Ingenuity http://www.ingenuity.com Intuitive web-based applications for quickly analyzing and accurately interpreting the biological meaning in your genomics data Wed, 23 Apr 2014 07:17:58 +0000 en-US hourly 1 http://wordpress.org/?v=3.5.1 AACR 2014, Data Complexity and a Host of Ingenious Genomic Presentationshttp://www.ingenuity.com/blog/events/aacr-2014-data-complexity-host-ingenious-genomic-presentations http://www.ingenuity.com/blog/events/aacr-2014-data-complexity-host-ingenious-genomic-presentations#comments Thu, 17 Apr 2014 21:13:46 +0000 Uma Asthana http://www.ingenuity.com/?p=4106 It was a real pleasure for the QIAGEN Silicon Valley team to attend this year’s annual meeting of the American Association for Cancer Research in San Diego. AACR can always be relied on for top-notch posters and presentations illustrating the … Read More

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It was a real pleasure for the QIAGEN Silicon Valley team to attend this year’s annual meeting of the American Association for Cancer Research in San Diego. AACR can always be relied on for top-notch posters and presentations illustrating the cutting edge in oncology, from basic and translational research all the way through to clinical trials.

A tour of the poster sessions was particularly gratifying for us.  Dozens of AACR posters reported results from Ingenuity Pathway Analysis or Ingenuity Variant Analysis. We are always proud of the scientific tools we’ve built, but there’s nothing quite like seeing really smart researchers deploying them in ways we never even dreamed of – it is a great motivator for the team here to know we are helping to make a contribution to the community.  The conference program reflected a remarkable range of applying genomics and proteomics to cancer research.  There was no shortage of presentations about genomic-driven investigations or patient studies looking at genetic alterations and therapeutic response.  If we needed any evidence, it was clear from AACR that genomic technologies in particular are growing as invaluable tools in the lab and the clinic.

Among so many thought provoking, ingenious sessions, it would be difficult to choose one favorite session, but one great lineup came during a forum entitled “How to Achieve a Cancer Knowledge Commons Database of Cancer Genetics” that was moderated by Tom Hudson of the Ontario Institute for Cancer Research and included David Haussler from the University of California, Santa Cruz, and Gaddy Getz from the Broad Institute of MIT and Harvard.  In a remark that nicely summed up the challenge of genomic data interpretation in cancer research, Hudson said, “Cancer is the high-water mark for genomics due to its complexity; other diseases cost less for data storage and analysis.”

The challenges inherent in building databases, storing the data, and interpreting them is no secret.  It’s something that we’ve been working on for a long time.  One of the primary ways we have been supporting leading-edge cancer researchers is by keeping pace with cancer-related findings in the biomedical literature, and integrating databases of high-quality, relevant, gene-to-disease associations into the Ingenuity Knowledge Base.

AACR-2014-poster

Scientific poster presented at AACR 2014 by Jean-Noel Billaud

Also during AACR2014, Ingenuity Scientist, Jean-Noel Billaud, presented – ‘Sample & Assay Technologies Integrated microRNA and mRNA signature associated with the transition from the locally confined to the metastasized renal cell carcinoma’.  Click here to download the PDF

For those of you who couldn’t be there this year, AACR has posted a nice collection of (free!) presentations from the meeting. Click here to access the presentations.   Many thanks to all of the AACR attendees who took the time to stop by our booth and learn more about Ingenuity Knowledge Base and how to use the Ingenuity product line in cancer research.

What was your experience at AACR 2014 and what was your biggest takeaway?  Share with us in the comments below.

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IU Scientist Deploys IPA in the Fight Against Triple-Negative Breast Cancerhttp://www.ingenuity.com/blog/customer-stories/iu-scientist-deploys-ipa-fight-triple-negative-breast-cancer http://www.ingenuity.com/blog/customer-stories/iu-scientist-deploys-ipa-fight-triple-negative-breast-cancer#comments Mon, 07 Apr 2014 17:30:26 +0000 Uma Asthana http://www.ingenuity.com/?p=4158 At Indiana University, Milan Radovich uses Ingenuity Pathway Analysis from QIAGEN to analyze breast cancer networks based on RNA-seq data. So far, his results promise to improve studies of genetic changes in tumors and may lead to new treatment options … Read More

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At Indiana University, Milan Radovich uses Ingenuity Pathway Analysis from QIAGEN to analyze breast cancer networks based on RNA-seq data. So far, his results promise to improve studies of genetic changes in tumors and may lead to new treatment options for triple-negative patients — and he’s just getting started. 

