Ingenuity http://www.ingenuity.com Intuitive web-based applications for quickly analyzing and accurately interpreting the biological meaning in your genomics data Tue, 20 Sep 2016 07:46:22 +0000 en-US hourly 1 http://wordpress.org/?v=4.0.13 Streamlined bioinformatics for RNA sequencing of liquid biopsieshttp://www.ingenuity.com/blog/news/streamlined-bioinformatics-for-rna-sequencing-of-liquid-biopsies http://www.ingenuity.com/blog/news/streamlined-bioinformatics-for-rna-sequencing-of-liquid-biopsies#comments Fri, 15 Apr 2016 11:38:47 +0000 http://www.ingenuity.com/?p=6668 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, … Read More

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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 afour-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 andnucleic 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).

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A retrospective look at cancer research effortshttp://www.ingenuity.com/blog/news/a-retrospective-look-at-cancer-research-efforts http://www.ingenuity.com/blog/news/a-retrospective-look-at-cancer-research-efforts#comments Fri, 15 Apr 2016 11:34:05 +0000 http://www.ingenuity.com/?p=6666 From IPA and Ingenuity® Variant Analysis™ to Biomedical Genomics Workbench and GeneReader, we’re honored to see that our products are on the front lines of the fight against cancer. Here’s a quick look at some of our customers’ most compelling … Read More

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From IPA and Ingenuity® Variant Analysis™ to Biomedical Genomics Workbench and GeneReader, we’re honored to see that our products are on the front lines of the fight against cancer. Here’s a quick look at some of our customers’ most compelling research.

As an assistant professor at the Indiana University School of Medicine, Milan Radovich’s career is still young, though he is making impressive strides in triple-negative breast cancer research. Using NGS and RNA-seq, he and his team are delving into how patients react to therapies and chemotherapy, allowing him to tailor treatment and discover promising new drug targets. His work with IPA determined that healthy breast tissue provides far better control than that taken from tumor-adjacent “normal” samples; in fact, this realization prompted the Komen Tissue Bank to change its recommendations for researchers. Radovich cites Upstream Regulator Analysis, Causal Network Analysis, and Molecular Activity Predictor as some of the powerful IPA features that enabled him to achieve these remarkable findings.

H. Sunny Sun from Taiwan’s National Cheng Kung University College of Medicine in Taiwan uses NGS and molecular diagnostics to learn more about colon cancer. Using exome and RNA sequencing, she and her team compared the gene mutation traits of local colon cancer patients with those featured in published papers. The resulting huge amounts of data were managed using CLC Biomedical Workbench, chosen by her team for its reliability.

At the Genomics Shared Resource at the UC Davis Comprehensive Cancer Center, technical director Cliff Tepper is responsible for sourcing solutions that can inform the work of both scientists and physicians. He has made several significant advances in cancer research by homing in on variants using Ingenuity Variant Analysis. He also used GeneRead DNAseq Targeted Panel to take a universal view of cancer, identifying a range of genes implicated in different types of cancer. In fact, Tepper gave a poster presentation at last year’s AACR about this very topic.

We are proud that these and other of our solutions are helping extraordinary scientists to make a difference in cancer research, and we look forward to learning more about their latest work at AACR.

Get more stories from our customers.

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CTCs as prognostic markers for metastatic breast cancerhttp://www.ingenuity.com/blog/news/ctcs-as-prognostic-markers-for-metastatic-breast-cancer http://www.ingenuity.com/blog/news/ctcs-as-prognostic-markers-for-metastatic-breast-cancer#comments Wed, 13 Apr 2016 11:11:25 +0000 http://www.ingenuity.com/?p=6664 Editor’s note: This is a cross-posted article from the Biomarker Insights blog. Please visit the original site for further information.  Circulating tumor cells (CTCs) are tumor cells circulating freely in the peripheral blood of patients. The characterization of CTCs is considered as … Read More

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Editor’s note: This is a cross-posted article from the Biomarker Insights blog. Please visit the original site for further information. 

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.

Interested in this technology? Download your copy of the webinar slides and watch the recording.

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.

