This week, Gentle said that it has expanded its portfolio to include InHelix, a new genome interpretation service, which the Leuven, Belgium-based company has launched to help medical geneticists and clinicians annotate and identify both novel and known pathogenic variants that underlie rare inherited diseases.
As reported by Clinical Sequencing News, BioInform’s sister publication, Gentle set up shop last November, offering a clinical exome sequencing test — priced at $1,990 — that provides carrier screening for more than 1,700 severe genetic diseases such as cystic fibrosis and sickle cell anemia, risk assessment for conditions such as colon and breast cancer, and looks for pharmacogenetic markers.
There has been "quite a lot of demand" for Gentle's test since it launched, according to Peter Schols, Gentle's CEO. And given the demand, the company decided to launch a separate informatics service, he told BioInform, to "offer more people access to our extensive database of markers as well as to our informatics pipeline."
The ideal client for Gentle's service will be geneticists in academic, pharmaceutical, and private sequencing labs who can do their sequencing in house but prefer to outsource the interpretation components of the analysis. "It’s more geared towards a medical genetics environment [and specifically] towards commercial labs that want to offer the same genome interpretation as we do for the Gentle test."
The new service uses a modified version of the analysis pipeline that Gentle uses internally to analyze the data that its test generates. The difference between the two informatics pipelines is that unlike the internal version of the system, which is tailored to identify known pathogenic variants, the InHelix pipeline is "more focused on diagnostics," Schols explained. Its tools let "our scientists flag variants as possibly pathogenic [and] compile a report with the most relevant variants for the diseases and for the phenotypes observed."
These results are based on a database of pathogenic markers culled from public and proprietary repositories such as the Human Gene Mutation Database as well as data from internal studies conducted by Gentle researchers. That information is "combined into one system that provides very rich annotations of variants, making it possible for geneticists to quickly identify disease-causing variants."
The depth of information in the database is one of the factors that Gentle believes sets its service apart from interpretation offerings provided by companies such as Knome and Codified Genomics, Schols said. "Our pipeline, as far as we know, includes more different data sources than any other service currently available in terms of coding and non-coding regions, [and] we have very good annotation." The company also expects that InHelix will benefit from the reputation that Gentle has built with customers who've purchased its test, he said.
To use the service, clients submit raw genetic data either as vcf or bam files as well as any phenotype data they can provide. Three weeks later, the company returns a report that includes a list of the most likely causal variants for the observed phenotypes, background information and literature references, some limited treatment information, as well as a description of the filtering and annotation procedure so that scientists can reproduce and verify InHelix's analyses.
Analyses start at $690 per sample for either whole exome or whole genome data. Gentle will interpret the first genome or exome submitted for free, giving prospective clients an opportunity to familiarize themselves with the service.