Cancer Crusader: IU Scientist, Milan Radovich,  Marches Ahead in the Fight Against Triple-Negative Breast Cancer

Radovich uses next-generation sequencing and genomic studies to learn more about  triple-negative breast cancer, which in reality is a catch-all for several different forms of cancer. With RNA and DNA sequencing, he aims to unravel the subtypes included in the triple-negative breast cancer category, and then determine which treatments and therapies will give patients the best possible outcome.

Still early in his career, Radovich has already reported findings that are likely to upend the way breast cancer research is conducted. His groundbreaking discovery that breast tissue taken from healthy patients serves as a better control than adjacent normal tissue from the cancer patient is challenging conventional wisdom in the cancer community.

That critical finding, just one of many coming out of his lab, was powered by IPA. “For so many years, IPA has been the go-to tool for network analysis,” Radovich says. “We primarily use it to do pathway, network, and upstream regulator analysis.” More recently, Radovich and his team have begun to use Ingenuity Variant Analysis as well, and will soon be launching studies designed to take advantage of both applications.

In a recent effort, Radovich and his team made real strides toward identifying genetic elements that are common across the various types of cancer bundled into the triple-negative group. “Out of 14,000 or so expressed genes, we were able to find with Ingenuity about 146 that acted as the common denominator — and a large proportion of them belong to a single network,” he says. With this new information, his lab is now moving ahead with mouse testing of drug targets that might influence that network.

IPA has played a pivotal role in these studies, says Radovich, who uses several bioinformatics tools, many of them developed at universities. “A company can invest in people who can really debug software and commit to quality control,” he says. “What you’re really buying with IPA is a high-quality database and a really well done tool that gives you faster time to results. You’ve got the confidence that the information it generates is right.” IPA features such as Upstream Regulator Analysis, Causal Network Analysis, and Molecular Activity Predictor go well beyond what publicly available tools can offer, he adds.

For more on Milan Radovich’s work on triple-negative cancer, check out this case study.

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Ingenuity Clinical at ACMG 2014http://www.ingenuity.com/blog/events/ingenuity-clinical-at-acmg-2014 http://www.ingenuity.com/blog/events/ingenuity-clinical-at-acmg-2014#comments Wed, 26 Mar 2014 12:56:48 +0000 Uma Asthana http://www.ingenuity.com/?p=4115 With the annual clinical genetics meeting of the American College of Medical Genetics and Genomics taking place in Nashville this week, the QIAGEN Silicon Valley blog staff chatted with Sean Scott who is leading our Ingenuity Clinical initiative.  Sean spends … Read More

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With the annual clinical genetics meeting of the American College of Medical Genetics and Genomics taking place in Nashville this week, the QIAGEN Silicon Valley blog staff chatted with Sean Scott who is leading our Ingenuity Clinical initiative.  Sean spends most of his time talking to clinical geneticists and lab directors to understand their unmet needs and requirements for NGS-based test interpretation and reporting — so we asked him to tell us about the key trends that he sees.  Here’s what he had to say. Sean Scott - General Manager of Clinical Informatics talking about 3 key trends in clinical lab that is addressed by Ingenuity Clinical

Scale Challenges on the Horizon:

As labs migrate from single-gene Sanger sequencing tests to multi-gene panels and exome or whole genome NGS-based tests, labs are inevitably going to encounter increased complexities in tests, phenotypes, and variants that will constrain their ability to effectively interpret and report out on these tests.

