Software Platform Provides Capabilities for Somatic Variation Analysis

An upgraded information-processing platform enables clinical genetics and molecular pathology laboratories to achieve higher performance and efficiency in somatic variation analysis of tumor-tissue sequencing data and in reporting of tissue-typing results, among other features.

Agilent Technologies (Santa Clara, CA, USA) has released its Cartagenia Bench Lab 5.0, a major new version that addresses inherent challenges of interpreting and reporting on genomic variants data. Cartagenia Bench Lab, registered as an exempt Class I Medical Device in the US, helps high-throughput diagnostic labs to validate and automate their variant assessment and reporting pipelines.


The software enables clinical geneticists and molecular pathologists to combine single nucleotide polymorphisms (SNPs); small insertions and deletions (INDELs); and copy number variations into one seamless analysis. Variant curation tools allow users to review variants, collaboratively build evidence, and securely share it with peers and data-sharing communities. With a range of new features for somatic variant classification, review, and curation, the 5.0 release represents a significant leap forward.

Cartagenia Bench provides direct access to over 100 curated and publicly available databases with information on actionable variants, trials, drugs, and therapy options such as CIViC, COSMIC, N-of-One, OncoMD, and CollabRx.

The software's variant curation tools enable labs to build an internal knowledge base of predictive, prognostic, diagnostic, and functional evidence of previously curated variants. By accessing tumor type-ontology and variant information from the curated and public databases, labs can efficiently implement their variant assessment standard operating procedure to more effectively filter variants and access knowledge based on the tumor's tissue type.

"Translating genomic data into actionable information is challenging,” said Herman Verrelst, Agilent vice president and general manager of the company's Genomics Solutions Division and Clinical Applications Division, “The 5.0 release offers molecular pathology labs access to clinical-grade analysis tools and knowledge — one of the key pain points for the implementation of next-generation sequencing (NGS) in routine oncology testing — to help them efficiently interpret sequencing data of tumor samples and provide actionable information by accessing publicly and curated databases containing peer reviewed evidence on diagnostic, prognostic, and therapeutic variants."

"Since we implemented our routine diagnostic pipeline on Agilent's bench platform, we've appreciated the close collaboration with the team and how they translate our needs into new software versions," said Petra Nederlof, head of Molecular Diagnostics, Netherlands Cancer Institute (Amsterdam).

"We are truly excited by our partnership with Agilent as it extends our reach into the global molecular pathology community," said Dr. Malachi Griffith from McDonnell Genome Institute, Washington University School of Medicine (St. Louis, MO, USA), "With the incorporation of the CIViC knowledge base in Agilent's bench platform, all users will now have direct access to the predictive, prognostic, and diagnostic evidence curated by CIViC domain experts."

Agilent will be showcasing Cartagenia Bench Lab 5.0 and other solutions at the NGS in Molecular Pathology Symposium, November 30-December 2, 2016, at the Netherlands Cancer Institute. "We're excited about co-organizing this event with Agilent," said Dr. Nederlof, "We have a strong agenda of international experts who will share expertise from their clinical diagnostic practices.” The symposium will include tracks on clinical variant assessment and lab reporting, automation, somatic variant classification, NGS panel composition, and data-sharing initiatives.

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