Scalable, fast, automated NGS solution for research of vaccines and therapeutics

Vaccines help train our immune system to protect us from infectious disease and recognize and combat against diseases such as cancer. Many questions still need to be answered, as researchers continue their efforts to develop new vaccines, improve vaccine efficacy and mitigate adverse events. How do we identify the right targets for vaccines? Are there biomarkers that can be used to predict vaccine efficacy? How do factors such as dosage amount or the microbiome impact immunes response to vaccines?

The advent of massively parallel next-generation sequencing (NGS) and the ability to quickly sequence and analyze DNA and RNA helps advance our understanding of the genetics behind vaccine response and enhance vaccine development research.

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Ion Torrent targeted NGS offers rapid, multi-dimensional genetic analysis at scale for vaccine research across the development workflow, from discovery to vaccine efficacy. Whether you need to study pathogen biology and target discovery or comprehensively analyze host immune response, Ion Torrent has the solution to help researchers quickly and cost-effectively study and improve vaccine development.

Benefits of using Ion Torrent targeted NGS for vaccine development research include:

  • Flexibility—one technology you can standardize across the vaccine research pipeline, enabling multiple applications and multi-dimensional analysis
  • Speed—rapid turnaround time for quick iteration to characterize the right candidates
  • Automation—easy adoption, lower user intervention, and improved lab efficiency
  • Accuracy—identify predictive biomarkers to potentially improve efficacy of vaccines, stratify samples by immune response for more efficient clinical research studies, help address vaccine safety, and potentially mitigate adverse events

SARS-CoV-2 Spotlight: The importance of studying viral variants in vaccine and therapeutics research


Sequencing the entire SARS-CoV-2 viral genome can generate new insights about the biology of SARS-CoV-2 and novel drug targets that could inform vaccine and therapeutics research. All viral mutations must be taken into consideration during vaccine or therapeutic development, or it may render a candidate less effective as the virus continues to evolve.

Ion Torrent NGS enables sequencing of the complete ​SARS-CoV-2 genome to identify key mutations for investigating community spread and ongoing evolution of SARS-CoV-2 with potential implications for vaccine research​. The Ion AmpliSeq SARS-CoV-2 Insight Research Assay is part of a fast, automated, and acccurate targeted NGS workflow that enables coronavirus typing in under a day, with coverage of >99% of the SARS-CoV-2 genome and variants, including all serotypes. This end-to-end solution also includes the assay and plug-in suite developed with researchers working to slow the spread of the virus.

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Ion Torrent solutions in the vaccine development research workflow

  • Identify pathogen and conduct genomic analysis to design vaccine
  • Identify antigen/neoantigen candidates
  • Characterization and optimization
  • Functional analysis for production
  • Stratify samples by immune response
  • Safety
  • Efficacy

NGS solutions

  • Pathogen analysis
  • Host analysis
    • Microbiome
  • Immune response analysis
    • Adaptive immunity
    • Innate immunity
    • Signaling pathways

Pathogen analysis and target discovery

Targeted NGS can help identify genetic patterns related to virulence, antigens and neoantigens that elicit an immune response, as well as genetic factors that may contribute to immunity or may lead to adverse events. Genetic information advances vaccine development research and could lead to therapeutics with greater specificity for better protection against infection or improve treatment outcome in the future for diseases such as cancer.

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Adaptive immunity—immune repertoire analysis

Vaccines enable our adaptive immune system to quickly recognize and fight against infectious disease, as well as boost our immune system to attack diseases such as cancer. An accurate, targeted NGS approach is needed to sequence these complex genetic rearrangements correctly and understand how the immune system evolves over time for disease causing agents like SARS-CoV-2, or understand the cancer immunity cycle to improve cancer vaccine therapies. Immune repertoire analysis also enables sample stratification for clinical research studies, facilitating interpretation and potentially improving vaccine efficacy.

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Innate immunity and signaling pathways

Innate immune response involves molecules such as interferons and cytokines, but their relative contributions to response and adverse events remain poorly understood. Targeted gene expression analysis provides a scalable cost-effective approach to understand how genes are regulated in response to antigens and vaccines. Characterizing innate immunity and the various immune signaling pathways may potentially help improve vaccine efficacy, minimize risk of adverse events and provide information on appropriate options.

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Microbiome analysis for vaccine research

The gut microbiome is considered our “second genome” and believed to influence human immunity including complex interactions in microbe-microbe and host-microbe relationships that may impact vaccine response and potentially vaccine efficacy. Targeted NGS can capture species information that may be critical due to their immunomodulatory and antiviral properties, including microbes that may not be culturable.

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Ion Torrent solutions for vaccine development research

Unlike other NGS approaches, Ion Torrent focused NGS solutions for vaccine development research provide the speed, scalability, and accuracy you need to spend more time developing vaccine solutions and less time looking for them.

analysis and
target discovery

Host immune response

Adaptive immunity and immune repertoire analysis

Innate immunity and signaling pathways

Microbiome analysis

  • SARS-CoV-2 research panel
  • Infectious disease research panels 
  • Custom and On-Demand targeted NGS panels
  • T-cell receptor (TCR) Beta assays 
  • B-cell receptor (BCR) IGH assays*
  • Targeted transcriptome gene expression kits* 
  • Immune Response Research Assay
  • Microbiome assay for health research
Learn more about SARS-CoV-2 and other pathogen assays ›Learn more about the immune repertoire response assays ›Learn more about our targeted RNA and transcriptome assays ›Learn more about the Microbiome Health Research Kit ›

*Available for human and mouse models

Complementary Ion Torrent NGS systems for vaccine development research

Ion GeneStudio S5 System

Scalable targeted NGS to support small and large projects
The Ion GeneStudio S5 system is a scalable, targeted-NGS workhorse with wide application breadth and throughput capability.

Ion Torrent Genexus System

Specimen to report in a single day with a hands-off, automated workflow*​
​The Genexus System is the first turnkey NGS solution that automates the specimen-to-report workflow and delivers results in a single day with just two user touchpoints.*​

For Research Use Only. Not for use in diagnostic procedures.