Clinical geneticists and lab directors can spend two to three hours, on average, classifying an observed variant in a case.  Particularly tricky variants can take upwards of five to seven hours to assess.  Standard practice is to score and classify observed variants based upon available clinical evidence in scientific literature — combined to some degree with various prediction algorithms — and labs spend a significant amount of time searching for relevant literature and non-published clinical evidence in databases and other sources that are often missing relevant articles and information.

This is an incredibly time-consuming, human-intensive, and error-prone approach. It’s not difficult to extrapolate out on the scale challenges when you run exome- or genome-based tests with today’s mostly manual approach.  Labs will not be able to hire enough clinical geneticists to handle this increased workload.  Next-generation sequencing has tremendous potential in the clinical environment; however, the market for NGS-based clinical testing will not develop quickly unless labs can streamline and scale their test interpretation and reporting workflow from variant annotation through scoring, classification, and reporting. Our goal is to greatly reduce the amount of time it takes an average lab to classify variants as well as to increase confidence in clinical assessment of the observed variant.

There are three basic components to our clinical decision support software:

  • Content manually curated from literature
  • Computational engine for the automated scoring and classification of variants
  • Workflow support for the review, assessment, and reporting of clinically relevant variants

Here at QIAGEN, our mission is to manually curate all relevant human mutation-related clinical evidence and then structure and model it to make it computable for automated variant scoring and classification.  With Ingenuity Clinical, we’ll provide support screening and diagnostic applications as well as hereditary /germline and somatic cancer test indications, where labs want to link clinically relevant somatic variants to approved drug indications and available clinical trials.  We aim to help labs bring more effective tests to market faster, reduce the costs associated with test interpretation, foster professional association standards, and better demonstrate the clinical utility of their lab-developed tests to ensure reasonable levels of reimbursement.

Internal Knowledge Is Key: 

Comprehensive coverage of literature and the clinical evidence embedded within it is a must-have for effective test interpretation.  While 80 percent of variant classification is based on scientific literature, the remaining 20 percent is based on domain expertise within the lab and the case history data these labs have accumulated. That knowledge may not be represented in the scientific literature, but it is just as useful and important as published information.  A lab’s ability to develop an internal case database can be a clear competitive advantage, improving its ability to make assessments and setting it apart from other clinical labs.  Ingenuity Clinical will enable labs to capture this internal information and incorporate it into the underlying clinical evidence to improve their interpretation capabilities.

ACMG Leads in Defining Guidelines: 

ACMG has been very proactive at defining guidelines for variant scoring and classification; they want consistency, quality metrics, and standards across labs. We’ve been working with ACMG to explore how we can help with their educational curricula and how we can help support their guidelines around variant interpretation. We are able to translate those guidelines into bioinformatics terms and implement them in our clinical decision support tool. This will be really important in ensuring standardization and compliance across labs. ACMG is very progressive for trying to drive standards for NGS-based testing, and we are glad to have a good working relationship with the association.

Many thanks to Sean for his insight! Please stop by booth #526 at ACMG to see a demo of Ingenuity Clinical, our newest product that is currently available through an early access program.

 

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Phoenix Here We Come! SOT 2014http://www.ingenuity.com/blog/events/sot-2014 http://www.ingenuity.com/blog/events/sot-2014#comments Sat, 22 Mar 2014 00:17:59 +0000 Uma Asthana http://www.ingenuity.com/?p=4071 Next week we’re headed to Phoenix to mix and mingle with more than 6,500 toxicologists from around the world, who are gathering for the Society of Toxicology (SOT) Annual Meeting (SoT 2014). In addition to the large gathering of toxicologists, there … Read More

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SOT Next week we’re headed to Phoenix to mix and mingle with more than 6,500 toxicologists from around the world, who are gathering for the Society of Toxicology (SOT) Annual Meeting (SoT 2014). In addition to the large gathering of toxicologists, there will be some 350 exhibitors discussing and demonstrating cutting-edge products, services, and technologies. We’ll be holding court in Booth #1121.  We are also hosting a workshop on Monday (3/24) from noon – 1:30 (free lunch!) in the Sheraton Deer Valley Room. We are most excited to discuss the advanced functionality of Ingenuity IPA-Tox, a toxicogenomics focused data analysis capability within IPA that provides focused toxicity and safety assessment information on compounds under investigation.  In addition, two relatively new advanced features of IPA that will be of interest to the SOT crowd are the BioProfiler and Casual Network Analysis tools:

