In order to provide the best software and product support for our customers, QIAGEN must periodically retire older versions of our software. This enables us to dedicate all our resources in delivering the latest features, enhancements and support to our current versions and latest solutions.
At this time, we would like to announce the pending end of life of QIAGEN Ingenuity Variant Analysis (IVA). On December 31, 2020, Adobe will end support of Flash Player, the web-based technology that powers IVA.
“Adobe is planning to end-of-life Flash. Specifically, we will stop updating and distributing the Flash Player at the end of 2020 and encourage content creators to migrate any existing Flash content to these new open formats.”
QIAGEN Digital Insights has evolved from the collection of world-class bioinformatics and scientific and clinical content properties, such as Ingenuity, CLC bio, Biobase, OmicSoft, and N-of-One. As such, there has been an effort to streamline the QIAGEN Digital Insights portfolio.
We have taken the opportunity to deprecate the Flash version of IVA while merging its functionality into QIAGEN Clinical Insights (QCI). This way we can streamline the QIAGEN Digital Insights portfolio while preserving the IVA workflows in an HTML5 compliant platform.
During the 2020 transition period, IVA users will have full access to the classic, Flash-based IVA platform. By mid-2020, an updated version of QCI will contain elements supporting many of the existing IVA workflows. Once this version of QCI becomes available, all IVA users will automatically have access to QCI as part of their IVA subscription within 2020. With access to both IVA and QCI, users will be able to learn how to perform IVA workflows within QCI and provide feedback to the development team.
After December 31, 2020, all IVA users must use the QCI platform, as the classic IVA Flash platform will be terminated after that date.
If you have any questions, please contact us at bioinformaticssales@qiagen.com.
Researchers across the world are using QIAGEN Digital Insights solutions to accelerate their work in a variety of applications
Powerful insights help innovate, integrate and translate scientific results into impactful discoveries. Many noteworthy papers cite QIAGEN Digital Insights solutions and demonstrate how our tools help drive research insights and discoveries. These papers use QIAGEN Ingenuity Pathway Analysis (IPA), QIAGEN CLC and/or QIAGEN OmicSoft to help drive success. The QIAGEN Digital Insights portfolio encompasses a comprehensive, easy-to-use toolbox that ensures continuity in NGS workflow. Here, we have curated a selection of just a few recent papers to offer a sense of the diversity of the research for which QIAGEN Digital Insights solutions makes a difference.
Next-generation sequencing profiles of the methylome and transcriptome in peripheral blood mononuclear cells of rheumatoid arthritis
First author: Chia-Chun Tseng
In honor of World Autoimmune Arthritis Day (May 20), check out this exciting research by C. Tseng and colleagues from Kaohsiung Medical University who use next-generation sequencing to understand how the methylome and transcriptome contribute to rheumatoid arthritis. Learn how they use QIAGEN IPA to investigate the interaction between genetics and epigenetics. Dig into their research paper here.
Interferon-β corrects massive gene dysregulation in multiple sclerosis: Short-term and long-term effects on immune regulation and neuroprotection
First author: Xuan Feng
Excellent research by Xuan Feng and colleagues at the University of Chicago who study the effects of interferon-β on correcting gene dysregulation in multiple sclerosis. Discover how the team uses QIAGEN IPA to investigate the short-term and long-term impact of IFN-β on immune regulation and neuroprotection. Check out their research here.
Cellular and molecular characterization of multiplex autism in human induced pluripotent stem cell-derived neurons
First author: Emily M. A. Lewis
Dr. E. Lewis and colleagues from Washington University School of Medicine attempt to model multiplex autism using iPS cells derived from a family with autism. Learn how the team uses QIAGEN IPA to uncover the significance of unique genetic signatures contributing to polygenic autism. Read their paper here.
Pathogenic pathways in early-onset autosomal recessive Parkinson's disease discovered using isogenic human dopaminergic neurons
First author: Tim Ahfeldt
Fascinating research by Dr. T. Ahfeldt and colleagues at the Icahn School of Medicine at Mount Sinai who try to understand the pathogenic pathways involved in early-onset autosomal recessive Parkinson's disease. See how they use QIAGEN IPA to understand the significance of these pathways in causing Parkinson’s in isogenic human pluripotent stem cell lines. Read their research here.
