New, powerful bioinformatics tool: The RNA-Seq Explorer Solution
Today we announced our new RNA-Seq Explorer Solution — a powerful bioinformatics tool that combines Ingenuity® Pathway Analysis™ and Biomedical Genomics Workbench® to generate clear insights for research into improved cancer detection, diagnosis, and treatment. One of the most compelling benefits of the RNA-Seq Explorer Solution is that it allows you to focus on biology, giving you the tools to drive your research forward and to publish novel findings. It transforms raw data from liquid biopsies — one of the most promising new ways to detect and characterize cancer — into clear, accurate, actionable insights. Ultimately, we believe that a powerful bioinformatics-driven liquid biopsy solution like this one will vastly improve precision medicine and cancer management.
Principal Scientist Jean-Noel Billaud is presenting data from this new solution at AACR at our theater presentation on Tuesday, April 19, at 3:00 p.m. We hope you’ll come by to hear the finer points of our new RNA-Seq Explorer Solution. You’re of course also welcome to stop by our booth #741 for at chat.
Get the full overview of our activites at AACR.
For more details on the RNA-Seq Explorer Solution, please read the official press release below.
Press release
QIAGEN launches streamlined bioinformatics for RNA sequencing of liquid biopsies
RNA-seq Explorer Solution generates clear insights for cancer ‘omics’ analyses
Hilden, Germany, and Germantown, Maryland, April 14, 2016 – QIAGEN N.V. (NASDAQ: QGEN; Frankfurt Prime Standard: QIA) today announced introduction of its unique RNA-seq Explorer Solution, a bioinformatics-driven approach to analysis and interpretation of “omics” data from liquid biopsy-based research. RNA-seq Explorer Solution is a new tool which integrates Ingenuity® Pathway Analysis™ Biomedical Genomics Workbench® and other QIAGEN bioinformatics solutions to generate clear insights for research into improved detection, diagnosis and treatment of cancer. The solution will be demonstrated at the American Association for Cancer Research (AACR) Annual Meeting in New Orleans.
“The RNA-seq Explorer Solution provides the most powerful bioinformatics tool for the analysis and interpretation of RNA sequencing data from liquid biopsies, including from tumor-derived exosomes. Next-generation sequencing of liquid biopsies, one of the most promising new ways of detecting and characterizing cancer, demands the highest-accuracy tools to make sense of inherently noisy data,” said Dr. Laura Furmanski, Senior Vice President and head of QIAGEN’s Bioinformatics Business Area. “QIAGEN’s streamlined RNA solution transforms raw data from liquid biopsies into valuable insights – a significant milestone for liquid biopsy analysis of indications such as cancer. The best bioinformatics will drive progress in precision medicine and cancer management.”
Liquid biopsy is a non-invasive method using samples of body fluids such as blood to detect and profile diseases such as cancer at the earliest stage, resulting in more successful prognosis and treatment. One liquid biopsy approach extracts DNA or RNA from tumor-derived exosomes, tiny enclosures that circulate in body fluids. In an RNA-seq workflow, scientists analyze and interpret exosomal RNA to determine gene expression profiles, identifying regulatory networks and potential isoforms of biological significance.
RNA-seq Explorer Solution facilitates simple, accurate discovery and validation of biomarkers, enabling researchers to go from raw data in FASTQ format to significant insights that home in on the genetic drivers of cancer. The solution draws upon QIAGEN’s Ingenuity Pathway Analysis (IPA), an all-in-one, web-based software application that enables analysis, integration and understanding of expression data. IPA is backed by the expert-curated Ingenuity Knowledge Base of highly structured, detail-rich biological and chemical findings. RNA-seq Explorer Solution also integrates QIAGEN’s Biomedical Genomics Workbench, a comprehensive data analysis platform that offers end-to-end workflows and tools for the alignment, normalization and statistical analysis of NGS experimental results.
In addition to demonstrating of the new RNA-seq solution at its booth at the AACR meeting, QIAGEN Bioinformatics recently released a four-part webinar series; the company will also have a sustained presence at the event. Click here for more details.
Leadership in liquid biopsies
RNA-seq Explorer Solution complements QIAGEN’s industry-leading liquid biopsy portfolio, which is spanning sample technologies, assay technologies and bioinformatics. It includes gold-standard solutions for the extraction of cell-free, circulating nucleic acids (cfDNA), circulating tumor cells (CTCs), and exosomes. In partnership with pharmaceutical companies, QIAGEN is developing and commercializing the broadest portfolio of companion diagnostics based on liquid biopsies, including the therascreen EGFR RGQ Plasma PCR kit, the first ever CE-IVD-marked blood-based test to guide treatment decisions for solid tumors.
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 September 30, 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, personalized healthcare, 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).
