QIAGEN Bioinformatics and NGS Solutions Enable Genomic Breakthroughs
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QIAGEN N.V announced that its Sample to Insight solutions, from next-generation sequencing (NGS) technologies to bioinformatics solutions for research and clinical testing, figure prominently in independent studies presented this week at the American Society of Human Genetics (ASHG) annual meeting in Orlando, Florida. The ASHG 2017 conference, from October 17-21, attracts leaders in research and clinical applications from around the world, offering scientific sessions on new technologies in molecular biology and discoveries regarding genomic influences on disease.
“Wide-ranging studies at ASHG demonstrate the applications of QIAGEN solutions in achieving insights across the continuum of from genomic research in academia and pharma to clinical molecular testing. The world’s leading researchers can depend on our Sample to Insight workflows to create valuable insights,” said Dr. Thomas Schweins, Senior Vice President of QIAGEN’s Life Science Business Area. “QIAGEN solutions – spanning areas such as automated sample processing, solutions for reliable detection of genetic variations as well as tools for the analysis and interpretation with market-leading bioinformatics – are enabling breakthroughs in molecular testing and thereby making improvements in life possible.”
Among the published abstracts for the ASHG 2017 conference that highlight QIAGEN solutions:
• Using next-generation sequencing to investigate causes of delayed development in children, researchers at the University of Technology Dresden and University Clinic Leipzig in Germany relied on QIAGEN’s CLC Biomedical Genomics Workbench bioinformatics software for variant calling, a critical step in interpreting genetic findings. (Abstract No. 1048, “It does not have to be the whole exome: Mendeliome sequencing increases the diagnostic yield in patients with unexplained intellectual disability by 30%.”)
• Researchers at the Mayo Clinic in Rochester, Minnesota, tested QIAGEN’s CLC bioinformatics software for variant calling of small genetic variations known as indels, short for insertions and deletions of base pairs in DNA. The study found QIAGEN’s CLC bioinformatics coupled with NGS delivered 95% accuracy in identifying insertions of less than 30 base pairs and deletions of less than 27 base pairs. (Abstract No. 1265, “Limits of indel detection using CLC alignment and variant calling.”)
• Counsyl, a clinical laboratory in South San Francisco, California, compared QIAGEN Clinical Insight (QCI) software for interpretation of NGS results from 1,900 variants in hereditary cancer and other diseases to manual interpretation by PhD scientists and genetic counselors. The study found QCI’s coverage of variants was “comprehensive” and concordant with the lab’s own analysis. Counsyl added, “QCI has significantly increased curation efficiency, as evidenced by ~75% time savings in a reference search process that can take up to 45 minutes,” supporting adoption of QCI for reference selection to free lab staff’s time for difficult cases. (Abstract No. 602: “Evaluation of QIAGEN Clinical Insight as a content resource for variant curation in a CLIA laboratory.”)
• Researchers at the Mayo Clinic screened more than 3,000 patients to see how many might have benefitted from an early warning from genetic testing and concluded that new tools for early detection and treatment could potentially improve survival from pancreatic cancer. The researchers relied on a customized 37-gene QIAseq Targeted DNA panel for NGS to detect gene variants indicating predisposition to cancer, the study found up to 8% of patients had the mutations. The Mayo researchers said the results suggest a need to revise guidelines for clinical genetic testing. (Abstract No. 666/F, “Prevalence of cancer predisposition gene mutations among unselected pancreatic cancer patients.”)
• Two epigenetic studies at Loughborough University in the United Kingdom examined the influence of exercise in altering DNA methylation and gene expression linked to inflammatory conditions. Using QIAGEN’s EpiTect LyseAll kits and Pyromark Q48 Autoprep assays, the scientists found significant changes in methylation of two genes post-exercise. (Abstract No. 1642, “DNA Methylation of TNF decreases after an intense bout of eccentric exercise,” and Abstract No. 1658, “DNA methylation of PPARGC1A is associated with cycling performance.”)