Comparative profiling of the synaptic proteome from Alzheimer’s disease patients with focus on the APOE genotype
First author: Raphael Hesse
Exciting Research by R. Hesse and Colleagues at the University of Edinburgh who start and end with QIAGEN NGS solutions from Sample to Insight. See how the QIAamp DNA Mini Kit helps extract DNA from brain tissue and how QIAGEN IPA helps the team understand the pathways involved in Alzheimer’s disease pathophysiology. Delve into the details in their paper here.
Tuberculous meningitis in children is characterized by compartmentalized immune responses and neural excitotoxicity
First author: Ursula K. Rohlwink
Tuberculous meningitis is the most severe form of TB with a high mortality rate. See how U. Rohlwink and colleagues at the University of Cape Town use QIAGEN IPA to help understand how the disease affects different compartments of the brain differently and cause neurotoxicity. Read the full Nature Communications article here.
De novo variants in exomes of congenital heart disease patients identify risk genes and pathways
First author: Cigdem Sevim Bayrak
Genetically heterogeneous diseases such as congenital heart disease (CHD) are ideally suited for pathway analysis to identify statistically significant key genes and their role in the disease pathogenesis. In this study, Bayrak and colleagues leverage QIAGEN IPA’s ability to take variant data from CHD patients to identify enriched pathways and develop a prioritized list of genes. Read the paper here.
Multi-'omics approach for studying tears in treatment-naïve glaucoma patients
First author: Claudia Rossi
Researchers use QIAGEN IPA to analyze the tears of glaucoma patients in this multi-'omics study aimed at better understanding primary open-angle glaucoma (PAOG). The team performed metabolomics and proteomics analyses to identify potential biomarkers that could help screen for this disease, which is the leading cause of irreversible blindness. Read the paper here.
Discovery and preclinical evaluation of anti-miR-17 oligonucleotide RGLS4326 for the treatment of polycystic kidney disease
First author: Edmund C. Lee
A team from Regulus Therapeutics use QIAGEN IPA to identify an anti-miRNA as a possible therapeutic in the treatment of autosomal dominant polycystic kidney disease (ADPSK), which is generally caused by mutations in PKD1 or PKD2. Discover how the team leveraged QIAGEN IPA’s extensive database of molecular interactions and biological findings to develop putative gene networks and pathways from gene expression data comparing disease data against their anti-microRNA treatment. Read the full Nature Communications paper here.
The circadian clock mutation promotes intestinal dysbiosis
First Author: Robin M. Voigt
Getting a good night’s sleep may be more important than you think. Fascinating research by Dr. R. Voight and colleagues at Rush University looks at the connection between sleep and intestinal dysfunction. Discover how the team uses QIAGEN IPA to tease out the relationship between the circadian rhythm and intestinal hyperpermeability. Read the full paper here.
Compromised metabolic reprogramming is an early indicator of CD8+ T cell dysfunction during chronic Mycobacterium tuberculosis infection
First author: Shannon L Russell
In honor of World Tuberculosis Day, check out this important research from the Africa Health Research Institute (AHRI) in Durban. They use QIAGEN IPA to look at how compromised metabolism can cause subpar T cell immunity against tuberculosis, and how pharmacological agents can help. Read the paper here.
Epigenetics meets proteomics in an epigenome-wide association study with circulating blood plasma protein traits
First author: Shaza B Zaghlool
Fascinating research by Dr. S. Zhaglool and colleagues at Weill-Cornell Medical College in Qatar, where they look at the connection between epigenetics and proteomics in an epigenome-wide study. See how the team uses QIAGEN IPA to understand the connection between DNA methylation and blood circulating proteins involved with inflammation control. Read the full Nature Communications article here.
Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins
First author: Tommy Tsan-Yuk Lam
Coronavirus researchers from Hong Kong University use QIAGEN extraction kits and QIAGEN CLC Genomics Workbench to identify SARS-CoV-2 in Malayan pangolins. Their research helps reveal how pangolins may have facilitated the coronavirus transfer to humans, causing the COVID-19 disease. Read their Nature publication here.
