Understanding correlations between mutations and therapeutic approaches

NGS methods enable efficient assessment of tumor mutational load and the identification of neoantigens

Tumor Mutational Load & Neoantigen Analysis

Sequencing the cancer exome and transcriptome provides information about mutations that may help determine the tumor's ability to evade the immune response, or identify tumor-specific neoantigens that can boost T cell-mediated immunity. Targeted sequencing methods provide an efficient, cost-effective alternative to whole-genome sequencing.

Innovative therapies have been developed to boost the immune response, such as checkpoint inhibitors, vaccines, and adoptive cell transfer. NGS applications have been helpful in developing these therapies, and understanding how genetic variants can influence their efficacy.

Using NGS to Aid the Immune System in Targeting Cancers

An overview of exciting new fields of immunotherapy research, and how NGS helps to move them forward.

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Tumor mutational burden (TMB) or tumor mutational load, the number of mutations within the coding region of a tumor genome, has been shown to correlate with response to immunotherapy treatment.

1-3 TMB has historically been assessed by whole-exome sequencing (WES),1-3 although recent studies have demonstrated that TMB can be effectively estimated using targeted sequencing panels.4-5

Mutations in protein coding genes of cancer cells are a source of potential neoantigens that the immune system can target. NGS has enabled the predictive selection of novel tumor antigens that can be applied to elicit a tumor-specific response. DNA and/or RNA is efficiently characterized by exome sequencing and/or transcriptome sequencing, and improved bioinformatics tools aid neoantigen selection by predicting the presentation of mutant peptides for recognition by the immune system.

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 mutational load and neoantigen 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.

Nextera Flex for Enrichment

Nextera Flex for Enrichment uses a fast, user-friendly workflow. On-bead tagmentation chemistry is combined with a simplified, single hybridization protocol to reduce total workflow time.

TruSeq DNA Exome

TruSeq DNA Exome is a cost-effective library preparation and exome enrichment solution.

TruSeq Stranded Total RNA Library Prep Kit

A robust, highly scalable whole-transcriptome analysis solution for a variety of species and sample types, including FFPE.

TruSeq RNA Exome

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

TruSight Tumor 170

TruSight Tumor 170 assesses both DNA and RNA for 170 genes associated with common solid tumors and Tumor Mutational Burden (TMB).

TruSight Oncology 500

Assay targeting multiple variant types, including tumor mutational burden (TMB) and microsatellite instability (MSI), even from low-quality samples.

NextSeq 550 Systems

Flexible configurations that support up to 12 exomes per run.

HiSeq 4000 System

High throughput and low cost for production-scale genomics.

NovaSeq Series

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 BaseSpace App

The Enrichment app rapidly aligns samples using Isaac and performs indel, SNV, CNV, and SV analysis and annotation.

pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens.

Genome Med 8 11 2016

Read Abstract

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade.

Science 351 1463-9 2016

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Atezolizumab as first-line treatment in cisplatin-ineligible patients with locally advanced and metastatic urothelial carcinoma: a single-arm, multicentre, phase 2 trial.

Lancet 389 67-76 2017

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Exome Sequencing

The exome represents the portion of the genome that potentially codes for proteins. Representing less than 2% of the genetic code, exome sequencing is a cost-effective alternative to whole-genome sequencing. It is a commonly used method for identifying neoantigens.1-3

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RNA Sequencing

RNA sequencing provides not only gene expression measurement, but also information on single nucleotide variants and splicing variants. The TruSeq RNA Access Kit is optimized for sequencing RNA from degraded samples, including FFPE tissues.

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Targeted Cancer Sequencing

For some applications, targeted sequencing panels may provide efficient assessment of mutational load.4,5

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Participant Stratification in Immuno-Oncology
Participant Stratification in Immunotherapy Research

Genomics scientists discuss how advances in immuno-oncology research resulting from NGS help better stratify subjects for clinical trials.

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  1. Rizvi NA, Hellmann MD, Snyder A, et al. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348 (6230):124-128.
  2. Snyder A, Makarov V, Merghoub T, et al. Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma. N Engl J Med. 2014;371(23):2189-2199.
  3. Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015;350(6257):207-211.
  4. Garofalo A, Sholl L, Reardon B, et al. The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016;8(1):79. doi:10.1186/s13073-016-0333-9.
  5. Campesato, L, Barroso-Sousa, R, Jimenez, L, et al. Comprehensive cancer-gene panels can be used to estimate mutational load and predict clinical benefit to PD-1 blockade in clinical practice. Oncotarget. 2015;6(33):34221-34227.

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