Do you spend hours cleaning up and integrating ‘omics data, yet still feel like you are drowning in it?

‘Omics data is a powerful resource to help drive innovation in biomarker and target discovery. If you work in drug development, you probably explore potential therapies by using ‘omics data to find new targets and indications. Yet it can be daunting to process, integrate and clean the data to make it meaningful. You’re probably working with data from both public portals and your internally-generated sources, each with its own sets of metadata and respective vocabularies. Perhaps it comes from several different drug discovery programs representing various diseases. The sheer volume and heterogeneity within ‘omics datasets can create a discouraging barrier to drawing meaningful conclusions.

Boost your bioinformatics capabilities

Have you ever thought of seeking the expertise and services of an experienced bioinformatics team to extend and speed up your ‘omics data processing capabilities?

QIAGEN Discovery Bioinformatics Services has the tools, knowledge and resources to help you quickly unravel the biology hidden in your ‘omics data. We supplement your workforce with experts from our bioinformatics team, including Ph.D.-qualified scientists, developers and project managers to provide a customized solution for your project. We do everything from secondary analysis services to in-depth analysis of biological data. We also take on high-quality content curation of literature, datasets and pathways. We can even build custom databases, which are specific collections of integrated ‘omics data with manually curated metadata.

Our services team helps biologists and bioinformaticians like you quickly answer questions relevant to your biomarker and target discovery projects. We do this by using our state-of-the-art software tools and high-quality manually curated content to query your ‘omics data to help answer your hypothesis-generating questions, such as:

• What is the expression pattern of my target(s)?
• In what tissue or disease is my target differentially expressed?
• What is the expression signature for my disease state?
• What are the different cell types across datasets, and how abundant are each one?
• What is the differential gene expression of monocytes in disease vs. control samples?

Once we run these queries, we can perform deeper meta-analyses on data collections to help you make more accurate hypotheses based on the biological context. Our queries and analyses save you countless hours organizing and visualizing internal pipelines and results, taking you directly down the biological path that makes most sense.

Example service project

A typical transcriptomic project that we take on is processing and storing bulk RNA-seq datasets, including single-cell RNA-seq. Sound familiar? Our QIAGEN Discovery Bioinformatics Services team will create a customized unified pipeline script to process your data and store it in a database framework. We pay special attention to statistical analysis, which can often be tricky when working with transcriptomic data. That’s because this type of data is often generated from heterogeneous samples composed of multiple cell types, and the counts data from a sample represents the average gene expression across all cell types. This heterogeneity is a major hurdle in statistical analysis. Differences in cell type proportions may prevent or bias the detection of cell type-specific transcriptional programs. To manage such challenges, our services team:

• Performs deconvolution of different cell types in the datasets and stores cell type abundance at sample-level resolution
• Provides a framework to run the samples in parallel using Amazon workspace to store the data
• Manually curates the metadata with controlled vocabularies in order to query and return quality-controlled samples and data
• Adds statistical comparisons using the curated metadata

Figure 1. Workflow for processing bulk RNA-seq data.

Quickly get the output you need

On all our projects, we work with you to determine the output and deliverables that best fit your needs. A typical example of what we provide for bulk RNA-seq data processing and storing is:

• A customized integrated 'omics data collection based on your internal data (‘internal Land’)
• A centralized database that biologists use for disease-focused queries, sources from your internal Land
• Custom scripts that enable analyses of both human and non-human data
• Combined information from multiple studies into a unified picture of biomarkers and disease signatures to help validate hypotheses
• Differential gene expression analysis to assess changes of candidate target gene related to a disease
• Signature-based analysis to gain insights into which diseases are relevant for target genes
• Assessment of relative cell type (cell state) abundance at sample-level resolution for multiple tissue types
• Investigation of differentially expressed genes and signatures at cell-type resolution

By working with QIAGEN Discovery Bioinformatics Services on projects like bulk RNA-seq data processing, you'll save time and increase accuracy. We help you quickly prioritize drug targets, biomarkers and compounds so you can readily gain a more robust and insightful understanding of complex diseases, to drive your next discovery.

Would you like to reduce the burden of working with ‘omics data to more quickly reach your next biomarker or target discovery? Could you use support with RNA-seq data processing and analysis? Let QIAGEN Discovery Bioinformatics Services lend a helping hand. Learn more about our range of bioinformatics services to extend and scale your in-house resources with our expertise and tailored bioinformatics services. Contact us today at QDIservices@qiagen.com to get your next project started. Together, we'll tame the 'omics data beast.

Need to expand your bioinformatics and curation expertise to harness the power of ‘omics data? Let QIAGEN Discovery Bioinformatics Services help.

Not all research teams have the time and in-house expertise to leverage the power of complex and high-volume ‘omics data, and many organizations lack workforce resources or server and infrastructure support. These limitations create bottlenecks, leaving research goals that don’t advance.

