office in Los Angeles. It raised $130,000 last May from local investors to fund alpha and beta versions of its first product, Afanasyev said. So far, more than 50 clients globally have used the solution to run more than 200 exome analyses. He also said that the company plans to develop and sell additional products, but it is not yet disclosing what those products will be or when they might be released.