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Cartagenia Launches Next-Generation Sequence Analysis Software for Clinical Labs

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By Uduak Grace Thomas

Cartagenia this week released a version of its Bench Lab software that is geared toward analyzing next-generation sequence data in clinical laboratories.

Leuven, Belgium-based Cartagenia said that its new product, dubbed Bench Lab NGS, focuses on standardizing the process of interpreting data. Prior to launching the software, the company ran a beta test program with about 10 European and US clinical laboratories in order to ensure that it met the needs of that market.

The product shares some of the same features as another Cartagenia product, Bench Lab CNV, which is used for analyzing structural variants in array CGH data. However, the NGS product consumes data in a slightly different format since structural variations are coded differently from molecular variations, Herman Verrelst, the company's CEO, explained to BioInform.

Additionally, Bench Lab NGS pulls in variant information from a different set of databases including the National Center for Biotechnology Information's Single Nucleotide Polymorphism Database and the Human Gene Mutation Database.

Verrelst said that Cartagenia has partnered with Interactive Biosciences to integrate Bench Lab NGS with Interactive's Alamut software, which includes visualization capabilities and an analytical engine for identifying and interpreting genetic mutations (BI 3/4/2011).

Customers are required to have separate licenses for each software tool in order to use Alamut's capabilities, Verrelst said.

Bench Lab NGS provides tools to store and annotate genomic variants and patient information, including phenotype data. It also allows researchers to explore genomic variant databases in order to identify and interpret disease mutations.

Bench Lab NGS helps users set up automated analysis and variant triage pipelines as well as validate clinical findings using information from existing datasets before incorporating their findings into routine practice.

It also provides researchers with a set of standard operating procedures for interpreting and reporting their findings; and it integrates these activities with laboratory information management systems and electronic health record systems.

Cartagenia isn't disclosing the cost of a license for Bench Lab NGS because the company intends to base its prices on the quantity of data that needs to be analyzed as well as the revenues the labs in question are able to generate using the system, Verrelst said.

The firm is adopting this approach because researchers within the tool's target customer base currently require analysis of only small volumes of NGS data, so placing too high a price tag on the software could drive away potential clients, he explained.

Similarly, he said the company will not charge large set-up fees to deploy the software in either of its two incarnations — as a cloud-based option or a local installation.

Its flexible price point and "close-to-free start-up fees" should make the system attractive to customers, he said.

Attractive pricing could make a difference in what is shaping up to be a competitive marketplace. Cartagenia recently opened a Boston office to expand its North American footprint (BI 3/23/2012), and competes with firms like GenomeQuest, Personalis, Omicia, and Knome, who all target a similar client base (BI 12/22/2011).

GenomeQuest has been particularly aggressive in courting the clinical market. Last month, the company secured Emory Genetics Laboratory as the eighth clinical lab to use its GQ-Dx software to support sequencing-based diagnostic tests (BI 2/24/12).

Verrelst said that Cartagenia's products were built specifically for use in clinical labs, however, which sets it apart from the rest of the pack.

While he declined to name any specific firms, he noted that "there are companies out there that have specific offerings focused on research settings and ... on other types of data analysis and they try to reinvent those systems to function in clinical settings."

Research-centric tools, he explained, are typically oriented toward gathering data on a cohort of patients as opposed to information from individual patients. They also don’t capture operational processes that are unique to clinical labs and may not have the same security requirements that are necessary for handling patient data, he said.

Cartagenia, on the other hand, is "not reconverted research software; we are tailored and focused on the operational context of our customers in [clinical] genetic labs," he said.

Verrelst noted that the software is also developed with an eye toward the validation processes that clinical labs are required to perform for their analysis workflows. Such labs have "strong requirements" for managing and providing access to data that exceed the capabilities of research tools, Verrelst said.

For example, he explained that clinical labs require user identification and management tools, data segregation, and secure systems that ensure that patient privacy is respected and only authorized users access the data. "These things are not present in the research setting" because in these cases "all the data is open and shared."

