Towards a deeper understanding of complex interactions governing the immune response

Next-generation sequencing (NGS) may help to discover factors that can impact the immune system’s ability to target tumors

Tumor Microenvironment and Immune Composition

Tumor tissues vary considerably in their microenvironment, and the existence of other cell types can influence the ability of the immune system to infiltrate and attack tumor cells. As promising new therapies evolve, there is an increasing need to identify cancer immunotherapy biomarkers to guide their appropriate application.

NGS can provide careful analysis of the cancer genome, and efficiently assess the tumor milieu as a real-time, highly sensitive monitor of immune marker expression in response to tumor growth or treatment. NGS analysis can be used to characterize the immune cell repertoire, identify various cell populations in the microenvironment, and comprehensively quantify gene expression of thousands of targets simultaneously.

Featured Publications: Cancer Immunotherapy Research

High-throughput sequencing has shown remarkable utility in cancer and immunology research, as well as in the development of individualized immunotherapy.

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Studies of epigenetic alterations in cancer, such as aberrant methylation and altered transcription factor binding, can provide insight into important tumorigenic pathways. As altered methylation often activates or silences genes, changes in the epigenome can affect gene expression and the rate of cancer progression.

NGS and microarray technologies can detect altered methylation patterns and other epigenetic changes in cancer.

Surveying the Chromatin Landscape with NGS

Researchers at Stanford University develop novel sequencing methods to understand the epigenome and its impact on cancer and immune disease.

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RNA analysis may help to identify aspects of the tumor microenvironment that can influence the effectiveness of checkpoint immunotherapies, such as inductive and inhibitory cytokines, and local recruitment of other cells types that can inhibit the T-cell response.

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Keeping Pace with Immuno-oncology Research Breakthroughs

NGS technology can accelerate biomarker identification and bring down costs for research subject screening and safety monitoring.

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Cancer researchers need simple-to-use bioinformatics applications to gain insights from complex genomic data. BaseSpace Cohort Analyzer allows biologists and researchers to make important discoveries without specialized bioinformatics skills. The retrospective analysis of clinical trial data can help inform future cancer research and drug development programs.

Learn more about BaseSpace Cohort Analyzer and BaseSpace Correlation Engine.

Informatics Applications for Immuno-oncology Research Using NGS

Improved informatics tools enable neoantigen discovery and tumor microenvironment analysis.

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Illumina offers several library preparation and sequencing options with access to data analysis options for tumor microenvironment analysis. Streamlined workflows and flexible kit configurations accommodate multiple study designs.

Approximately 90% of the world’s sequencing data are generated using Illumina sequencing by synthesis (SBS) chemistry.*

Click on the below to view products for each workflow step.

TruSeq Exome

TruSeq Exome Library Prep Kit is a cost-effective library preparation and exome enrichment solution.

RNA Access

The TruSeq RNA Access library prep kit provides a low-cost solution for analyzing human RNA isolated from limited or low-quality samples, including FFPE.

Illumina Bio-Rad® SureCell™ WTA 3′ Library Prep Kit for the ddSEQ™ System

Transcriptome profiling of hundreds to tens of thousands of single cells in a single experiment.

TruSeq DNA Methylation Kit

Whole-genome bisulfite sequencing libraries from as little as 50 ng DNA.

NextSeq Series

Flexible configurations that support up to 12 exomes per run.

HiSeq 2500 System

High throughput on a scalable platform for sequencing dozens to hundreds of cancer exomes per run.

HiSeq 3000/HiSeq 4000 Systems

Patterned flow cell technology results in high throughput, low price per sample, and enhanced speed and performance.

NovaSeq 6000 System

Flexibility and unprecedented throughput for virtually any genome, sequencing method, and scale of project.

BaseSpace RNA-Seq Apps

Immuno-Oncology filter for RNA sequencing analysis.

Enrichment App

Uses the Isaac Genome Alignment Software and the Isaac Variant Caller for exome data analysis.

Cancer immunotherapy. A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells.

Science 348 803-8 2015

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Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes.

Nat Biotechnol 33 1152-8 2015

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The epigenetic landscape of T cell exhaustion.

Science 354 1165-1169 2016

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Genomic Technologies for Cancer Research
Genomic Technologies for Cancer Research

Learn the numerous ways that genomic technologies can be applied to tumor biology.

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Immuno-oncology Informatics Applications Using NGS
Immuno-oncology Research Informatics Applications Using NGS

Improved informatics tools enable neoantigen discovery and tumor microenvironment analysis

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*Data calculations on file, Illumina, Inc, 2015.