Circulating tumor cells (CTCs) are tumor cells circulating freely in the peripheral blood of patients. The characterization of CTCs is considered as a real-time “liquid biopsy” that provides an ongoing picture of a patient’s cancer status, offering valuable insight into personalized anticancer therapy.
CTCs are very rare and highly heterogeneous, possessing tumor-specific antigenic and genetic characteristics. One of the most commonly used techniques to isolate CTCs is based on the enrichment of tumor cells that express epithelial cell adhesion molecules (EpCAM). This approach, however, can overlook CTC subpopulations that have undergone an epithelial-mesenchymal transition (EMT). It is believed that this EMT process allows the dissemination of CTCs from primary tumors into the circulation. During the EMT process, CTCs lose their epithelial characteristics and acquire more mesenchymal-like phenotypes.
QIAGEN has developed an advanced system that allows enrichment of these cancer cell subtypes from patient blood samples. To accomplish this, we use an antibody-conjugated magnetic bead isolation followed by molecular profiling of captured CTCs. This innovative approach is based on a unique mix of antibodies directed against various tumor cell-associated antigens. By using this technique, you will be able to identify cellular changes in antigen profiles once they develop an EMT or tumor stem cell phenotype, thereby ensuring that your enrichment includes these potentially crucial cells for analysis. This system has been widely used in characterizing cancer progression for targeted therapies.
In a recent investigation from the lab of Dr. Sabine Kasimir-Bauer, Maren Bredemeier and colleagues used the panel AdnaTest EMT-2/Stem Cell Select (QIAGEN Hannover GmbH, Germany) to enrich and profile the expression of 46 genes in CTCs of metastatic breast cancer (MBC) patients. The study was based on 2×5 ml blood from 45 MBC patients and 20 healthy controls, collected at the time of disease progression (T0) and at 2 consecutive clinical stagings (T1 and T2).
One interesting finding is that the multidrug resistant protein gene MRP1 showed a significant difference in expression in overall responders to treatment vs overall nonresponders. In order of significance, VEGFR1, keratin (KRT) 19, EGFR, MET1, ALDH, progesterone receptor (PR), UPA, cathepsin D, KIT1 and Ki67 were differentially expressed in CTCs of patients who had developed liver metastasis as compared to patients without liver metastasis. The patients with liver metastasis showed a significantly lower level of estrogen receptor (ER), PR, HER2, mammaglobin and KRT19 compared to other patients. These preliminary results indicated that CTCs can not only be used as a monitoring tool to guide anticancer therapy, but also allow prediction of the site of metastasis, which may enable a more precise therapeutic decision.
To get more information about this application in MBC research, visit Poster 19, Section 23, at 1 p.m. – 5 p.m., on Sunday, Apr 17, 2016 at AACR in New Orleans.
Find more details about our activities at AACR.
Liquid biopsies show promise for cancer research, but technical challenges remain
Preparing for this year’s annual meeting of the American Association for Cancer Research (AACR), we’ve been thinking about some of the most promising recent technology trends in oncology. One of our favorites is the advances in liquid biopsies as a way to earlier monitor cancer progression, and get a better sense of the genetic variation or expression profile present in a primary tumor or metastatic sites.
Most liquid biopsy studies look for one of three materials: cell-free DNA (cfDNA), circulating tumor cells (CTCs), or exosomes. As its name suggests, cfDNA is the genetic material released into the bloodstream from tumor cells that get lysed during apoptosis or some other process. CTCs are intact cells; in addition to the genetic information they can reveal about a tumor, they’re appealing because they may be cultured for a more sophisticated, longer-term analysis of how these cells function. Exosomes are vesicles released by cells as part of a cell-to-cell signaling network, among other important functions. They may contain RNAs or proteins produced by tumors or other cancerous cells. As scientists make inroads in liquid biopsy studies, it is becoming clear that a comprehensive picture of cancer requires information from as many of these sources as possible.
The biggest challenges with liquid biopsies right now involve finding signal in the noise. This occurs in two different phases: first, when blood or plasma is originally drawn from a patient. The cfDNA, CTCs, and exosomes from cancer cells are wildly outnumbered by material from healthy cells. Typically, liquid biopsies yield vanishingly small samples of interest for cancer research; significant efforts are underway to help solve this problem. A related challenge takes place in data analysis, where again the signal, identifying the driver variant or elucidating mechanisms driving the expression profile, from DNA or cells originating from a tumor can be very difficult to find in the wild-type noise. Analysis and interpretation solutions are being used to overcome this challenge as well.
We believe that liquid biopsies have the potential to transform the diagnosis and treatment of cancer patients. We’re delivering solutions that can help scientists conduct, analyse, and interpret liquid biopsy studies with greater precision and reliability.
We look forward to hearing more about this topic at AACR.
For additional updates, please visit the Biomarker Insights blog or see the schedule for our activities at AACR.