Influenza A viruses are transmitted via the air from the nasal respiratory epithelium of ferrets
First author: Mathilde Richard
In honor of Global Hand Hygiene Day, remember to wash your hands! Check out this paper by researchers at Erasmus University Medical Center, who use QIAGEN CLC Genomics Workbench to investigate how influenza and other respiratory viruses are transmitted from nasal tracts using ferrets as a model. Read their full paper in Nature Communications.
Discovery of a subgenotype of human coronavirus NL63 associated with severe lower respiratory tract infection in China, 2018
First author: Yangun Wang
Learn about the critical research by Dr. Y. Wang and team from Guangzhou Medical University who studied a subgenotype of human coronavirus, NL63. They used QIAGEN CLC Genomics Workbench to investigate how this virus undergoes continuous mutation and has the potential to cause severe lower respiratory tract infection in humans. Read their research here.
Discovery of bat coronaviruses through surveillance and probe capture-based next-generation sequencing
First author: Bei Li
Dr. B. Li and colleagues from Wuhan Institute of Virology have been observing bats for potential coronavirus outbreaks after the SARS and MERS incidents. With the current pandemic, better surveillance practices are necessary to predict and mitigate the emergence of these viruses in humans. See how the team uses QIAGEN CLC Genomics Workbench and QIAGEN extraction kits in a capture-based NGS approach to overcome cost challenges. Discover their research here.
The splicing factor hnRNP M is a critical regulator of innate immune gene expression in macrophages
First author: Kelsi O. West
Great research from Texas A&M HSC where K. West and colleagues look at how pre-mRNA splicing decisions influence or are affected by macrophage activation. See how they use QIAGEN CLC Genomics and QIAGEN IPA to understand this link to the innate immune response in this Cell reports paper.
Microbiota dysbiosis and its pathophysiological significance in bowel obstruction
First author: Shrilakshmi Hedge
April is IBS awareness month. Check out this intriguing research by S. Hegde and colleagues from UTMB who look at how bowel obstruction may cause changes to the gut microbiota composition. See how the team utilizes a complete Sample to Insight approach using QIAGEN's extraction kits for bacterial DNA and RNA and QIAGEN CLC Microbial Genomics Module to identify bacterial species affected
Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signaling
First author: Thomas Aga Legøy
Exciting research from the University of Bergen, where a team uses every part of the QIAGEN RNA-seq solution from Sample to Insight. See how QIAGEN CLC Genomics Workbench, QIAGEN IPA and other QIAGEN products help the team understand the development process of human-induced pluripotent stem cells into pancreatic islet cells. You can access the full Scientific Reports paper here.
Genetic aberrations in iPSCs are introduced by a transient G1/S cell cycle checkpoint deficiency
First author: Ryoko Araki
Crucial research for cell replacement therapy by Dr. R. Araki and colleagues from the National Institute of Radiological Sciences (NIRS) in Japan where they study how point mutations in reprogrammed pluripotent stem cells prevent their therapeutic application. Learn how the team uses QIAGEN CLC Genomics Workbench to understand how a cell cycle checkpoint deficiency causes a cancer-like state in these cells. Read the full Nature Sciences article here.
Immunomodulatory activity of humanized anti–IL-7R monoclonal antibody RN168 in subjects with type 1 diabetes
First author: Kevan C. Herold
Diabetes breakthrough research by Dr. K Herold and team in collaboration with Pfizer at the Yale School of Medicine who used a humanized monoclonal antibody to block cytokine IL-7, which is critical for T cell development and function. Learn how the team used QIAGEN OmicSoft Array Suite to investigate how blocking IL-7 affects immune cells and could help treat diabetes. Get the details by accessing the full paper here.
Nucleus accumbens pathways control cell-specific gene expression in the medial prefrontal cortex
First author: Takatoshi Hikida
Hikida and colleagues at Osaka University try to tease out the molecular connections between different regions of the brain. Learn how the team uses QIAGEN OmicSoft Suite and QIAGEN IPA to understand how knocking down gene expression of D1 and D2 receptors in the neurons of the nucleus accumbens affects gene expression in the neurons of the medial prefrontal cortex. Get the details in this Scientific Reports paper.
