During our workshop at this year’s AGBT conference, scientist Chris Mason from Weill Cornell Medicine intrigued the audience with a look at several ongoing projects in his lab. Mason is best known in the genomics field for PathoMap, a study of the microbial inhabitants of New York City, and for the NASA twins study, which uses an integrative ’omics approach to analyze the effects of space travel by comparing twin astronauts — one in space and one here on Earth. He has also done considerable RNA methods work and was the first to coin the word “epitranscriptome.” His team has been using QIAGEN tools, and he shared his experiences with our solutions.
One of Mason’s major efforts is MetaSUB, or PathoMap on steroids. For MetaSUB, scientists are analyzing microbial communities in 45 cities around the world, using subways and other urban infrastructure to get a better understanding of how microbes live, move, and pass among humans. Among other things, these studies are shedding light on important traits such as drug resistance; non-resistant and antibiotic-resistant bacteria could be found living in the same subway station in New York. As part of this project, the lab has been using CLC Genomics Workbench and CLC Microbial Genomics Module to analyze 16S rRNA data. Thanks to our recent partnership with CosmosID, our solution will soon have whole metagenome taxonomic analysis capabilities as well. Mason’s team is also working on the Extreme Microbiome Project to conduct similar studies in unusual locations around the world.
A similar approach, including CLC Genomics Workbench, is being used to study previously collected patient samples that were never successfully cultured. Mason said 20 to 30 percent of patients with infectious disease fall into this category — waiting for weeks for culturing of their samples, only to get inconclusive results. This project will sequence 250 such samples and use metagenomics to determine the microbial content.
In separate work, the Mason lab is using RNA-seq to look at differentially expressed genes in clinical samples. One project used the QIAseq Targeted RNA Panels to look at samples from leukemia patients taken at the time of diagnosis and again at relapse. The goal was to find genes consistently dysregulated at relapse — something that previous exome studies had failed to detect. The protocol worked well even with samples as small as 10 nanograms, and the all-in cost of about 50 cents per target gave a good option for quickly and affordably measuring gene expression. This study led to the validation of 104 genes that appear to be a signature of relapse in these patients.
One of the essential features of the QIAseq panels is the ability to add unique molecular identifiers, or barcodes, to each molecule prior to library prep, according to Mason. This step helps scientists detect PCR artifacts and correct ratios later in the workflow, making the process more robust and reliable.
Thanks to Chris Mason for an excellent talk about some of the fascinating research going on in his lab!
Watch the presentation on Targeted RNA sequencing, Urban Metagenomics, and Astronaut Genomics:
https://clcbio.23video.com/v.ihtml/player.html?token=753d018adc990f968d90e9d98b3c65b5&source=embed&photo%5fid=13129410Learn more about our solution for metagenomics
Learn more about QIAseq Targeted RNA Panels
The 17th annual Advances in Genome Biology and Technology meeting was a whirlwind of stellar talks, great posters, and - of course - fabulous parties.
While all the talks were terrific, some really resonated with us. In the opening session, David Haussler made the case for sharing genomic data and rare variant information as much as possible, a message that we loved hearing as co-founders of the Allele Frequency Community. We believe that data sharing is essential for genomic medicine to have the kind of impact we all anticipate. In another talk, Stephan Schuster announced the launch of the GenomeAsia 100K, a new project to sequence 100,000 people in Asia for a better understanding of the genetic diversity in that population. We’re excited to see what this new trove of data contributes to the global genomics community.
Our team was busy during the conference and one of the highlights of our efforts was the lunch workshop featuring Chris Mason from Weill Cornell Medicine. He presented updates on some of his more unique projects, including efforts to sequence pathogens across New York City and more extreme environments and to unravel the biological effects of space travel through a study of twin astronauts. Mason has been beta testing the QIAseq Targeted RNA Panels, and during his presentation, he highlighted the benefits of the panels in delivering digital RNA sequencing for gene expression analysis, and he shared results from that metagenomics work as well. It was a great workshop thanks to Mason and all the attendees who took the time to join us!
We also participated in the software demo session, showcasing our QIAGEN Ingenuity® Variant Analysis™ application for sequencing data interpretation. With the connections to the Ingenuity Knowledge Base and HGMD, it relies on meticulously curated genomic and biological data to help scientists quickly home in on variants of interest to get at the root cause of disease or other phenotypes. We provided software demos at our hospitality suite as well, and we’d like to thank all the people who stopped by.