• To improve detection of low-frequency variants in cancer, QIAGEN scientists created a Sample to Insight solution using QIAseq targeted panels to incorporate unique molecular identifiers (UMIs) for NGS, followed by data analysis with the Biomedical Genomics Workbench software. Applying this innovative workflow to several datasets, the team significantly increased sequencing quality (Q scores) and achieved more accurate estimates of variant frequency. (Abstract No. 1333, “Leveraging unique molecular identifiers to improve low-frequency variant calling in QIAseq V3 panels.
“Wide-ranging studies at ASHG demonstrate the applications of QIAGEN solutions in achieving insights across the continuum of from genomic research in academia and pharma to clinical molecular testing. The world’s leading researchers can depend on our Sample to Insight workflows to create valuable insights,” said Dr. Thomas Schweins, Senior Vice President of QIAGEN’s Life Science Business Area. “QIAGEN solutions – spanning areas such as automated sample processing, solutions for reliable detection of genetic variations as well as tools for the analysis and interpretation with market-leading bioinformatics – are enabling breakthroughs in molecular testing and thereby making improvements in life possible.”
Among the published abstracts for the ASHG 2017 conference that highlight QIAGEN solutions:
• Using next-generation sequencing to investigate causes of delayed development in children, researchers at the University of Technology Dresden and University Clinic Leipzig in Germany relied on QIAGEN’s CLC Biomedical Genomics Workbench bioinformatics software for variant calling, a critical step in interpreting genetic findings. (Abstract No. 1048, “It does not have to be the whole exome: Mendeliome sequencing increases the diagnostic yield in patients with unexplained intellectual disability by 30%.”)
• Researchers at the Mayo Clinic in Rochester, Minnesota, tested QIAGEN’s CLC bioinformatics software for variant calling of small genetic variations known as indels, short for insertions and deletions of base pairs in DNA. The study found QIAGEN’s CLC bioinformatics coupled with NGS delivered 95% accuracy in identifying insertions of less than 30 base pairs and deletions of less than 27 base pairs. (Abstract No. 1265, “Limits of indel detection using CLC alignment and variant calling.”)
• Counsyl, a clinical laboratory in South San Francisco, California, compared QIAGEN Clinical Insight (QCI) software for interpretation of NGS results from 1,900 variants in hereditary cancer and other diseases to manual interpretation by PhD scientists and genetic counselors. The study found QCI’s coverage of variants was “comprehensive” and concordant with the lab’s own analysis. Counsyl added, “QCI has significantly increased curation efficiency, as evidenced by ~75% time savings in a reference search process that can take up to 45 minutes,” supporting adoption of QCI for reference selection to free lab staff’s time for difficult cases. (Abstract No. 602: “Evaluation of QIAGEN Clinical Insight as a content resource for variant curation in a CLIA laboratory.”)
• Researchers at the Mayo Clinic screened more than 3,000 patients to see how many might have benefitted from an early warning from genetic testing and concluded that new tools for early detection and treatment could potentially improve survival from pancreatic cancer. The researchers relied on a customized 37-gene QIAseq Targeted DNA panel for NGS to detect gene variants indicating predisposition to cancer, the study found up to 8% of patients had the mutations. The Mayo researchers said the results suggest a need to revise guidelines for clinical genetic testing. (Abstract No. 666/F, “Prevalence of cancer predisposition gene mutations among unselected pancreatic cancer patients.”)
• Two epigenetic studies at Loughborough University in the United Kingdom examined the influence of exercise in altering DNA methylation and gene expression linked to inflammatory conditions. Using QIAGEN’s EpiTect LyseAll kits and Pyromark Q48 Autoprep assays, the scientists found significant changes in methylation of two genes post-exercise. (Abstract No. 1642, “DNA Methylation of TNF decreases after an intense bout of eccentric exercise,” and Abstract No. 1658, “DNA methylation of PPARGC1A is associated with cycling performance.”)
• To improve detection of low-frequency variants in cancer, QIAGEN scientists created a Sample to Insight solution using QIAseq targeted panels to incorporate unique molecular identifiers (UMIs) for NGS, followed by data analysis with the Biomedical Genomics Workbench software. Applying this innovative workflow to several datasets, the team significantly increased sequencing quality (Q scores) and achieved more accurate estimates of variant frequency. (Abstract No. 1333, “Leveraging unique molecular identifiers to improve low-frequency variant calling in QIAseq V3 panels.
