NEW YORK (GenomeWeb) – Bangalore, India-based Leucine Rich Bio has developed and is preparing to launch a new cloud-based software-as-a-service solution dubbed CtoG to help clinical genetics laboratories identify potentially harmful mutations in data from their next-generation sequencing-based tests.
The company has been offering bioinformatics analysis and consulting services since its launch in June but CtoG is its first commercial product. When the software goes on sale on Nov. 17, it will provide algorithms to explore, identify, and interpret clinically relevant mutations, and will report the results in a manner that is both clinician- and bioinformatician-friendly, Kumar Sankaran, the company's CEO and co-founder, told BioInform.
CtoG uses some common open source algorithms to handle the sequence alignment and variant calling portions of the analysis process, and then uses a proprietary algorithm to rank potentially pathogenic variants, he said.
It's this bespoke ranking method along with an internally-developed database of manually curated information culled from published literature that will set Leucine Rich Bio's offering apart from competing SaaS offerings, according to Sankaran.
"We are targeting the interpretation," he said. And in order to do that well "a lot [of] data needs to be captured from literature. So, we've done manual curation and built our own database [and then] on top of that, we've developed a ranking algorithm which we think is more robust and consistent across data."
Leucine Rich Bio's Human Genome Variation Database (HGVD) contains curated content about mutation function gathered from sources such as published genome-wide association studies. It includes information on variants' clinical significance, associated phenotypes, as well as data on drug response. The company’s algorithm uses this information to rank variants based on criteria such as mutation function, impact on disease, and variant impact on protein structure and function. The report that’s returned to customers contains the list of relevant suspect variants along with supporting information from the literature, as well as more in-depth information about the informatics analysis for more tech-savvy clients to dig into.
At present, the company's database contains content that supports analysis in rare genetic diseases cases, so it will initially target laboratories that offer this kind of testing, Sankaran said. But by the end of the year, it will have included in its database curated information related to cancer so it can also cater to laboratories offering NGS-based oncology tests, he said. The company also plans to keep adding content that supports other disease-based tests.
Leucine Rich Bio has been testing the software in a private beta for some months, where researchers have been providing feedback on things such as its consistency and accuracy when it's run on different datasets as well as on data from different sequencing platforms. The company is using this feedback to fine tune the system prior to full launch, after which it will continue the beta, Sankaran said.
Meanwhile, the firm is fleshing out the details of its pricing. Initially, it will charge a per-sample price, which will vary depending on whether the sample in question is whole genome or whole exome, Sankaran said. The tentative price per sample is between $25 and $200 depending on the kind of analysis that’s needed, he said.
The company is also on the market for cloud providers to host its system. It is currently mulling several options, looking specifically for a vendor whose infrastructure complies with the Health Insurance Portability and Accountability Act as well as considering what system its clients want, according to Sankaran.
Leucine Rich Bio will also keep offering its existing stable of services. The six-person firm currently offers whole genome and exome and RNA-seq analyses to help customers identify disease-associated mutations and select more appropriate therapies for their patients. It uses the same infrastructure that underlies CtoG but can be tailored to meet clients' needs, for example, to analyze data from non-human models, Sankaran said. Pricing for Leucine Rich Bio's service offering is flexible depending in part on the nature of the project — that is, human versus non-human data.
CtoG will have to compete with SaaS solutions from companies like Strand, which recently launched its StrandOmics interpretation software; Tute Genomics, which offers a cloud-based interpretation engine based on the ANNOVAR software; and Russian firm iBionom, which launched a beta version of its clinical genome interpretation software earlier this year. It will also have to contend with interpretation service providers such as Belgian firms Diploid and Gentle, which both offer variant interpretation services; Codified Genomics, whose interpretation service is based on informatics capabilities from Baylor College of Medicine; as well as companies like Knome that offer both services and software for clinical contexts.