Ingenuity http://www.ingenuity.com Intuitive web-based applications for quickly analyzing and accurately interpreting the biological meaning in your genomics data Mon, 29 Jun 2015 04:28:56 +0000 en-US hourly 1 http://wordpress.org/?v=4.0.5 RNA-Seq Summit: Unlocking the transcriptome in Bostonhttp://www.ingenuity.com/blog/events/rna-seq-summit-unlocking-transcriptome-boston http://www.ingenuity.com/blog/events/rna-seq-summit-unlocking-transcriptome-boston#comments Tue, 23 Jun 2015 16:36:34 +0000 http://www.ingenuity.com/?p=6176 As we ease into summer, we are looking forward to getting together with the RNA-seq research community at the 3rd annual Hanson Wade RNASeq Summit 2015 in Boston later this month (June 23-25) . We are proud sponsors of this relatively new … Read More

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As we ease into summer, we are looking forward to getting together with the RNA-seq research community at the 3rd annual Hanson Wade RNASeq Summit 2015 in Boston later this month (June 23-25) . We are proud sponsors of this relatively new meeting which brings together researchers from around the world to share their experience and the latest science in the analysis and application of RNA-seq in basic research, drug discovery and development.

RNA-seq offers significant advantages over existing high throughput methods for gene expression analysis, including more precise measurement of transcript levels, the ability to distinguish different isoforms, and a broader dynamic range to quantify gene expression levels.  It is precisely these advantages, however, that make interpretation of RNA-seq data a daunting task.

QIAGEN’s portfolio of bioinformatics solutions offers powerful tools to accurately interpret and distill large RNA-Seq data sets. QIAGEN’s Ingenuity Pathway Analysis (IPA), for example, enables you to quickly identify significant differentially expressed isoforms between condition and control samples, and interpret the impact of expression changes in the context of biological processes, disease and cellular phenotypes, and molecular interactions.

For those of you who will be at this year’s meeting, Senior QIAGEN Field Application Scientist Sean Prince will discuss these solutions at the RNA-Seq Summit in a presentation on Wednesday (June 24) and a RNASeq workshop on Thursday (June 25):

Wednesday, June 24

  • 2:10pm ET: Application of the QIAGEN Bioinformatics Complete RNA-Seq workflow in a West Nile Virus infection Case Study

Thursday June 25

  • 2:00pm ET: Maximize Your Biological Interpretations With QIAGEN Bioinformatics Complete RNA-Seq Workflow

You can register for the workshop by clicking below:

Register

Can’t make it to the RNA-Seq Summit this year? You can click on the link to download our West Nile Virus Case Study Poster.

Our blog and website also have a number of informative RNA-seq-specific resources where you can learn more about our portfolio of products and how researchers are using them to investigate things like  West Nile Virus infection and breast cancer networks.

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At Stanford Discovery Walk, IPA for Posterityhttp://www.ingenuity.com/blog/news/stanford-discovery-walk-ipa-posterity http://www.ingenuity.com/blog/news/stanford-discovery-walk-ipa-posterity#comments Tue, 09 Jun 2015 16:14:31 +0000 http://www.ingenuity.com/?p=6118 Stanford University is renowned for its beautiful campus, but it wasn’t the lovely foliage or grand architecture that had us inspired the other day. On a recent visit to campus, we spotted odes to our very own application, images from … Read More

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Stanford Discovery Walk, IPA in Posterity!

Stanford University is renowned for its beautiful campus, but it wasn’t the lovely foliage or grand architecture that had us inspired the other day. On a recent visit to campus, we spotted odes to our very own application, images from Ingenuity Pathway Analysis (IPA), etched into granite!

A few years ago, Stanford unveiled the Discovery Walk, a series of artistic renderings that pay tribute to important biomedical advances from the past 150 years. These black granite panels cover a row of benches that make up a walkway about the size of a city block. Among the notable advances are an fMRI brain scan, a DNA double helix, and a leukemia cell seen through a microscope.

Stanford Discovery Walk, IPA in Posterity!

But the one we’re especially proud of is a depiction of an IPA network derived from gene expression effects from anti-CD3 therapy. Permanently preserved in stone! That’s really cool.

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And just around the corner, we found an etching from a different Stanford lab highlighting the role of MYC as a key transcription factor in a cellular network.

