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CeGaT and Genomatix Finalists of Boston Children’s Hospital’s CLARITY Challenge

Published: Friday, November 09, 2012
Last Updated: Friday, November 09, 2012
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Free exomes project for six families and new variant analysis software.

CeGaT (Center for Genomics and Transcriptomics) GmbH, the Department of Prostate Cancer Research, Institute of Pathology, University Hospital Bonn and Genomatix Software GmbH were announced as finalist (Top 3) of the CLARITY challenge, organized by Boston Children’s Hospital.

The challenge was started in April 2012 by sending raw genome sequence data and medical records of three families (children and their immediate relatives) to 30 teams worldwide including BGI, NIH and other well-known genome centres.

Two of the patients had undiagnosed neuromuscular diseases, the other a cardiovascular disorder. In all cases current diagnostic tests gave negative results.

The aim of the CLARITY challenge was not only to solve the three cases but also to standardize methods for analyzing, interpreting, reporting and, ultimately, using genomic information in a clinical setting (

To achieve this, CeGaT and Genomatix Software successfully combined their expertise and services to solve the cases within the time limit given and identify best methods and practices to provide meaningful results to medical doctors, patients and their families.

The team was the only one to correctly flag every likely genetic mutation in all three families.

Saskia Biskup, Managing Director of CeGaT says: "I would like to take the opportunity to thank the organizers and sponsors for setting up the CLARITY challenge. It is a fantastic way to motivate and improve the necessary interaction between researchers and clinicians in order to bring next-generation sequencing to the "next" level. We are delighted that we have been selected as a finalist from the thirty competing teams. We were able to provide useful information for all three families, where the underlying genetic defect could be identified for the first time. In addition this gave us the opportunity to test CeGaT's interdisciplinary approach and know-how in the areas of technology, bioinformatics, biology, and medicine in a competitive setting. The CLARITY challenge has reassured us that our interdisciplinary approach is the future of diagnostics."

CeGaT and Genomatix will now offer their complete genetic analysis service to another six families (six trios or 18 exomes) for free.

The families will be selected on the basis of clinical manifestations with a yet unknown genetic cause. This free exomes project will build on the experiences gained in the CLARITY challenge and hopefully allow patients to find better treatment options by understanding the cause of their diseases.

Its goal is to follow the CLARITY mission to improve the clinical relevance of genetic analysis in hospitals.

Hospitals and doctors who are interested in registering patients for this project will find more information on the CeGaT website ( starting Nov 07, 2012.

Genomatix has announced the pre-release of geneGrid, a web application designed to help medical researchers identifying pathogenic genomic variations in humans.

The GeneGrid technology allows one to annotate and filter thousands of genomic variations within seconds and is supported by a large body of medical and genomics data.

In addition, GeneGrid is integrated with many established Genomatix tools, such as the Genomatix Pathway System (GePS) and the Genomatix Genome Browser.

Prior to its official release, GeneGrid was successfully used in the CLARITY challenge.

"With GeneGrid we enable medical researchers to find novel and known variants that are medically relevant. We knew that geneGrid was based on a solid technology, but applying it in the CLARITY challenge showed us how powerful it really is in a clinical setting." says Jochen Supper, Head of Computational Biology at Genomatix.

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