Bleomycin hydrolase regulates the release of chemokines important for inflammation and wound healing by keratinocytes
First author: Rebecca Riise
A team at AstraZeneca use QIAGEN OmicSoft DiseaseLand to help them study the role of bleomycin hydrolase in inflammation and wound healing. Find out how they discover a novel role for this cysteine protease in the regulation of cytokine secretion. Read this Scientific Reports paper here.
To request information on the QIAGEN Digital Insight solutions, contact bioinformaticssales@qiagen.com.
We are excited to announce our acquisition N-of-One, Inc., a privately-held U.S. molecular decision support company and pioneer in clinical interpretation services for complex genomic data.
The addition of N-of-One will enable QIAGEN to significantly expand its decision-support solutions while offering a broader range of software, content and service-based solutions. It will also enable QIAGEN to provide customers with greater access to valuable genomic data assets and service offerings.
N-of-One’s technology-enabled, yet human-driven, services and the proprietary MarkerMine™ database are planned to be integrated into QIAGEN Clinical Insight (QCI), enhancing this industry-leading clinical offering with medical interpretation and real-world evidence insights and offering robust decision support in oncology.
The proprietary database, services and processes of N-of-One produce case-specific reports based on data generated with molecular tests, including next-generation sequencing (NGS) technologies, and deliver clinical evidence for biomarkers and a list of therapeutic options for consideration. N-of-One also provides patient-specific clinical trial matching services and a somatic cancer database with more than 125,000 anonymized patient samples. This data will be added to the patient samples currently available in QCI, further increasing QIAGEN’s position in offering by far the largest genomics knowledge base.
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Day One kicked-off with numerous informational sessions, including talks on the role of AI in clinical decision-making, the importance of standardization for reimbursement, and the tremendous potential of genomic profiling in disease prevention, diagnosis, and treatment.
Dan Richards, Vice President of Biomedical Informatics at QIAGEN, spoke about the clinician's current challenge of curating all the evidence he or she needs to confidently sign-off on variant reports before they go to the prescribing physician. QIAGEN Clinical Insight (QCI) and N-of-One were featured as solutions providing options for either in-house curation with tailored workflows or on-demand curation services.
On Tuesday morning, the conversation continued with a panel hosted by Sean Scott, Chief Business Officer of Clinical Genomics and Bioinformatics at QIAGEN, that discussed the emergence and application of real-world evidence in the clinical setting, especially in precision diagnostics and clinical trial protocol design.
The panel consisted of Raju K Pillai, MD, Hematopathologist and Molecular Pathologist at City of Hope National Medical Center, James Hadfield, Director and Principal Diagnostic Scientist at AstraZeneca, and Sheryl Krevsky Elkin, Chief Scientific Officer of N-of-One.
Also on Tuesday morning, Mary Napier, Associate Director of NGS Strategy at QIAGEN, gave a timely talk on how diagnostic labs and pharma companies can gain a comprehensive understanding of tumor mutational burden signature by implementing our new QIAseq Tumor Mutational Burden panel.
What does she mean by "comprehensive"?
Find out here!
Thank you to everyone who visited the QIAGEN booth, we truly enjoyed talking to all of you about the industry challenges, and changes you see happening now and in the future.
See you at our next event:
Advances in Genome Biology and Technology (AGBT) 2019 in Marco Island, Florida!
February 27th - March 2nd
Want to know more about our clinical solutions and real-world evidence?
Stop by booth #1557 at ASH to explore our complete Sample to Insight solution for interrogating 25 genes for variants with known significance to clonal myeloid malignancies.
Coupled with QIAGEN Clinical Insight (QCI) Analyze and Interpret, QIAGEN’s secondary and tertiary NGS analysis platform that provides seamless variant detection, interpretation and reporting based on actionability tiers from the 2017 AMP/ASCO/CAP guidelines, the streamlined solution enables sub-classification and prognostic assessment of hematological malignancies, including leukemia, Non-Hodgkin lymphoma, Hodgkin lymphoma and multiple myeloma.
