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:

Learn more about our solution for metagenomics
Learn more about QIAseq Targeted RNA Panels

We're excited to announce new partnerships to expand the use of our bioinformatics solutions for microbiome, metagenomics and other applications.

We've signed an agreement with genomics big data company CosmosID, Inc. to allow our users of CLC Genomics Workbench to access and integrate CosmosID’s metagenomics analysis platform. Furthermore, an agreement with Trigent Solutions Inc. enables streamlined access to our bioinformatics solutions for centers of the U.S. Food and Drug Administration.

For more information on the partnerships, please read the official press release below.

Press release

New agreements underscore QIAGEN’s leadership in bioinformatics

FDA centers and researchers gain access to QIAGEN’s enhanced solutions for applications including microbial and microbiome analysis

Hilden, Germany, and Aarhus, Denmark, February 2, 2016 – QIAGEN N.V. (NASDAQ: QGEN; Frankfurt Prime Standard: QIA) today announced new partnerships to enhance the profile and expand the use of its market leading bioinformatics solutions for microbiome, metagenomics and other applications.

QIAGEN Bioinformatics signed an agreement with genomics big data company CosmosID, Inc. to allow users of QIAGEN’s CLC Genomics Workbench to access and integrate CosmosID’s metagenomics analysis platform into their QIAGEN bioinformatics platform. CosmosID’s platform allows users to identify and characterize microbial communities from whole genome shotgun data and to determine their relative abundance. The new plug-in expands the range of metagenomic and microbiome applications supported by QIAGEN’s microbial genomics solution enabling researchers in fields such as infectious disease, animal health, agriculture, environmental and food safety to use shotgun metagenomics analysis for routine testing employing next-generation sequencing.

Metagenomics and microbiome research, which look at the impact of microbial diversity on environment and human health, are growing very rapidly. At the end of 2015, QIAGEN acquired MO BIO Laboratories, Inc., a leader in sample technologies for microbiomes.

Furthermore, QIAGEN announced a contract awarded to its partner Trigent Solutions Inc. that enables streamlined access to QIAGEN’s bioinformatics solutions for centers of the U.S. Food and Drug Administration. Products available to FDA centers include software for infectious disease research and outbreak analysis, such as CLC Genomics Workbench, CLC Microbial Genomics Module, CLC Genome Finishing Module, as well as solutions in human genomics, such as Biomedical Genomics Workbench, Ingenuity^® Variant Analysis^TM, and Ingenuity^® Pathway Analysis^TM.

The contract expands QIAGEN’s long-standing bioinformatics relationship with the FDA from one Center of Excellence to seven centers, spanning human health and food safety applications. The products and services provided to the FDA also enable uploading and sharing of public health data with U.S. and international institutions via the National Center for Biotechnology Information (NCBI) SRA database of biological sequencing data to combat infectious outbreaks both on national and global levels.

“We are excited about the latest agreements”, said Dr. Laura Furmanski, Senior Vice President and head of QIAGEN’s Bioinformatics Business Area. “They are leveraging the reach and profile of our leading portfolio of bioinformatics solutions that enable a growing number of customers to analyze vast amounts of data from next-generation sequencing – and to arrive at actionable insights.”

To learn more about QIAGEN’s bioinformatics business, please visit https://digitalinsights.qiagen.com.

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 https://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).