  • BioProfiler: With BioProfiler, you can quickly profile a disease or phenotype by understanding its associated genes and compounds. You can also identify genes known to be causally relevant as potential targets or identify targets of toxicity, associated known drugs, biomarkers and pathways.
  • Causal Network Analysis: This new feature provides a comprehensive approach to identifying upstream molecules that control the expression of the genes in your datasets. Expanding beyond “direct” or “single hop” relationships between upstream regulator and target molecules in the dataset, Causal Networks uncovers regulator networks that connect to the dataset targets.

If you’re headed to Phoenix, SOT 2014 Annual meeting, and would like to meet with us, come by our booth or contact us. We’d be interested to hear about your work and answer any questions you may have about IPA-Tox and how it might help advance your toxicology projects.

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New Scientific Webinar from Nature on Genomicshttp://www.ingenuity.com/blog/science/genomics-webinar-from-nature http://www.ingenuity.com/blog/science/genomics-webinar-from-nature#comments Thu, 20 Mar 2014 16:13:54 +0000 Bryant Macy http://www.ingenuity.com/?p=4045 If you missed the recent QIAGEN sponsored scientific webinar from Nature, it’s now available for viewing on Nature’s website. “Realizing the promise of genomics through rapid innovation in biological analysis and interpretation Discover how intuitive web-based applications can help scientists quickly … Read More

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If you missed the recent QIAGEN sponsored scientific webinar from Nature, it’s now available for viewing on Nature’s website.

“Realizing the promise of genomics through rapid innovation in biological analysis and interpretation

Discover how intuitive web-based applications can help scientists quickly analyze and accurately interpret the biological meaning in their genomic data.

In the last few years, researchers and clinicians have been faced with the challenge of how to effectively sort through and accurately understand the biological meaning from their genomic data.

Now, web-based applications such as QIAGEN’s Ingenuity Platform can be used to better comprehend complex biological systems, answer questions, analyze and interpret data.

In this webinar, the audience discovers how Ingenuity Pathway Analysis (IPA) and Ingenuity Variant Analysis softwares are used by researchers to provide new insight into and quick interpretation of their scientific findings.

The speakers, John Martignetti and Garry Nolan, discuss how these software solutions were applied to their respective research areas to more effectively search, explore, visualize, analyze and interpret biological findings related to genes, proteins and small molecules.”

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For Clinical Labs, Manually Analyzing Variants Remains Painful and Laborioushttp://www.ingenuity.com/blog/products/manual-variant-analysis-clinical-labs http://www.ingenuity.com/blog/products/manual-variant-analysis-clinical-labs#comments Tue, 18 Mar 2014 16:05:13 +0000 Bryant Macy http://www.ingenuity.com/?p=4037 Here at QIAGEN Silicon Valley located in Redwood City, CA where Ingenuity™ web-based apps are developed, we are always working on ways of improving the filtering, prioritizing and interpreting human genetic variation.  To help us understand how this process takes … Read More

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Here at QIAGEN Silicon Valley located in Redwood City, CA where Ingenuity™ web-based apps are developed, we are always working on ways of improving the filtering, prioritizing and interpreting human genetic variation.  To help us understand how this process takes place in clinical labs, we sat down with our resident expert, Tara Love, who previously spent several years at Correlagen and LabCorp as a variant analysis expert.

Tara Love, PhD, Clinical Geneticist, QIAGEN

Tara Love, PhD, Clinical Geneticist, QIAGEN

Tara, who is now a clinical geneticist here at QIAGEN, earned her PhD in genetics from Tufts University and completed a postdoc in cancer genetics at the Dana-Farber Cancer Institute before she moved to commercial genetic testing.

At LabCorp, Tara’s group analyzed variants from Sanger and next-generation sequencing-based gene panels related to hereditary disease that were often requested by doctors looking to confirm a diagnosis. She would receive an annotated packet of information about the sequence results pointing to regions of interest, identified variants, and other relevant data based on a comparison to the human reference genome.