Stanford Discovery Walk, IPA in Posterity!

To help you locate the Discovery Walk at Stanford University, here is the map:

Discovery_Walk_map

Next time you happen to be at Stanford, we hope you stop to check it out, take a picture with you in the frame and share it with us! If you have to elbow some people out of the way to get a glimpse, don’t worry about it — it’s probably just the QIAGEN Bioinformatics team gawking at this great honor!

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New Product – QIAGEN® Clinical Insight Launched!http://www.ingenuity.com/blog/news/new-product-qiagen-clinical-insight-launched http://www.ingenuity.com/blog/news/new-product-qiagen-clinical-insight-launched#comments Thu, 04 Jun 2015 16:47:49 +0000 http://www.ingenuity.com/?p=6103 We are very pleased to announce the general availability of QIAGEN® Clinical Insight, the most comprehensive, scalable bioinformatics platform for clinical labs interpreting and reporting on genomic variants identified using next-generation sequencing. The first two supported applications are in oncology, … Read More

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We are very pleased to announce the general availability of QIAGEN® Clinical Insight, the most comprehensive, scalable bioinformatics platform for clinical labs interpreting and reporting on genomic variants identified using next-generation sequencing. The first two supported applications are in oncology, for somatic and hereditary cancer testing.

The secure QCI web application rapidly classifies variants, identifies treatment options and performs geographical clinical trial matching. The platform’s interpretation tools are supported by a unique evidence-based approach, which evaluates genomic variants in the context of published biomedical literature, professional association guidelines, publicly available databases and annotations, drug labels and clinical trials. QCI also provides access to the Allele Frequency Community, the world’s largest repository of ancestral and ethnic diversity data.

In creating this platform, we gathered input from more than 100 clinical testing labs and worked with 50 of them to evaluate the QCI content and software in their workflows for laboratory-developed tests. One of the clinical collaborators that evaluated QCI was Dr. Madhuri Hegde, Professor of Human Genetics at the Emory University School of Medicine and Executive Director of the Emory Genetics Laboratory (EGL):

“Clinical labs developing and offering NGS-based clinical tests are confronted with two key challenges: the complexity of translating genetic information into actionable insights for ordering physicians and the time and effort it takes to interpret and report clinically relevant variants. Through its collaboration with EGL and other leading labs on the design and validation of its new QCI offering, QIAGEN has developed a deep understanding of these unmet needs. QCI supports both germline and somatic test indication which is important to labs offering diverse test indications. And it provides full platform and assay agnostic interpretation and reporting workflow support which enables clinical testing labs to reduce time and cost associated with NGS based testing.”

QCI is the latest addition to QIAGEN’s portfolio of bioinformatics solutions that are driving the growth of next-generation sequencing for clinical research and diagnostic labs. For more information on QCI visit our webpage.

Please sign up if you are interested in learning more about QIAGEN Clinical Insight:

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Dartmouth Bioinformatician Uses Dual Stressors, IPA for New Findings in Evolutionhttp://www.ingenuity.com/blog/customer-stories/dartmouth-bioinformatician-uses-dual-stressors-ipa-new-findings-evolution http://www.ingenuity.com/blog/customer-stories/dartmouth-bioinformatician-uses-dual-stressors-ipa-new-findings-evolution#comments Fri, 29 May 2015 15:30:38 +0000 http://www.ingenuity.com/?p=6083 New research from Thomas Hampton, a senior bioinformatics analyst at the Geisel School of Medicine at Dartmouth College, and collaborators used a dual-stressor system to discover important aspects of evolution in a fish with unique phenotypic plasticity. QIAGEN’s Ingenuity Pathway … Read More

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Thomas Hampton, Senior Bioinformatics Analyst, Geisel School of Medicine - Dartmouth College

Thomas Hampton, Senior Bioinformatics Analyst, Geisel School of Medicine – Dartmouth College

New research from Thomas Hampton, a senior bioinformatics analyst at the Geisel School of Medicine at Dartmouth College, and collaborators used a dual-stressor system to discover important aspects of evolution in a fish with unique phenotypic plasticity. QIAGEN’s Ingenuity Pathway Analysis (IPA) helped them make the connection.

In the study, the team collaborators used IPA to characterize genes underlying an important biological mechanism in Fundulus heteroclitus, a type of killifish. Their results were published in Molecular Biology and Evolution in a paper entitled “Natural Selection Canalizes Expression Variation of Environmentally Induced Plasticity-Enabling Genes.”

