Leuven, March 27, 2012 – Cartagenia, the global leader in supplying diagnostic
knowledge, analytic software and database systems to genetic labs and
clinicians, today announced the commercial release of its BENCH lab NGS
solution for clinical NGS data analysis.
The new product is tailored to support the adoption of Next Generation
Sequencing technology in routine clinical practice and focuses on standardizing
the data interpretation process.
NGS technology brings opportunities for parallelizing genetic testing utilizing
targeted gene panels, whole-exome or whole-genome approaches. NGS is also
changing the way in which labs, clinicians and gene testing service facilities
work. Using NGS introduces new challenges for storing and accessing complex
data, identifying clinically relevant and validated genetic variants, and providing
high quality and consistent lab reports.
Labs need to maintain turn-around times, interpret hundreds or even thousands
of genetic variants of varying significance, and guarantee clinical quality of the
lab report. To keep ahead of volumes, labs need to automate and standardize
their diagnostic workflow with state-of-the art tools.
Clinicians need to guarantee standard of care and confidently counsel, making it
a necessity to have up-to-date and – where possible – clinically validated
knowledge resources always available.
Hospitals and core facilities need integrated tools that work with technologies
from multiple vendors, integrate with IT systems, and link to external referrers
electronically, yet are flexible enough to handle technologies changing over time.
Store and explore, validate and automate
The BENCH lab NGS solution provides unparalleled feature functionality to
support the four essential steps in robust and reliable NGS data analysis:
Store and annotate genomic variants and patient information: Manage
storage complexity of large data volumes, large numbers of variants,
samples and patients, including detailed phenotype information.
- Explore and identify disease mutations: Efficiently search and explore
the genomic variant database and identify disease mutations.
Automatically consult heterogeneous information sources, public
databases and algorithms for interpretation. Build pipelines, explore and
confirm diagnostic hypotheses.
- Validate clinical findings and interpretation workflows: Assist in validating
clinical findings, set up automated analysis and variant triage pipelines,
and clinically validate them on existing data sets before introducing them
in routine practice.
- Automate lab reporting: Implement standard operating procedures for
interpretation and reporting into automated clinical use. Automatically
and confidently generate lab reports. Integrate with LIMS and EHR
Beta test use program
The product was created to the same standard as BENCH lab CNV,
Cartagenia´s proven product for structural variant analysis on array CHG data,
which has enjoyed tremendous success over the past years. BENCH lab NGS
similarly focuses on increasing lab efficiency and supporting the daily routine of
Part of the product validation process was done in close collaboration with key
customers. Cartagenia runs a comprehensive beta test program, in which over
10 leading labs worldwide are participating, validating the product in multiple
clinical domains and utilizing a range of sequencing strategies. In the beta test
program, participating labs provide NGS data (gene panels, exomes and whole
genomes), patient case information, and operational diagnostic workflow
GeneDx (Gaithersburg, MD) is validating BENCH lab NGS as an efficient
storage system for variants annotated by an in-house pipeline for its Next Gen
Sequencing panels. Use cases include phenotype driven search of annotated
variants to identify clinically relevant mutations in context of multiple testing
indications, with integration of results / findings to a reporting system, and a joint
analysis of both CNV assay results and molecular variations, allowing
encompassing search and reporting across genotyping platforms.
The Genome Diagnostics unit of the Medical Genetics center at UMC Utrecht,
The Netherlands, is validating diagnostic workflows in Primary Immune
Deficiencies (PID), for which they have developed a target capture kit,
incorporating phenotype in variant selection and triage. With UMC Utrecht and 7
collaborating large clinical genetics groups, Cartagenia is standardizing
requisition forms to tailor PID clinical information capture, for subsequent
incorporation into phenotype-driven variant triage and classification.
In a parallel track, Cartagenia and UMC Utrecht are co-developing general
purpose diagnostic workflows around a 300+ gene targeted sequencing assay
(covering diagnostically validated as well as putative genes), using masking
functionality and the in silico assay design system available in BENCH lab NGS.
This allows variant sub-setting and tailored report automation targeted to a
specific pathology or reason for referral.
At the DNA Diagnostics Laboratory of the Department of Clinical Genetics at
AMC, Amsterdam, The Netherlands, a similar domain-specific approach was
taken, with a primary focus on cardiomyopathies. A key issue in disease-specific
variant interpretation is dealing with managed variant lists, where a lab can
annotate previously seen variants and automate reporting when variant
observations occur in new samples. With AMC, attention was also paid to
developing score-card based methods effectively combining multiple algorithms
that provide effect prediction scores, strengthening the quality of overall effect
prediction for variants of unknown significance.
With the DNA Diagnostics lab at the Hospices Civils de Lyon, CHU Lyon,
France, Cartagenia is looking into supporting analysis of large families for
diagnosis of autosomal or X-linked recessive disorders. Other unique areas of
collaboration include comparative analysis in cancer versus normal tissue.
Amongst a number of other applications, Cartagenia is working with Centre for
Medical Genetics at the University Hospital of Brussels (UZ Brussel),
Belgium, to support analysis of primary cardiac arrhythmias and mitochondrial
disorders. The latter are more challenging because of the wide clinical spectrum,
the mode of inheritance and the different types of variants (nuclear and
mitochondrial homo- versus heteroplasmic mutations).
With the Genomics Core at Life and Brain GmbH, Bonn, Germany, Cartagenia
is working is the area of Oncology. Although multiple specific pathologies were jointly addressed, the most prominent use case with L&B is on sequencing and
interpreting a panel of relevant genes involved in Familiar Adenomatous
Polyposis (FAP). The BENCH lab NGS platform is tailored towards automated
in-silico masking, variant reporting on known disease-bearing mutations, and
automated clinical reporting on diagnostically relevant findings.
Herman Verrelst, CEO of Cartagenia: “I would like to explicitly thank our
customers and partners for providing us with a wealth of input and clinical
information. Through-out the process, we were tremendously motivated by the
consistent positive feedback from our beta users. We have now a mature
product that we bring to the market with the utmost confidence. The BENCH lab
NGS solution was developed under stringent requirements of an ISO 13485
certified Quality Management System and will be marketed in the USA as an
exempt Class 1 Medical Device, subject to FDA general controls and software
quality system regulations for medical devices.”
The BENCH lab NGS solution is immediately available. Cartagenia will be
exhibiting, discussing and presenting the new system at the ACMG 2012 Clinical
Genetics Meeting at the Charlotte Convention Center, March 27-31, BOOTH
More information can be found at:
www.cartagenia.com/products or www.cartagenia.com/ACMG2012
Cartagenia supplies diagnostic knowledge, software and database systems, and
related services to genetic labs and clinicians, enabling them to perform
clinically relevant genetic analyses quickly and efficiently, and offer patients and
carers high-quality genetic interpretation and counselling.
T +32 16 40 40 66