That’s when Tara and her group of analysts would spring into action analyzing variants.  Their first tools were Google and PubMed, which they used to search for the variants to find papers citing them. “My main objective was to gather as much information as possible on each variant,” Tara says. Next, they had to go through each paper that came back to extract useful information: for the patients reported in the paper, which disease did they have? Were they heterozygote or homozygote? “The more evidence we could gather like that could support the idea that it may be a causal or benign variant,” she adds.

A follow-up step was to visit various databases and websites that offer tools to predict the consequence of amino acid changes based on the DNA variant, as well as RNA splicing tools. These tools would provide suggestions on how that change would be expected to affect the entire protein, a clue for Tara and her team as they tried to establish a link between the variant detected and the patient’s phenotype. The drawback: “This task had to be done manually, one at a time, for the different sites where these prediction programs were housed,” Tara says.

Understandably, this hands-on process took quite a bit of time. For genetic variation that could not be found in any papers, Tara says the average time spent per variant was about half an hour.  For variants that were in the literature, the average was more like two hours — with the most time ever spent on a single variant clocking in at 24 hours due to tremendous complexity. To meet clinical lab standards, every analysis had to be confirmed by another person on the team.

The process is “just not scalable” for sequencing exomes or whole genomes, Tara adds. With that much data, she says, clinical lab teams will need a reliable method for rapidly filtering out common variants to help analysts focus on variants that are more likely to be causative. Ideally, that same method would also quickly identify known pathogenic variants. “The goal should be for analysts to only have to score variants of unknown significance,” she says.

The process Tara described is the same whether it’s a major commercial testing lab or a small academic clinical lab. “Analyzing the variants in this way is a necessity whether you’re small or big,” she says. “Everybody who does this sort of testing needs help.”

We have long recognized this need and are working to help clinical geneticists with this challenge. Ingenuity Variant Analysis can already be used to identify variants likely to be drivers of disease. Also, we are developing Ingenuity Clinical, a new clinical decision support product for clinical geneticists and lab directors that aids in the interpretation of variants observed in genomic sequencing data. Ingenuity Clinical aims to provide a seamless easy-to-use solution for the clinical laboratory to rapidly assess the meaning of variants.

If you’ll be attending the American College of Medical Genetics meeting in Nashville this month, we’d be happy to provide a demo of the early-access Ingenuity Clinical decision support system. Please stop by booth #526.

If you won’t be at ACMG, please sign up here to get more information about Ingenuity Clinical.

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AJHG Paper Makes Data Available via Ingenuity Variant Analysis for Interactive Reviewhttp://www.ingenuity.com/blog/customer-stories/cell-paper-makes-data-available-via-ingenuity-variant-analysis-interactive-review http://www.ingenuity.com/blog/customer-stories/cell-paper-makes-data-available-via-ingenuity-variant-analysis-interactive-review#comments Wed, 05 Mar 2014 18:08:36 +0000 Bryant Macy http://www.ingenuity.com/?p=4020 Data sharing is a critical component of any research project, and it’s something we’ve made easier with the interactive Share and Publish features within Ingenuity Variant Analysis. Many research teams have taken advantage of this functionality to share data with … Read More

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Data sharing is a critical component of any research project, and it’s something we’ve made easier with the interactive Share and Publish features within Ingenuity Variant Analysis. Many research teams have taken advantage of this functionality to share data with colleagues or the entire community in the case of papers they’ve submitted for publication. A recent example comes from a team led by Peter Krawitz of the Charité University Medicine in Berlin.

In the American Journal of Human Genetics (AJHG, a Cell Press journal), Krawitz and colleagues recently published an exome study of individuals thought to be harboring mutations affecting proteins involved in the synthesis of glycosylphosphatidylinositol (GPI) anchors. In recent years, mutations in eight genes involved in the GPI-anchor-synthesis pathway have been shown to cause a wide phenotypic spectrum of disorders with intellectual disability and seizures; these range from syndromic forms with characteristic physical malformations and minor anomalies to nonsyndromic forms. Congenital disorders that are caused by an impairment of GPI-anchor synthesis and maturation are now classified as congenital disorders of glycosylation, a diverse class of metabolic diseases.