The paper sheds light on a poorly understood but critical trait in killifish, and would not have been possible without conducting a dual-stressor study, Hampton says. Such studies are rare in science because of concerns about confounding variability, but Hampton and his team were able to carefully craft their experiments and use IPA to determine the meaning of the gene expression data they generated. The result is a new look at the scale of evolution in killifish, which may contribute to a better appreciation of how evolution functions in other organisms too.

Hampton and his collaborators, including Joseph Shaw at Indiana University and John Colbourne at the University of Birmingham, chose to study killifish for a most unusual trait: the fish is equally happy in fresh water or in salt water, due to its ability to change the morphology and function of its gills as needed to adjust for salinity levels in the water. “This is really special. They can remodel their gills on a week-to-week basis,” Hampton says. “This would be like if anytime we needed to fly, we just sprouted a pair of wings.”

During the experiment, the team interrogated gene expression with custom arrays to reveal what was going on during gill remodeling. But in this case, expression analysis was not terribly insightful. “The kinds of genes engaged in this plasticity response were not that interesting, viewed from a distance,” Hampton says. “It looks like a bunch of different genes that are not related to anything that makes a tremendous amount of sense.”

Fortunately, the team used IPA to dig deeper, looking at the genes on a network level. “We found that the genes that facilitate phenotypic plasticity seem to be less connected to other genes, almost as if they’re in their own little world, ready to be activated in one direction or another to facilitate this process without a lot of cross-talk from other systems,” Hampton says. “That’s what Ingenuity helped us figure out. It’s an interesting result that suggests that evolution has acted not just on genes but on gene networks to make phenotypic plasticity happen.”

For more information on the study and on how Hampton uses IPA, check out the full case study here.

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BGI will offer QIAGEN’s Ingenuity Variant Analysis to 10,000-plus customershttp://www.ingenuity.com/blog/news/bgi-will-offer-qiagens-ingenuity-variant-analysis-10000-plus-customers http://www.ingenuity.com/blog/news/bgi-will-offer-qiagens-ingenuity-variant-analysis-10000-plus-customers#comments Wed, 27 May 2015 15:51:27 +0000 http://www.ingenuity.com/?p=6068 We wanted to share some exciting news with you from earlier this month in case you might have missed it.  On May 5th we announced the expansion of our collaboration with BGI, the world’s largest genomics organization.  Moving forward, all of … Read More

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BGI+IVAWe wanted to share some exciting news with you from earlier this month in case you might have missed it.  On May 5th we announced the expansion of our collaboration with BGI, the world’s largest genomics organization.  Moving forward, all of BGI’s customers will receive sequencing data generated from their samples through Ingenuity Variant Analysis’ secure, web-based platform for analysis and interpretation of sequencing data.

This is an exciting news that makes Variant Analysis initially available to BGI’s customers in China, Hong Kong and Taiwan, with plans to expand to other regions throughout the year. BGI collaborates with more than 10,000 organizations and 30,000 partners worldwide, providing sequencing services for thousands of research projects, including large-scale genome initiatives.

Yingrui Li, Chief Scientist of BGI, said of the news: “We welcome this opportunity to expand our relationship with QIAGEN for the benefit of BGI collaborators around the world. Coupling BGI’s world-class sequencing with the deep bioinformatics of Ingenuity Variant Analysis will give researchers an enhanced, integrated way to seamlessly move quickly from raw data to valuable insights.”

We are honored that Variant Analysis continues to be recognized by the world’s leading sequencing service providers as a value-added data interpretation solution for their customers. In March 2015, QIAGEN also announced a reseller agreement with GATC Biotech, a leading European provider of DNA and RNA sequencing, to provide access to Ingenuity Variant Analysis as part of GATC’s sequencing services.

Please visit our website for more information on Ingenuity Variant Analysis.  Please visit www.genomics.cn for more information on BGI’s services.