We had a great time in Orlando and we’re for sure looking forward to AGBT meeting next year – hope to see you there!
Learn more about QIAGEN Ingenuity Variant Analysis
Read more about the new QIAseq Targeted RNA Panels
It's a pleasure to announce an expansion of our portfolio of Sample to Insight solutions for next-generation sequencing (NGS) with the introduction of more than 170 new QIAseq Targeted RNA Panels for gene expression profiling.
Innovative molecular barcode technology and built-in control assays coupled with world-leading RNA isolation technologies, integrated NGS library preparation and Ingenuity® Pathway Analysis™ software, provide a unique solution for efficient RNA sequencing, using any NGS sequencer.
For more information on the QIAseq Targeted RNA Panels, please read the official press release below.
Press release
QIAGEN launches targeted RNA panels for next-generation sequencing
Sample to Insight workflows deliver more efficient, accurate gene expression profiling
Hilden, Germany, and Germantown, Maryland, February 11, 2016 – QIAGEN N.V. (NASDAQ: QGEN; Frankfurt Prime Standard: QIA) today announced the introduction of more than 170 new QIAseq Targeted RNA Panels for gene expression profiling, expanding QIAGEN’s portfolio of Sample to Insight solutions for next-generation sequencing (NGS). The panels enable researchers to select from over 20,000 human genes and lncRNA to survey expression fold changes and discover interactions between genes, cellular phenotypes and disease processes.
The new QIAseq Targeted RNA Panels use innovative molecular barcode technology and built-in control assays to empower researchers with true digital RNA sequencing and accurate gene expression results. Coupled with world-leading RNA isolation technologies, integrated NGS library preparation and Ingenuity® Pathway Analysis™ software, the panels provide a unique Sample to Insight solution for efficient RNA sequencing, using any NGS sequencer. Data analysis and insights are integrated into the QIAseq panels with easy-to-use, comprehensive analysis modules that require no bioinformatics expertise.
“Our QIAseq panels make RNA sequencing more accurate and reproducible with molecular barcode-based sequencing addressing the challenges posed by of low-abundance transcripts, PCR duplicates and amplification bias. These are important new tools for NGS researchers,” said Brad Crutchfield, Senior Vice President and head of QIAGEN’s Life Sciences Business Area. “QIAGEN is leading the way in providing NGS solutions to take labs from Sample to Insight.”
QIAseq Targeted RNA Panels cover an extensive range of disease- and signaling pathway-focused genes, with each panel targeting 100 to 500 genes. The content is based on the latest recommendations from relevant medical and scientific literature. The panels also can be customized to include other genes of clinical and biological interest, with flexibility to analyze from 12 to 1,000 genes simultaneously.
QIAGEN has collaborated with key leader in genomic discovery in the development of the new QIAseq panels to validate product performance in a wide range of applications, including translational and clinical research. Dr. Chris Mason, Associate Professor at Weill Cornell Medicine and one of the early users of QIAseq Targeted RNA Panels, will be presenting application data of the new panels at the Advances in Genome Biology and Technology (AGBT) meeting in Orlando, Fla., on February 11.
QIASeq panel technology combines the flexibility and throughput of NGS with the accuracy of qPCR. The panels use only 20 nanograms of starting RNA material to analyze hundreds of genes. The molecular barcode technology, proprietary assay design algorithms and chemistry provide industry-leading specifications: >97% specificity (reads on target), >95% uniformity (bases covered by at least 20% of the mean coverage depth), and sensitivity to detect 1 RNA copy per cell for QIAseq RNA panels.
QIAGEN serves next-generation sequencing customers worldwide with solutions from Sample to Insight. The company’s sample preparation workflows, including tools for difficult challenges such as single-cell analysis and studies of microbial diversity, are the industry’s most respected. Its Enzymatics products are used in an estimated 80% of all NGS workflows. QIAGEN also provides a portfolio of NGS oncology gene panels compatible with any platform. The GeneReader NGS System was launched in late 2015 as the world's first truly Sample to Insight NGS workflow from primary sample to final report – providing a simpler, more cost-effective way for clinical testing to take advantage of NGS technology and improve outcomes.
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, personalizedhealthcare, 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).