QCI Interpret for myeloid malignancies offers a specialized workflow that guides prognostication and treatment decisions. With features that incorporate cytogenetic information, World Health Organization (WHO) somatic frequencies, and variant-level prognostic evidence from the QIAGEN Knowledge Base, QCI Interpret helps you assess actionability through multiple levels of information.
Meet and talk with our experts at ASH 18, booth #1557!
Featured Products and Solutions
Check out our Sample to Insight oncohematology solutions here.
See you in San Diego!
Your QIAGEN team
Continuing our series looking at recent publications citing products from QIAGEN Bioinformatics, today we recap several fascinating papers from customers who made use of Ingenuity® Pathway Analysis™ to understand the meaning of changes in gene expression.
Long-Term Mild, rather than Intense, Exercise Enhances Adult Hippocampal Neurogenesis and Greatly Changes the Transcriptomic Profile of the Hippocampus
First author: Koshiro Inoue
In this PLoS One publication, scientists from the University of Tsukuba and other institutes in Japan used rats to understand why mild exercise shows benefits to spatial memory while intense exercise does not. Focusing on a stress biomarker, they performed microarray analysis and found that mild exercise regulated more genes. IPA reported that genes influenced by mild exercise were mostly connected to lipid metabolism and protein synthesis, while intense exercise was linked to a negative effect on hippocampal neuroadaptation.
Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction
First author: Cielito Reyes-Gibby
MD Anderson Cancer Center scientists report in this BMC Systems Biology paper a study of the genetic basis for alcohol, smoking, and opioid addiction. Using IPA, they found candidate genes as well as common pathways; for example, ERK1/2 was connected in all of the addiction networks.
Targeting of multiple oncogenic signaling pathways by Hsp90 inhibitor alone or in combination with berberine for treatment of colorectal cancer
First author: Yen-Hao Su
Published in Biochimica et Biophysica Acta – Molecular Cell Research, this paper demonstrates the use of heat shock protein 90 inhibitors to treat colorectal cancer, also finding that herbal medicine berberine can improve drug sensitivity. A separate data supplement shows results from IPA that contributed to a global molecular network of the significant genes studied.
Macrophage Gene Expression Associated with Remodeling of the Prepartum Rat Cervix: Microarray and Pathway Analyses
First author: Abigail Dobyns
Scientists from Loma Linda University School of Medicine and the University of Edinburgh describe in this PLoS One paper a study of differences in cervical physiology between pregnant and nonpregnant rats. IPA was used to determine that changes in resident macrophages indicate networks of genes that are collectively up- or down-regulated prior to birth. Associated pathways were linked to wound healing and inflammation.
Serial expression analysis of breast tumors during neoadjuvant chemotherapy reveals changes in cell cycle and immune pathways associated with recurrence and response
First authors: Mark Jesus M. Magbanua, Denise M. Wolf, Christina Yau
Scientists from the University of California, San Francisco, published in Breast Cancer Research the results of a breast cancer transcriptome study designed to elucidate response to neoadjuvant chemotherapy. Gene expression data were analyzed with IPA to map genes to pathways and gene ontology groups, revealing that poor response was linked to lower expression of cell cycle inhibitors.
(1) Characterization of a novel chicken muscle disorder through differential gene expression and pathway analysis using RNA-sequencing and (2) Messenger RNA sequencing and pathway analysis provide novel insights into the biological basis of chickens’ feed efficiency
First authors: Marie Mutryn and Nan Zhou
This pair of papers from scientists at the University of Delaware and Maple Leaf Farms are both highly accessed publications in BMC Genomics. The first uses RNA-seq to study an emerging muscle disorder seen recently in chickens. IPA was used to interpret the 1,500 genes differentially expressed between affected and unaffected chickens and resulted in new leads about the biological mechanism behind the disorder. In the second paper, RNA-seq data was generated to help explain the differences between chickens with high or low feed efficiency. The team used IPA for functional and canonical pathways, molecule activity prediction, and analysis of upstream regulators.
