Ingenuity® Pathway Analysis (IPA®) is a powerful analysis and interpretation tool for uncovering network interactions and identifying new targets or candidate biomarkers within the context of biological systems. Here, we’ve rounded up a handful of the most interesting recent papers that have cited its use.
A University of Manchester-based research team developed this report on better understanding the pathology of keloid disease, an aggressive, locally invasive form of tumor. With the intention to apply a novel, three-method approach to this disease, the team used IPA to enrich the intersecting data. “IPA was chosen as the primary mode of enrichment analysis as all pathways, ontologies and interactions are manually curated and have supporting literature data behind them, thus providing a very robust and standardised platform for interpreting differential gene lists from transcriptomic studies,” the authors wrote. The team concluded that this research will not only provide an investigative starting point for other heterogeneous dermatological conditions, but also that it may have clinical implications for the future management of keloid disease.
The April issue of Oncotarget included a compelling report on advances in prostate cancer research. Prostate cancer is common among men from Western countries and is a major contributor to cancer-related deaths. Compiled by a German team, the report detailed a study of TMPRSS2:ERG (T/E) gene fusion variants, which are present in 50% of tumors and are the most frequent somatic alteration. They used IPA and the underlying QIAGEN Knowledge Base for functional annotation and pathway enrichment of differentially regulated genes, finding important signaling pathways. This research enabled the team to confirm the value of using ALK1-blocking agents to stall progress of certain prostate cancers.
Typically caused by intrauterine inflammation, preterm birth is a leading cause of neonatal mortality. Infants who survive have an increased risk for lifelong disabilities. A Baltimore-based team used the established mouse model of intrauterine inflammation-induced preterm birth and deployed IPA to analyze the transcription profiles, which helped identify Nuclear erythroid 2-related factor 2 (Nrf2) as a prominent upstream regulator. The scientists determined that Nrf2 — a transcription factor that regulates the response to oxidative and inflammatory stress — was a contributor to susceptibility for not only preterm birth but also a variety of environmental diseases, ranging from cigarette smoke-induced emphysema to allergen-induced asthma and polymicrobial sepsis. Their paper ran in Scientific Reports and urges future human studies to confirm the theory that pharmacological activation of Nrf2 might reduce inflammation and oxidative stress, the leading indicators of preterm birth.
Arthritis Research and Therapy recently ran a study focused on candidate genes for rheumatoid arthritis from a group of researchers at the Karolinska Institutet/University Hospital in Solna, Sweden. The report detailed the team’s process to identify new candidate genes and molecular pathways that are potentially involved in rheumatoid arthritis pathogenesis and which might be tested in the future as drug targets. The scientists used IPA’s experimental evidence database (human, mouse, and rat) for network construction and analysis, finding that out of 377 genes from rheumatoid arthritis-associated loci, 22 were differentially expressed, suggesting that at least three new candidate genes are involved in disease development: ERBB2, TP53 and HTOP1.
A French team looked at ways in which the meat industry might trim feed costs for pig meat production, aiming to describe shared and specific molecular responses in different tissues of pigs for residual feed intake. They used IPA to visualize plausible regulatory networks that included expression changes and to generate functional hypotheses and identify central molecules in small sub-networks. The team found that non-productive functions in metabolic tissues are likely important processes for feed efficiency — so dietary compounds with both anti-inflammatory and anti-oxidant activities might improve feed efficiency for pigs. They published their findings in BMC Genomics.
If you’re willing to share how you are using QIAGEN Bioinformatics tools in your workflow, we’d love to hear about it! Please contact us here; we’d also be happy to arrange a trial of Ingenuity Pathway Analysis.
It's a pleasure to announce an expansion of our portfolio of Sample to Insight solutions for next-generation sequencing (NGS) with the introduction of more than 170 new QIAseq Targeted RNA Panels for gene expression profiling.
Innovative molecular barcode technology and built-in control assays coupled with world-leading RNA isolation technologies, integrated NGS library preparation and Ingenuity® Pathway Analysis™ software, provide a unique solution for efficient RNA sequencing, using any NGS sequencer.
For more information on the QIAseq Targeted RNA Panels, please read the official press release below.
Press release
QIAGEN launches targeted RNA panels for next-generation sequencing
Sample to Insight workflows deliver more efficient, accurate gene expression profiling
Hilden, Germany, and Germantown, Maryland, February 11, 2016 – QIAGEN N.V. (NASDAQ: QGEN; Frankfurt Prime Standard: QIA) today announced the introduction of more than 170 new QIAseq Targeted RNA Panels for gene expression profiling, expanding QIAGEN’s portfolio of Sample to Insight solutions for next-generation sequencing (NGS). The panels enable researchers to select from over 20,000 human genes and lncRNA to survey expression fold changes and discover interactions between genes, cellular phenotypes and disease processes.
