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.
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.
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.
TruSeq Exome Library Prep Kit 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.
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.TruSight Tumor 170
TruSight Tumor 170 assesses both DNA and RNA for 170 genes associated with common solid tumors and Tumor Mutational Burden (TMB).
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.
*Data calculations on file, Illumina, Inc, 2015.