QIAGEN Discovery Bioinformatics Services can reduce the burden of broadening your in-house bioinformatics capabilities. We offer complete Sample to Insight workflows and tools which work together to reveal deep insights into your biological questions. Our team uses best-in-class bioinformatics tools and solutions from QIAGEN Digital Insights to support your projects and goals, whatever your needs may be.

Discover the benefits of partnering with a leading provider of bioinformatics tools and services for discovery research scientists:

• Access the QIAGEN Digital Insights team’s experience and expertise, with 30 years of knowledge and 400 industry experts
• Utilize industry-leading software and knowledge bases
• Leverage our deep customer base and market knowledge
• Over 20 years of trusted data and database security
• Scalable Sample to Insight solutions available from a single trusted partner

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Confronted with challenges to advancing their research, Nofima turned to QIAGEN Discovery Bioinformatics Services for quality results, fast

Dr. Philip James, Ph.D., Senior Researcher at a small research institute called Nofima, was confronted with several challenges associated with access to analytics tools when studying the effect of diet on gene regulation in sea urchins, including processing and pathway analysis of RNA-seq data. He also needed to put the results into a biological context.

Dr. James found partnering with QIAGEN Discovery Bioinformatics Services a reliable and convenient way to extend in-house resources, with our expertise and tailored bioinformatic services ensuring time savings and high-quality results.

Inspirational and groundbreaking science is often unorthodox and tricky, even concerning bioinformatics research. Follow the journey of partnering with QIAGEN Discovery Bioinformatics Services, from initial contact and delivery of data analysis to submission for publication.

Read Nofima's story here.

QIAGEN Discovery Bioinformatics Services offer custom solutions that help translate discovery from your data. This includes tailored plugin development for QIAGEN CLC Genomics Workbench and QIAGEN CLC Genomics Server, helping to extend and customize the feature sets of these NGS analysis solutions.

The QIAGEN Antibody Analysis Suite is one of the custom solutions developed by the QIAGEN Discovery Bioinformatics Services team. This automated, high-throughput tool enables a detailed analysis of antibody sequences and includes the ability to customize to ensure that it fits the exact needs of specific workflows. The Antibody Analysis Suite is used for the characterization of antibody repertoires involved in the discovery and development of therapeutic and diagnostic antibodies and often includes DNA sequence analysis. In vitro display and selection, for example, requires sequence analysis at several steps in the process. First, to test initial library diversity and quality, and subsequently to ensure proper selection and thorough characterization of final clones. The QIAGEN Antibody Analysis Suite provides a tool for detailed analysis that:

• Accelerates the research process
• Removes manual and error-prone steps
• Is user-friendly and integrated
• Can be customized to match specific needs

The Antibody Analysis Suite is a collection of tools that can be fully integrated with the powerful QIAGEN CLC Genomics bioinformatics platform, seamlessly providing endless options for further up- or downstream analysis. The Antibody Analysis Suite can help you:

• Automate and standardize your workflow for heavy and light chain annotation with QC reports
• Build an internal database
• Provide detailed reports and visuals of gene segment usage and mutations with annotation of antibody-specific features
• Automatically annotate antibody heavy and light variable domains and alignments of both DNA and amino acid sequences to proprietary or public databases of germline DNA sequences, or rearranged variable domain sequences
• Understand details regarding V, D and J allele usage and mutations found compared to these; junction sequences; FR and CDR region lengths and sequences, presented in tables and visual displays for further investigation, such as multiple alignments across selected input sequences
• Efficiently identify antibody clones per sample
• Create phylogenetic visualizations and dendrograms
• Perform robust phylogenetic analysis framework that supports metadata-based visualization, as well as sequence clustering
• Analyze results from protein and DNA samples, in parallel
• Determine V, D and J allele usage: Each antibody VH or VL domain is compared to a database of germline sequences of V, D and J alleles, to identify the best hit for each of those gene segments. The alignment of the V segment to its closest germline V segment is displayed in one of many customizable, graphical views
• Perform multiple amino acid alignments: The VH and VL domains of each translated antibody sequence are aligned to a collection of pre-existing, annotated heavy and light domains
• Annotate VH and VL domains: Each sequence is annotated with antibody-specific features, including CDR regions, junction region, specific V, D and J segments and numerous combinations of these
• Quality control your sequences: Each sequence will be checked in terms of frame-shifts and stop codons, as well as missing features, such as conserved amino acids, segments or other motifs
• Group and assemble multiple sequence reads per antibody clone: If an antibody sequence is composed of multiple underlying DNA sequence reads, these can be grouped and assembled prior to analysis
• Create in-house comparisons and databases: Capabilities to make private BLAST databases and protein alignments, such that all analyses can be performed in-house and with proprietary or downloaded public data
• Fully supported to run locally, on servers or cloud environments

Visit us here for more information and request a consultation from our experts today!