The new QIAseq Targeted RNA Panels use innovative molecular barcode technology and built-in control assays to empower researchers with true digital RNA sequencing and accurate gene expression results. Coupled with world-leading RNA isolation technologies, integrated NGS library preparation and Ingenuity® Pathway Analysis™ software, the panels provide a unique Sample to Insight solution for efficient RNA sequencing, using any NGS sequencer. Data analysis and insights are integrated into the QIAseq panels with easy-to-use, comprehensive analysis modules that require no bioinformatics expertise.
“Our QIAseq panels make RNA sequencing more accurate and reproducible with molecular barcode-based sequencing addressing the challenges posed by of low-abundance transcripts, PCR duplicates and amplification bias. These are important new tools for NGS researchers,” said Brad Crutchfield, Senior Vice President and head of QIAGEN’s Life Sciences Business Area. “QIAGEN is leading the way in providing NGS solutions to take labs from Sample to Insight.”
QIAseq Targeted RNA Panels cover an extensive range of disease- and signaling pathway-focused genes, with each panel targeting 100 to 500 genes. The content is based on the latest recommendations from relevant medical and scientific literature. The panels also can be customized to include other genes of clinical and biological interest, with flexibility to analyze from 12 to 1,000 genes simultaneously.
QIAGEN has collaborated with key leader in genomic discovery in the development of the new QIAseq panels to validate product performance in a wide range of applications, including translational and clinical research. Dr. Chris Mason, Associate Professor at Weill Cornell Medicine and one of the early users of QIAseq Targeted RNA Panels, will be presenting application data of the new panels at the Advances in Genome Biology and Technology (AGBT) meeting in Orlando, Fla., on February 11.
QIASeq panel technology combines the flexibility and throughput of NGS with the accuracy of qPCR. The panels use only 20 nanograms of starting RNA material to analyze hundreds of genes. The molecular barcode technology, proprietary assay design algorithms and chemistry provide industry-leading specifications: >97% specificity (reads on target), >95% uniformity (bases covered by at least 20% of the mean coverage depth), and sensitivity to detect 1 RNA copy per cell for QIAseq RNA panels.
QIAGEN serves next-generation sequencing customers worldwide with solutions from Sample to Insight. The company’s sample preparation workflows, including tools for difficult challenges such as single-cell analysis and studies of microbial diversity, are the industry’s most respected. Its Enzymatics products are used in an estimated 80% of all NGS workflows. QIAGEN also provides a portfolio of NGS oncology gene panels compatible with any platform. The GeneReader NGS System was launched in late 2015 as the world's first truly Sample to Insight NGS workflow from primary sample to final report – providing a simpler, more cost-effective way for clinical testing to take advantage of NGS technology and improve outcomes.
About QIAGEN
QIAGEN N.V., a Netherlands-based holding company, is the leading global provider of Sample to Insight solutions to transform biological materials into valuable molecular insights. QIAGEN sample technologies isolate and process DNA, RNA and proteins from blood, tissue and other materials. Assay technologies make these biomolecules visible and ready for analysis. Bioinformatics software and knowledge bases interpret data to report relevant, actionable insights. Automation solutions tie these together in seamless and cost-effective molecular testing workflows. QIAGEN provides these workflows to more than 500,000 customers around the world in Molecular Diagnostics (human healthcare), Applied Testing (forensics, veterinary testing and food safety), Pharma (pharmaceutical and biotechnology companies) and Academia (life sciences research). As of December 31, 2015, QIAGEN employed approximately 4,600 people in over 35 locations worldwide. Further information can be found at http://www.qiagen.com.
Certain of the statements contained in this news release may be considered forward-looking statements within the meaning of Section 27A of the U.S. Securities Act of 1933, as amended, and Section 21E of the U.S. Securities Exchange Act of 1934, as amended. To the extent that any of the statements contained herein relating to QIAGEN's products, markets, strategy or operating results, including without limitation its expected operating results, are forward-looking, such statements are based on current expectations and assumptions that involve a number of uncertainties and risks. Such uncertainties and risks include, but are not limited to, risks associated with management of growth and international operations (including the effects of currency fluctuations, regulatory processes and dependence on logistics), variability of operating results and allocations between customer classes, the commercial development of markets for our products in applied testing, personalizedhealthcare, clinical research, proteomics, women's health/HPV testing and nucleic acid-based molecular diagnostics; changing relationships with customers, suppliers and strategic partners; competition; rapid or unexpected changes in technologies; fluctuations in demand for QIAGEN's products (including fluctuations due to general economic conditions, the level and timing of customers' funding, budgets and other factors); our ability to obtain regulatory approval of our products; difficulties in successfully adapting QIAGEN's products to integrated solutions and producing such products; the ability of QIAGEN to identify and develop new products and to differentiate and protect our products from competitors' products; market acceptance of QIAGEN's new products, the consummation of acquisitions, and the integration of acquired technologies and businesses. For further information, please refer to the discussions in reports that QIAGEN has filed with, or furnished to, the U.S. Securities and Exchange Commission (SEC).