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ITTM and QIAGEN provide new tranSMART functionalityhttp://www.ingenuity.com/blog/news/ittm-and-qiagen-provide-new-transmart-functionality http://www.ingenuity.com/blog/news/ittm-and-qiagen-provide-new-transmart-functionality#comments Wed, 13 Apr 2016 11:07:25 +0000 http://www.ingenuity.com/?p=6662 We’re pleased to announce our partnership with Information Technology for Translational Medicine (ITTM). We have partnered to develop a prototype of a connector for transferring data from tranSMART to IPA for further analysis and back to tranSMART for visualization. For … Read More

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We’re pleased to announce our partnership with Information Technology for Translational Medicine (ITTM). We have partnered to develop a prototype of a connector for transferring data from tranSMART to IPA for further analysis and back to tranSMART for visualization.

For more information about the connector and our partnership, please read the official press release from ITTM below.

 

Press release

ITTM logo

ITTM and QIAGEN provide new tranSMART functionality

ITTM S.A. in partnership with QIAGEN

Boston, MA, April 6th, 2016

Information Technology for Translational Medicine, S.A. (ITTM S.A.) announced today that it has partnered with QIAGEN to develop the first prototype of a connector between tranSMART and Ingenuity Pathway Analysis (IPA®). The connector will be provided to the tranSMART Foundation to further strengthen the development of the tranSMART platform. tranSMART is a global open-source bio-medical knowledge management platform and the new application is available on the latest tranSMART version release 1.2.4.

Scientists who have access to both platforms will be able to transfer data from tranSMART to IPA® for further analysis. The results of the IPA Core Analysis are being transferred back to tranSMART for visualization. IPA® is a web-based software application for the analysis, integration, and interpretation of data derived from ‘omics experiments, such as RNAseq, small RNAseq, microarrays including miRNA and SNP, metabolomics, proteomics, and small- scale experiments that generate gene and chemical lists.

“We wanted to provide a flexible solution that fits the requirements of our pharma partners. We plan to further develop the prototype and to provide additional integration solutions for our customers in the future.” Dr. Andreas Kremer, Managing Director of ITTM S.A.

“This is a great example how one can use Ingenuity Pathway Analysis’ programming interfaces to integrate our unique and best in class content and interpretation capabilities in pathway analysis and genomics into a knowledge ecosystem covering other areas of knowledge”, said Dr. Frank Schacherer, VP for QIAGEN Bioinformatics.” ITTM has proven to be an excellent partner for tranSMART integration and customization.”

About ITTM S.A.

ITTM S.A. is a spin-off company of the Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg. They provide data integration and knowledge management solutions and services to all bio-medical research areas. It focuses especially on translational medicine studies and clinical trials, in which heterogeneous data need to be curated, linked and integrated. ITTM S.A. offers cutting-edge clinical and multi-omics data analysis, visualization and text-mining solutions. For more information about ITTM, please visit the website at http://www.ittm-solutions.com.

About QIAGEN Redwood City

As QIAGEN’s Center of Excellence in Biological Analysis and Interpretation, QIAGEN Redwood, City (formerly Ingenuity Systems) is a leading provider of biomedical information and analysis solutions for the exploration, interpretation and analysis of complex biological systems in life science research and molecular diagnostics. These innovative solutions offered by QIAGEN are used by tens of thousands of researchers and clinicians at hundreds of leading pharmaceutical, biotechnology, academic, diagnostic and clinical institutions worldwide. Further information can be found at http://www.qiagenbioinformatics.com.

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Transcriptome analysis of pancreatic cancer exosomeshttp://www.ingenuity.com/blog/webinar/transcriptome-analysis-of-pancreatic-cancer-exosomes http://www.ingenuity.com/blog/webinar/transcriptome-analysis-of-pancreatic-cancer-exosomes#comments Wed, 13 Apr 2016 11:03:24 +0000 http://www.ingenuity.com/?p=6660 Webinar: Transcriptome analysis of pancreatic cancer exosomes involved in metastatic progression Pancreatic cancer is one of the most lethal malignancies with a poor prognosis. Liquid biopsies are non-invasive methods for diagnostics to detect early stage cancer resulting in more successful treatment. … Read More

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Webinar: Transcriptome analysis of pancreatic cancer exosomes involved in metastatic progression

Pancreatic cancer is one of the most lethal malignancies with a poor prognosis. Liquid biopsies are non-invasive methods for diagnostics to detect early stage cancer resulting in more successful treatment. One liquid biopsy technique is the detection of RNA from tumor-derived exosomes.