 

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Conference Presentation: A Systems Biology Approach to Viral Research (West Nile Virus Case Study)http://www.ingenuity.com/blog/webinar/conference-presentation-systems-biology-approach-viral-research-west-nile-virus-case-study http://www.ingenuity.com/blog/webinar/conference-presentation-systems-biology-approach-viral-research-west-nile-virus-case-study#comments Tue, 28 Apr 2015 16:13:16 +0000 http://www.ingenuity.com/?p=5935 QIAGEN scientists, Jean-Noel Billaud, Ph.D. and Stuart Tugendreich, Ph.D., recently completed a demonstration project on how Biomedical Genomics Workbench and Ingenuity Pathway Analysis (IPA) can be used together to create a systems biology approach to exploring host response in West … Read More

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West Nile Virus Poster FINAL

Understanding West Nile Virus Infection: The QIAGEN Bioinformatics Solution: Biomedical Genomics Workbench + Ingenuity Pathway Analysis (IPA).

QIAGEN scientists, Jean-Noel Billaud, Ph.D. and Stuart Tugendreich, Ph.D., recently completed a demonstration project on how Biomedical Genomics Workbench and Ingenuity Pathway Analysis (IPA) can be used together to create a systems biology approach to exploring host response in West Nile Virus infection. Their findings were presented by Dr. Billaud at the 2015 Molecular Med Tri-Con meeting during the Genome and Transcriptome Analysis track.

West Nile Virus is a neurotropic virus that is transmitted via mosquito bite. Infection is a worldwide health issue and the most common cause of epidemic viral encephalitis in North America. Despite the potentially devastating health impacts of infection, its viral pathogenesis is still incompletely understood and there are no approved therapies for use in humans.

Utilizing RNA-Seq data generated by researchers at Yale University,[1] Billaud and Tugendreich evaluated gene pathways and cellular response to explore the difference in immune response between susceptible and resistant individuals.

One of the exciting hypotheses they generated was around the role that the CLEC7A gene plays in the progression of life-threatening encephalitis. This gene has been described as a host susceptibility factor required by West Nile Virus, but there are still questions about its larger role. Using the Molecule Activity Predictor (MAP) tool within IPA, for example, they were able to interrogate sub-networks and canonical pathways associated with CLEC7A and generate scenarios by selecting a molecule of interest, indicating up or down regulation, and simulating directional consequences of downstream molecules and the inferred activity upstream in the network or pathway.

“One of the things we were able to demonstrate was that if you can inhibit CLEC7A you could potentially reduce the risk of West Nile Virus-associated encephalitis. There is much more testing and validation that has to be done, but it’s the kind of finding that would be compelling enough to warrant further investigation of this gene as a therapeutic target,” said Tugendreich.

Watch a recording from recent webinar for more information on this study: IPA Webinar West Nile Virus – Leveraging IPA and RNA-seq Data For Infectious Disease Research.


 

[1] Qian F, et al. Identification of Genes Critical for Resistance to Infection by West Nile Virus Using RNA-Seq Analysis. Viruses. 2013 Jul; 5(7): 1664–1681. Published online 2013 Jul 8. doi:  10.3390/v5071664. Accessed at: http://www.mdpi.com/1999-4915/5/7/1664 .

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TGF-β3 Protein Structure Demonstrates Variant-to-3D Structure Functionhttp://www.ingenuity.com/blog/customer-stories/tgf-%ce%b23-protein-structure-demonstrates-variant-3d-structure-function http://www.ingenuity.com/blog/customer-stories/tgf-%ce%b23-protein-structure-demonstrates-variant-3d-structure-function#comments Tue, 28 Apr 2015 05:26:32 +0000 http://www.ingenuity.com/?p=6008 A new functionality in QIAGEN® Biomedical Genomics Workbench can be used in conjunction with Ingenuity® Variant Analysis™ to identify causal variants, which disrupt protein/drug binding or have an impact on the protein 3D structure.  The user gains an insight not … Read More

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A new functionality in QIAGEN® Biomedical Genomics Workbench can be used in conjunction with Ingenuity® Variant Analysis to identify causal variants, which disrupt protein/drug binding or have an impact on the protein 3D structure.  The user gains an insight not only if a variant is probably causal, but also why.

The new tool, Link Variant to 3D Protein Structure, together with the new protein 3D viewer, offers a quick method for investigating the likely impact of a putative causal variant on the protein 3D structure. For each variant, the Biomedical Genomics Workbench combs through known protein structure information in the PDB database to predict the effect on structure, even for novel mutations. The tool also allows users to generate hypotheses for the effect of a mutation based on what part of the protein it changes. By eliminating the need to query a publicly available protein structure database for each mutation and then build a homology model, this tool dramatically accelerates a user’s ability to find the likely structural effect of DNA and RNA changes.