Cartagenia plans to eventually combine Bench Lab NGS and Bench Lab CNV into a single platform because it believes that next-generation sequencing platforms will soon be used to identify structural variants, Verrelst said.

He added that the company is also working to include other types of data including data from fluorescence in situ hybridization tests.

"The plan is to provide a universal genomics platform to our customers to cover all different workflows and all different data that are generated on various systems," he said.

Vetting the System

Prior to launching Bench Lab NGS, Cartagenia ran a beta test program in which researchers from about 10 clinical laboratories put the platform through its paces using NGS data, patient case information, and operational diagnostic workflow descriptions. The labs tested the system with targeted sequencing, exome sequencing, and whole-genome sequencing data.

Among the participants was GeneDx, a Gaithersburg, Md.-based laboratory, which used Bench Lab NGS to store variants annotated by an in-house pipeline for NGS panels, Cartagenia said.

GeneDx researchers used the system to conduct and report a phenotype-driven search of annotated variants with the aim of identifying clinically relevant mutations in the context of multiple testing indications. They also used the system to analyze copy number variant assay results and molecular variations.

Meanwhile, the genome diagnostics unit of the University Medical Center, Utrecht, in the Netherlands is working on validating diagnostic workflows in primary immune deficiencies, or PIDs that incorporate phenotype in variant selection and triage. They have also developed a target capture kit for PID's.

Hans Kristian Ploos van Amstel, who heads the genome diagnostics unit at UMC Utrecht, told BioInform this week that the center uses Sanger sequencing and Life Technologies' SOLiD 5500 sequencer to generate data for the project. The group is also looking into using Life Tech's Ion Torrent benchtop sequencers.

He explained that as part of the analysis, his group used an internal pipeline that handles the raw data from the sequencers and generates a list of variations with quality scores. This information is then fed into Cartagenia's software.

"[Our] in-house pipeline gives some interpretation of the mutations ... and some possible deleterious mutations," but "to get it together with clinical data and laboratory data ... we [needed] another platform and that’s where Cartagenia comes in," he said.

Prior to the development of this platform, "we had to do it by hand," he said. "You can do that for single genes but if you have a lot of data that’s too difficult."

Meanwhile, Cartagenia worked with researchers at UMC Utrecht and seven clinical genetics groups to create standardized requisition forms to capture PID clinical information.

Cartagenia and UMC Utrecht are also co-developing general-purpose diagnostic workflows around a 300-gene targeted sequencing assay that covers diagnostically validated and putative genes. The assay uses a masking functionality and in silico assay design system in Bench Lab NGS.

Using the assay and Bench Lab NGS, researchers will be able to select subsets of variants and then generate tailored reports for particular pathologies, Cartagenia said.

Also involved in the beta was the DNA diagnostics laboratory at the Academic Medical Center in Amsterdam. The researchers there worked on an approach for dealing with managed variant lists associated with cardiomyopathies that would allow a lab to annotate previously seen variants and automate reporting when variant observations occur in new samples.

The team also used the platform to generate score-card based methods of making predictions about variants of unknown significance, Cartagenia said.

The company also worked with the DNA diagnostics lab at a French hospital, where researchers worked on diagnosing autosomal or X-linked recessive disorders in large families. The researchers also ran comparative analysis in cancer versus normal tissue.

Another beta customer was the Center for Medical Genetics at the University Hospital in Brussels, Belgium, which used the software to support the analysis of primary cardiac arrhythmias and mitochondrial disorders.

Finally, Cartegenia worked with the genomics core at Life and Brain, a lab based in Bonn, Germany, focusing on sequencing and interpreting a panel of genes associated with familial adenomatous polyposis — an inherited condition in which cancerous growths form in the epithelium of the large intestine.


Have topics you'd like to see covered in BioInform? Contact the editor at uthomas [at] genomeweb [.] com.

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