In this webinar you can learn how bioinformatics solutions can be used to analyze and interpret RNA-sequencing results from these exosome experiments, providing additional hypothesis on regulatory networks and potential isoforms of biological significance. We’ll examine the transcriptome of pancreatic tumor-derived exosomes that induce the formation of a liver metastatic niche, and demonstrate how our solutions can provide deep biological understanding in this process.

Find out how to:

  • Streamline RNA-sequencing alignment and analysis using configured workflows for the fast track to biological interpretation
  • Analyze exosome gene expression signatures to pinpoint significant genes associated with early detection of pancreatic cancer
  • Identify significantly differentially expressed isoforms and their association to pancreatic cancer
  • Generate novel regulatory networks as hypotheses suggesting drivers of the expression changes observed in these tumor producing exosomes to better understand pancreatic cancer drivers

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QIAGEN partners with IT leaders on novel infrastructure for genomicshttp://www.ingenuity.com/blog/news/qiagen-partners-with-it-leaders-on-novel-infrastructure-for-genomics http://www.ingenuity.com/blog/news/qiagen-partners-with-it-leaders-on-novel-infrastructure-for-genomics#comments Wed, 13 Apr 2016 10:56:14 +0000 http://www.ingenuity.com/?p=6658 At Bio-IT World we had the pleasure to demonstrate the results of our work with the information technology leaders Intel and BioTeam. Our collaborations create infrastructure solutions that make population-scale genomic analysis feasible for more researchers. We’ve been working together with Intel … Read More

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At Bio-IT World we had the pleasure to demonstrate the results of our work with the information technology leaders Intel and BioTeam.
Our collaborations create infrastructure solutions that make population-scale genomic analysis feasible for more researchers. We’ve been working together with Intel to bring world-class infrastructure together with industry-leading genome analysis tools to enable massively scalable whole genome analysis at lower cost. Together with BioTeam we’re creating a proof-of-concept high-performance computing (HPC) appliance.
For more details about the partnerships, please read the official press release below.
Press release
QIAGEN partners with IT leaders on novel infrastructure for genomics
Demonstrates high-performance computing and genome analysis solutions at Bio-IT World 
 

Boston, Massachusetts, and Hilden, Germany, April 5, 2016  QIAGEN N.V. today announced it will demonstrate the result of its work with information technology leaders Intel and BioTeam at Bio-IT World. Together these collaborations create infrastructure solutions that make population-scale genomic analysis feasible for more researchers. QIAGEN Bioinformatics has worked with Intel to develop a computational solution and reference architecture for whole genome analysis, and with BioTeam to create a proof-of-concept high-performance computing (HPC) appliance. QIAGEN is demonstrating both of these solutions at the Bio-IT World Conference and Expo from April 5-7 in Boston.

By combining our industry-leading genome analysis applications with hardware solutions from leaders like Intel and BioTeam, QIAGEN Bioinformatics is providing world-class infrastructure to help scientists reveal actionable insights from genomic data,” said Dr. Laura Furmanski, Senior Vice President and head of QIAGEN’s Bioinformatics Business Area. “While next-generation sequencing is a momentous advance, society cannot realize the full potential without a corresponding ability to analyze NGS data quickly and accurately. Researchers and clinicians need cost-effective, comprehensive tools for calling and interpreting variants across whole human genomes, and we are providing these novel solutions.”

QIAGEN’s collaboration with Intel developed a reference architecture designed to produce high-volume whole genome data analysis, keeping up with the world’s highest-capacity sequencers, helping NGS scientists keep their sequencing pipelines running smoothly and efficiently. This offering leverages QIAGEN’s CLC Genomics Server software on a compute cluster of 32 Intel® Xeon® processor E5 family based nodes. It provides built-in analysis tools, scalability, fast connection and parallel storage, using Intel Enterprise Edition for Lustre, the world’s largest parallel storage system. In tests, the solution analyzed data quickly and for as little as $22 per genome. It will be described in a conference presentation at Bio-IT World from 3:30-3:50 p.m. on April 6.

“The collaboration with QIAGEN Bioinformatics targets the vexing challenges presented by soaring demand for genome analysis, commonly faced by NGS scientists,” said Ketan Paranjape, GM Life Sciences at Intel. “Optimized solution architectures for these workloads enable researchers to keep pace as sequencers process more genomes than we could have imagined, even a few years ago — all while taking advantage of open systems to save money as well.”