To try Ingenuity Pathway Analysis, request a trial.
Did we miss your paper? Please contact us; we would love to feature you!
Over the years, scientists around the world have been using our bioinformatics solutions in their research. We feel privileged that our applications have been assisting scientists in uncovering greater insights, landmark discoveries, and helping further the research that has a direct impact on humanity.
We are starting a new blog series to showcase some of these research papers from QIAGEN Bioinformatics customers. Here, we recap a handful of recent publications that used Ingenuity® Variant Analysis™ to help make sense of complex or hereditary disease phenotypes.
The use of whole-exome sequencing to disentangle complex phenotypes
First author: Hywel J Williams
This paper in the European Journal of Human Genetics comes from University College London’s GOSgene group, including lead author Hywel Williams, one of our featured researchers. Published in June, “The use of whole-exome sequencing to disentangle complex phenotypes” reports the identification of a causative mutation in two children with a previously uncharacterized disease marked by abnormal bronchial widening and peripheral neuropathy. The team used Ingenuity Variant Analysis to study exome sequence data, extracting the variants most likely to be causative. For more information on this paper, click here.
Alternating Hemiplegia of Childhood: Retrospective Genetic Study and Genotype-Phenotype Correlations in 187 Subjects from the US AHCF Registry (PLoS One)
First author: Louis Viollet
In May, a large team of scientists from institutions around the world report an ambitious effort to stratify patients with AHC, a neurological disorder associated with repeated bouts of temporary paralysis. The researchers analyzed mutations and genotype-phenotype correlations in nearly 200 patients, then used Ingenuity Variant Analysis to evaluate mutations detected in sequence data. In addition to finding novel mutations associated with the disorder, the team also determined that one known variant was linked to earlier onset and more severe symptoms, potentially offering a more accurate prognostic indicator (biomarker?) for newly diagnosed patients. You can read more about this work here.
A nonsense mutation of human XRCC4 is associated with adult‐onset progressive encephalocardiomyopathy
First author: Leonardo Bee
In the April issue of EMBO Molecular Medicine, scientists from Italy, the UK, and the US used exome sequencing to study twins with a progressive neurological syndrome; symptoms included cognitive impairment and depression, and both twins also had dilating cardiomyopathy. The publication reports the discovery of a homozygous nucleotide change affecting a protein associated with DNA repair. Ingenuity Variant Analysis was used to zero in on variants in the XRCC4 gene known to be involved in DNA repair. Using Ingenuity Variant Analysis’ Path to Phenotype™ investigators were able to link impairment of the XRCC4 gene to the subject’s observed developmental disorders. To learn more, click here.
Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS
First author: Karyn Meltz Steinberg
In March, scientists from Washington University in St. Louis and the University of Sydney published this paper in Nature Scientific Reports. In it, they describe exome sequencing of 44 trios of patients with ALS and their unaffected parents. Using Ingenuity Variant Analysis as well as other analysis tools, they found a number of homozygous recessive and de novo variants that may be implicated in the disease. “This trio study indicates that rare private recessive variants could be a mechanism underlying some case of sporadic ALS, and that de novo mutations are also likely to play a part in the disease,” the authors report. Learn more about this work here.
Impaired Telomere Maintenance and Decreased Canonical WNT Signaling but Normal Ribosome Biogenesis in Induced Pluripotent Stem Cells from X-Linked Dyskeratosis Congenita Patients
First Author: Bai-Wei Gu
Finally, this May PLoS One publication from researchers at the Children’s Hospital of Philadelphia reports the use of induced pluripotent stem cells from patients with dyskeratosis congenita, a rare syndrome affecting bone marrow. By comparing these cell lines to ones with knocked-in wild type genes correcting the dysfunction, the scientists could analyze changes in telomere activity associated with the syndrome. The team used both Ingenuity Variant Analysis and Ingenuity Pathway Analysis (IPA) to look at mutations and gene expression data, finding decreased WNT signaling in mutant cells. Research paper is available here.
Did we miss your paper? Please contact us; we would love to feature you!
