Next generation sequencing (NGS) has significantly advanced omics research, enabling high-throughput sequencing of DNA and RNA at unprecedented scale and depth offering a powerful tool to unravel the genetic basis of diseases and biological processes. While the technology has become indispensable for drug discovery workflows (Satam et al., 2023), costly equipment and the high level of expertise required to run it presents a challenge for many scientists. Outsourcing NGS services to specialized providers thus makes the technology accessible for everyone. In our previous blog, we explored key considerations to choose the NGS service partner that is right for your project. In the following article, we will focus on bridging the gap between NGS data generation and sophisticated analysis as well as data interpretation for drug discovery workflows.
Bridging the Gap: End-to-End NGS Services Solutions for Drug Discovery
Once your NGS experiment is run and the results are delivered, data analysis presents the next challenge. Service providers mostly offer primary and secondary data analyses options for their customers, i.e., demultiplexing, read processing, mapping (including QC steps) and quantification, e.g., read counting, transcript concentration estimation, and if needed differential expression analyses. Depending on the provider, the results are often delivered in form of a static report, including visuals. Some providers also offer plug-and-play data analysis platforms, such as Kangooroo.com for interactive data visualization for expression analyses. However, data interpretation and complex tertiary analysis are usually left to the client or are part of a custom analysis service that is billed in addition to the wet lab project.
This is where specialized data analysis providers offer unique benefits and make even complex analysis accessible! Combining data generation and analysis within an end-to-end solution can accelerate scientific projects by using established workflow combinations and algorithms allowing end users to access their data easily in a secure environment.
Key Benefits for End-to-end Solutions for Sequencing and Data Analysis
- Streamlined Workflow: By streamlining the process and ensuring full compatibility of the data generated with the data analysis platform of choice, you can significantly reduce turnaround times and expedite your research.
- Enhanced Data Quality: The combination of consistent and robust data generation with optimized and validated analyses minimizes variability and inconsistencies, ensuring the highest quality results.
- Deeper Insights: Advanced algorithms and data visualization tools empower clients to explore their data in detail: identification of expression patterns is straightforward and becomes intuitive with the right tools. Projects can be easily shared between collaborators using highly secure file servers - fostering innovation and sharing of results and driving follow-up studies across sites more efficiently.
- Expert Support: Dedicated data analysis providers can offer expertise from experimental design to data interpretation. Data analysis consultation is the cornerstone to planning successful sequencing projects and delivering the results to drive your project forward!
How to Find a Data Analysis Provider to Accelerate Drug Discovery Projects?
The combination of abundant data generated in omics experiments and advanced analytics is reshaping drug discovery workflows, increasing efficiency and reducing the required time to achieve results. To fully leverage the potential of data science, researchers and organizations are adapting their processes and workstyle to tap into the full potential of data driven discoveries. While larger organizations may establish in-house data science teams, smaller companies often outsource not only wet lab work but also data analysis to specialized experts. In an era where drug discovery is becoming increasingly complex, embracing data science is essential to drive innovation and accelerate the development of transformative medicines (Ferrero et al., 2020). Therefore, it is paramount that wet lab service partner and the selected data analysis partner integrate into a seamless, close-knit workflow and are fully synergistic.
Using curated plug-and-play data analysis platforms allow the user to harness the potential of complex analysis while keeping full control of the data, the experimental setup and workflow selected. This is particularly useful when data needs to be shared securely with groups and partner organizations in different locations or when it is planned to transfer the wet lab workflow in-house for future upscaling. Lexogen NGS Services for example uses technologies developed in the company available as kits and bulk reagents, making a future transfer of complete workflows very easy by foregoing home-brew technologies and relying on fully quality controlled kits and reagents produced according to ISO13485 standards.
Depending on the needs of the client, several providers exist with different platforms and capabilities.
KANGOOROO
Lexogen’s cloud-based Kangooroo Platform offers user-friendly, fast and convenient analysis of data generated with Lexogen kits, for example QuantSeq 3′ expression profiling, LUTHOR 3′ single-cell and ultra-low input RNA-Seq or CORALL for whole transcriptome analysis. Users can explore their data with interactive visualization for expression studies. The use of Kangooroo is complementary with the purchase of Lexogen RNA-Seq kits.
ROSALIND
PanHunter
BigOmics Playground
BigOmics Analytics is a swiss company specialized in advanced bioinformatics solutions dedicated to empowering researchers to unlock the full potential of their omics data. BigOmics’ data analysis platform, Omics Playground, offers a user-friendly interface and powerful tools for exploring complex datasets. With a focus on RNA-Seq, proteomics, and and metabolomics (beta) data, BigOmics Analytics helps researchers to accelerate drug discoveries or identify novel biomarkers with robust and reproducible results using best-in-class methods and algorithms.
Apart from differential expression, gene set enrichment and pathway analysis, BigOmics also offers biomarker and drug connectivity analysis – making the platform extremely useful for various stages within drug discovery workflows. Fast access to data insights can streamline experimental sequences to enable timely follow-up experiments to validate findings overall streamlining the process and advancing promising candidates with unprecedented speed – especially when wet lab work can also be expedited, e.g., by collaborating with a trusted NGS Service provider.
The Drug Connectivity Analysis module, which you can test by creating a trial account, relies on curated large-scale perturbation databases, e.g., Connectivity Map (CMap) from the Broad Institute or NIH’s Library of Integrated Network-based Cellular Signatures (LINCS) containing over 1.5M expression profiles from thousands of small molecules and genetic reagents in multiple cell types. Accessing this vast amount of information through intuitive tools such as the Omics Playground enables scientists to integrate insights with their own data sets and drive the discovery of novel therapeutics.
Summary - Expedite Discoveries by Outsourcing NGS to Trusted Partners
Embracing end-to-end solutions for wet lab NGS services and advanced data analysis capabilities, significantly accelerates drug discovery and brings transformative medicines to patients faster (Ivanisevic and Sewduth, 2023). End-to-end solutions from a trusted provider or by enlisting specialized wet lab and data analysis experts in a collaborative way allow end users to tap the full potential of omics to drive their discoveries.
- Expedite Discoveries: Combining data generation with best-in-class analysis can significantly reduce turnaround times, streamline experiment sequences and deliver insights fast.
- Expert Support: Trusted providers offer expertise from design to interpretation and consultation for follow-up studies to advance discoveries.
- Exceptional Data Quality: Consistent and robust data generation, with established quality control steps throughout the wet lab and bioinformatics process paired with optimized and curated data analysis maximizes the quality of your results.
- Reliable Insights: Streamlined processes, advanced algorithms, and interactive, collaborative data visualization can significantly increase the success rate to advance promising candidates at unprecedented speed.
Embrace the future of omics research, choose an end-to-end omics solution.
References
Ferrero E, Brachat S, Jenkins JL, Marc P, Skewes-Cox P, Altshuler RC, Gubser Keller C, Kauffmann A, Sassaman EK, Laramie JM, Schoeberl B, Borowsky ML, Stiefl N. (2020) Ten simple rules to power drug discovery with data science. PLoS Comput Biol.16(8):e1008126. DOI: 10.1371/journal.pcbi.1008126. PMID: 32853229; PMCID: PMC7451597
Ivanisevic, T., & Sewduth, R. N. (2023). Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers. Proteomes, 11(4), 34. DOI: 0.3390/proteomes11040034
Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday, S., Mishra, A. K., Das, G., & Malonia, S. K. (2023). Next-Generation Sequencing Technology: Current Trends and Advancements. Biology, 12(7), 997. DOI: 10.3390/biology12070997
Written by Dr. Yvonne Goepel