BioTeam and QIAGEN’s proof-of-concept appliance packages CLC Genomics Server with the BioTeam Appliance scientific computing platform to provide a cost-effective, high-performance offering. The flexible, customizable solution delivers a system that maps the computational requirements of the CLC Bio software to an infrastructure that complements its capabilities. The BioTeam Appliance demo at Bio-IT World will be at the QIAGEN Bioinformatics booth (#229) from 1:30-1:45 p.m. on April 6.

“Bioinformatics is an ideal market for high-performance computing, and our simple, end-to-end appliance removes a significant barrier to adoption for many customers,” said Stan Gloss, Founding Partner and Chief Executive Officer at BioTeam. “Our plug-and-play solution enables scientists to focus on research rather than on creating complex IT systems from scratch. We look forward to continuing development of this proof-of-concept model with the QIAGEN Bioinformatics team.”

About BioTeam

BioTeam is a high-performance consulting practice dedicated to delivering objective, technology agnostic solutions to the life science researchers. We leverage the right technologies customized to our client’s unique needs in order to enable them to reach their scientific objectives.

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, 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).

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Liquid biopsies show promisehttp://www.ingenuity.com/blog/news/liquid-biopsies-show-promise http://www.ingenuity.com/blog/news/liquid-biopsies-show-promise#comments Wed, 13 Apr 2016 10:47:56 +0000 http://www.ingenuity.com/?p=6656 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 … Read More

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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.

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Scalable whole genome analysishttp://www.ingenuity.com/blog/news/scalable-whole-genome-analysis http://www.ingenuity.com/blog/news/scalable-whole-genome-analysis#comments Wed, 13 Apr 2016 10:36:25 +0000 http://www.ingenuity.com/?p=6654 New resource available: Pairing QIAGEN Bioinformatics tools with Intel technology for scalable whole genome analysis Scalable whole genome analysis We’ve been working together with Intel to bring world-class infrastructure together with industry-leading genome analysis tools to enable massively scalable whole … Read More

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New resource available: Pairing QIAGEN Bioinformatics tools with Intel technology for scalable whole genome analysis

Scalable whole genome analysis

We’ve been working together with Intel to bring world-class infrastructure together with industry-leading genome analysis tools to enable massively scalable whole genome analysis at lower cost. Now, we have released a new white paper detailing the reference architecture and other technical information for our joint solution.

Designed to help NGS scientists keep their sequencing pipelines running smoothly even at capacity – all while saving money and producing better results – our solution provides whole genome analysis for as little as $22 per genome. It meets the computational and analysis demands of Illumina’s HiSeq X Ten, but Intel’s 32-node offering can save researchers up to $1.3 million in total ownership costs compared to the 85-node cluster recommended by the vendor for a BWA+GATK variant calling pipeline.

Here’s a quick look at what makes our solution different:

  • Built-in analysis tools: The system uses Biomedical Genomics Server solution.
  • Scalability: Designed to scale on-demand for computing, networking, and storage, the cluster allows labs to manage capacity easily and cost-effectively.
  • Proven accuracy: While efficiency and cost-effectiveness is an important factor for NGS data analysis, accuracy in both variant calling and interpretation for the solution is proven to be among the best.
  • User friendly: The solution masks the complexity of cluster computing with the easy-to-use Biomedical Genomics Workbench.
  • Fast connection to data: We used a high-speed interconnect system based on Intel True Scale Fabric to link the compute nodes and centralized storage, providing up to 40 Gbps of bandwidth per port.
  • Parallel storage: The solution incorporates Intel Enterprise Edition for Lustre, the world’s leading parallel storage system, to keep all the nodes, cores, and threads operating at high efficiency.

For more details, check out the full white paper.

Our tests showed that the 32-node system could process and analyze 48 genomes in 24 hours, on average – enough capacity to handle all the data produced by a HiSeq X Ten. We also tested the system with exome data and successfully analyzed approximately 1,440 human exomes every 24 hours.

Together with Intel we were presenting this joint solution at the Bio-IT World 2016 conference in a presentation addressing the growing demand for population-scale genomics.

 

If you’d like to learn more but are not able to attend the conference, please feel free to email us.
More information about Bio-IT World

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