To show its effectiveness on a rare disease case, we went back to one of our favorite Ingenuity Variant Analysis data sets, the TGF-β3 data set generated by Dr. Hugh Rienhoff in his analysis of his daughter’s DNA. We loaded the causative mutation into Biomedical Genomics Workbench and used the new functionality to find out why the mutation in TGF- β3 is likely the disease causing one. In less than two minutes, we got the protein structure, which clearly illustrates how the mutation induces an amino acid change that breaks a disulfide bond and clashes with the surrounding protein structure. This suggests that this protein, which is probably non-functional, is damaged in a region required in the assembly of the larger protein complex.

These findings were experimentally validated by Dr. Rienhoff.

Picture from 3D Viewer in BxGWB

Pictures from the 3D viewer in the workbench. The protein chain affected by the mutation is shown in blue ribbon representation.

The leftmost picture shows the protein reference structure. Three disulfide bridges establishing a highly structured part of the protein are shown in sticks, and the cysteine being mutated is labeled (Cys409).

The rightmost picture shows the mutated amino acid (Tyr409) in space-filling, to illustrate how the increased size of the side chain will not fit inside the rigid structure. The amino acid is colored to show clashing atoms in red.

Picture2 from 3D Viewer in BxGWB

Picture from the 3D viewer in the workbench.

The protein chain affected by the mutation is shown in ribbon representation and the amino acid (Tyr409) resulting from the mutation is shown in ball-n-sticks and colored to show clashing atoms in red. Other protein chains from the larger protein complex are shown as molecular surfaces (blue and yellow). The mutation will disrupt an otherwise very stable part of the protein, forming an interface to the protein chain shown in blue surface.

You can read more about Dr. Rienhoff’s case study in our Featured Researcher section.

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Time to celebrate the Double Helix – DNA Day!http://www.ingenuity.com/blog/science/time-celebrate-double-helix-dna-day http://www.ingenuity.com/blog/science/time-celebrate-double-helix-dna-day#comments Wed, 22 Apr 2015 16:15:57 +0000 http://www.ingenuity.com/?p=5990 This year’s DNA Day celebration is happening a day early, on April 24th, presumably because this is one of the few holidays best celebrated with colleagues. Here at QIAGEN Bioinformatics, we’ll be raising a glass to the team that determined … Read More

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dnaday2015

This year’s DNA Day celebration is happening a day early, on April 24th, presumably because this is one of the few holidays best celebrated with colleagues. Here at QIAGEN Bioinformatics, we’ll be raising a glass to the team that determined the structure of DNA 62 years ago as well as to the massive global collaboration of scientists responsible for completing the first draft of the human genome a dozen years ago.

We’re thrilled that the National Human Genome Research Institute has continued annual celebrations for DNA Day, which was first designated in the U.S. as a one-time holiday back in 2003. This year, NHGRI highlighted a national Pinterest challenge to engage K-12 students in learning about DNA. Meanwhile, the American Society of Human Genetics is hosting its tenth annual essay contest for DNA Day, open to students in grades 9-12.

In the corridors of QIAGEN Bioinformatics, we like to think we celebrate DNA every day. Our applications and platforms are geared toward helping scientists glean more information from each genome they study, from filtering and interpreting genetic variants to predicting how those DNA changes might affect protein structure. As DNA data becomes increasingly important for patient care, we strive to provide extra layer of knowledge  to help scientists and clinicians find meaningful answers more quickly. You can read some of our customer case studies in our Featured Researcher section. Considering that the first snippets of DNA were sequenced with the most rudimentary tools only 40 years ago, it’s quite remarkable how much the community is achieving with DNA studies today. From accurately linking disease risk to genetic variants to understanding elements like epigenetics, advances and knowledge are developing at a breakneck pace. Recent innovations in gene and genome editing have been downright extraordinary. Truly, we’re witnessing one of the most fascinating revolutions humans have ever experienced.

For our part, we’ll keep pushing the boundaries of what’s possible with automated interpretation and analysis based on elegantly curated data and knowledge. Given how rapidly the field is moving, we can’t wait to see what’s new and exciting on DNA Day next year! Share in the comments, how you will be celebrating The DNA Day!

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