BARCELONA, Spain – QIAGEN announced two milestones in its delivery of solutions for clinical analysis and interpretation of hereditary diseases with whole exome and genome data.

Widely enabling GATK best practices without technical or bioinformatics skills

Beginning this month, pipeline scripts that implement the Broad Institute’s GATK best practices — a widely-used solution for variant calling — can be easily used in QIAGEN’s Biomedical Genomics Workbench with its Biomedical Genomics Server Solutions. This combination forms part of QIAGEN’s Hereditary Disease Solution. In addition, the variant-interpretation capabilities of QIAGEN’s Hereditary Disease Solution were assessed at the recent Critical Assessment of Genome Interpretation (CAGI) 4 event for clinical accuracy using the clinical panel in the Johns Hopkins Challenge. The Company will be showcasing these advances and its extensive portfolio of software solutions at the European Human Genetics Conference in Barcelona, May 21-24.

QIAGEN’s plugin for GATK incorporation and pipeline scripts expand access to the GATK best practices for exomes and whole genome variant analysis for single samples within its Biomedical Genomics Workbench. Requiring no advanced bioinformatics skills, this configuration allows clinical researchers and clinicians to:

Run GATK according to the best practices recommended by the Broad Institute for whole exome sequencing or whole genome sequencing in combination with Ingenuity Variant Analysis as an end-to end variant calling and interpretation workflow from the workbench;

Combine GATK results with variants called using CLC variant-calling pipelines to identify variants missed previously; and

Visualize and validate results without importing VCF and BAM files within a single product.

“The Broad’s GATK pipeline is a community standard, and is cited in more than 90 percent of papers,” said Michael Barmada, Associate Professor Human Genetics, Director at the Center for Computational Genetics, University of Pittsburgh. “I am very excited that GATK is now integrated into the Biomedical Genomics Workbench, making it as easily accessible as the other tools provided by QIAGEN. This signifies an expanding commitment to clinical researchers and clinicians who want to quickly and comprehensively call variants and create interpretation workflows with community-standard tools in an easy-to-use environment.”

QIAGEN Bioinformatics’ Hereditary Disease Solution performs best in clinical accuracy at this year’s CAGI 4 challenge

The QIAGEN Bioinformatics Hereditary Disease Solution for exomes, genomes, and large gene panels performed best in clinical accuracy at the CAGI 4 conference for the second consecutive year. For the challenge, each participant was provided variant calls for 83 genes from a cohort of 106 patients with a range of clinical presentations and tested for assignment of patients to their correct disease class. Dr. Sohela Shah, Principal Genome Scientist for Advanced Clinical Testing at QIAGEN Bioinformatics, demonstrated the variant interpretation capabilities of QIAGEN’s Hereditary Disease Solution and its extensibility for whole exome and genome analysis.

“We are excited to have participated in this study and to demonstrate our superior capabilities for variant interpretation,” said Dr. Michael Hadjisavas, VP of Clinical Genomics Program, QIAGEN Bioinformatics. “Our capabilities and investments in developing these solutions will become increasingly relevant as the research and clinical community scales from panels to exomes and ultimately to whole genomes for personalized medicine. This trend will continue to demand the use of our highly sophisticated computational solutions with the perpetually curated QIAGEN Knowledge Base to predict phenotypic impacts of genomic variation. CAGI 4 was an ideal showcase for these capabilities within our Hereditary Disease Solution.”