In the paper, Krawitz and colleagues identified four different mutations in three unrelated families by using independent strategies. In family A, recruited based on the physical features of postnatal microcephaly, a combination of traditional microarray-based autozygosity mapping and exome sequencing identified a missense variant in PGAP3, a gene linked to GPI-anchor maturation, as the only likely candidate. In families B and C, mutations were uncovered in the same gene via a targeted sequencing approach in a cohort of individuals ascertained specifically for intellectual disability and hyperphosphatasia.

In this study, scientists screened rare variants using the interactive filter cascade in Variant Analysis, which helped them to eliminate common and non-deleterious variants. Ultimately, they homed in on variations in the homozygous region of chromosome 17 and predicted that they were deleterious. The data supporting their findings have been made available for review by the authors and can be found online. People wishing to view the analysis can access it with a free Variant Analysis account.

The process of publishing these data required a simple click of the Publish button by the research team. This first step allowed the authors to embargo the custom URL until their manuscript was accepted and published. They were then able to update it with the final title and journal and click “release” once the paper was published. Releasing a data set allows Ingenuity to make the data publicly and perpetually accessible via the custom URL the researchers created. The analysis parameters used in the published study will persist with the data set, meaning each time it is accessed,  users will see how others have analyzed it.

To learn more about the Share and Publish features of Variant Analysis, please visit the product page or contact us.

Paper citation:

Mutations in PGAP3 Impair GPI-Anchor Maturation, Causing a Subtype of Hyperphosphatasia with Mental Retardation

The American Journal of Human Genetics – 6 February 2014 (Vol. 94, Issue 2, pp. 278-287)

Malcolm F. Howard, Yoshiko Murakami, Alistair T. Pagnamenta, Cornelia Daumer-Haas, Björn Fischer, Jochen Hecht, David A. Keays, Samantha J.L. Knight, Uwe Kölsch, Ulrike Krüger, Steffen Leiz, Yusuke Maeda, Daphne Mitchell, Stefan Mundlos, John A. Phillips, Peter N. Robinson, Usha Kini, Jenny C. Taylor, Denise Horn, Taroh Kinoshita, Peter M. Krawitz

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Interpretation Was in the Limelight at AGBThttp://www.ingenuity.com/blog/events/interpretation-limelight-agbt http://www.ingenuity.com/blog/events/interpretation-limelight-agbt#comments Wed, 19 Feb 2014 22:15:40 +0000 Bryant Macy http://www.ingenuity.com/?p=3974 We enjoy heading to Marco Island every year for the Advances in Genome Biology and Technology meeting, so it was no surprise that we had a great time there this year. But the AGBT organizers added something to make the … Read More

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We enjoy heading to Marco Island every year for the Advances in Genome Biology and Technology meeting, so it was no surprise that we had a great time there this year. But the AGBT organizers added something to make the event even more exciting for us: software demonstrations!

This year for the first time, AGBT attendees got to sit down with various software developers and take their tools for a test drive. We were delighted to participate in this event and had fun talking to so many people who wanted to see what QIAGEN’s Ingenuity tools could offer their research pipelines.

Indeed, sequence data interpretation drove a key part of the conversation at AGBT this year — a sea change for a meeting that has always been so focused on the nuts-and-bolts sequencing technologies. Many of the talks included descriptions of new analysis tools being developed or pleas for better applications, particularly for scientists who have to share reports with clinicians. As AGBT presentations center more and more on clinical applications of NGS data, this need for high-quality interpretation and easy-to-use reporting tools will only grow.

AGBT always kicks off community discussions that last well into the year, and we are glad to join in this important focus on accurate and efficient interpretation of genetic data. For anyone who didn’t get a chance to attend the software demo session, try the latest free previews of Variant Analysis for DNA-seq or IPA (or iReport) for RNA-seq data analysis and interpretation.

Also, thanks to all the conference attendees who made our time in Marco Island so memorable!

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