GenomeScan^® OncoNeoantigen

Multi-Omics. Deeper Biology. Personalized Oncology.

What is OncoNeoantigen?

OncoNeoantigen is a cutting-edge sequencing service that identifies patient-specific neoantigens—mutated proteins unique to cancer cells capable of triggering targeted immune responses—by integrating Whole Genome Sequencing (WGS) and RNA sequencing. This approach provides high-resolution insights into the tumor’s mutational and transcriptional landscape, enabling accurate somatic mutation detection, expression validation, and neoantigen prioritization based on immunogenic potential.

How can I help you?

Connect with Stefanie, our Head of Oncology

Sample type required:

Tumor Samples

FFPE (Formalin-Fixed Paraffin-Embedded)
Fresh Frozen Tissue

Matched Normal Samples

Blood
Saliva
Adjacent healthy Tissue

Key Documents

Service Specification Sheet

Sample Submission Guide

Case Study

Why GenomeScan^® OncoNeoantigen is the smart choice for your clinical research?

Integrated workflow

GenomeScan^® OncoNeoantigen combines tumor-normal Whole Genome Sequencing (WGS) with RNA sequencing in a seamless, ISO-accredited pipeline. This dual-omic approach enables:

High-confidence somatic mutation calling
Expression validation of mutated genes
Neoantigen prioritization based on immunogenic targets

Optimized for low-input and degraded samples, the platform delivers biologically rich, clinically actionable insights to support personalized immunotherapy development.

Ultra-Deep Sequencing

Our platform ensures comprehensive genomic and transcriptomic profiling with:

1 billion paired-end reads per tumor (WGS)
300 million paired-end reads for matched normal tissue (WGS)
200 million paired-end reads for tumor (RNA-seq)

This depth enables robust detection of somatic variants, structural alterations, CNVs, and transcriptome-wide expression, even from challenging FFPE samples.

Designed for Challenging Samples

GenomeScan^® OncoNeoantigen is purpose-built for real-world clinical material, maintaining high performance across:

FFPE and Fresh Frozen tissues
Low-yield biopsies
Rare or archival tumor samples

This makes it ideal for retrospective studies, rare cancer types, and limited or degraded specimens.

Tissue Contamination Control

Accurate neoantigen discovery requires high tumor purity. To ensure data integrity:

All samples undergo pathologist review and tumor cell percentage (TCP) assessment
Microdissection is performed when needed to enrich tumor content and enhance analytical precision

Integration with Clinical Workflows

Under ISO/IEC 17025 accreditation, GenomeScan^® OncoNeoantigen meets the highest standards for:

Technical competence
Reproducibility
Regulatory compliance

Validated protocols and transparent reporting ensure compatibility with clinical trials, translational research, and pharma R&D pipelines.

Accelerated turnaround for time-critical applications

Speed is essential in personalized immunotherapy. Our platform leverages:

Advanced sequencing technologies
Automated workflows
Streamlined bioinformatics

This enables rapid data delivery, supporting faster decision-making and accelerated immunotherapy development.

Workflow: From Biopsy to Neoantigen Discovery

GenomeScan^® OncoNeoantigen follows a structured, end-to-end sequencing pipeline that ensures data quality and biological relevance at every step:

OncoNeoantigen in Clinical Trials: Personalized Targets, Smarter Therapies

Personalized Cancer Vaccines

Revolutionize cancer treatment with personalized vaccines tailored to each patient’s unique tumor profile.

OncoNeoantigen enables precise identification of tumor-specific neoantigens through integrated genomic and transcriptomic analysis, supporting the development of individualized cancer vaccines. These vaccines are designed to elicit robust, patient-specific immune responses by targeting mutations unique to each tumor, enhancing therapeutic precision and minimizing off-target effects.

Adoptive T Cell Therapy (ACT)

Identify and validate neoantigen targets to engineer highly specific CAR-T cells.

OncoNeoantigen can help you to identify and validate expression-validated neoantigen targets suitable for engineering T-cell receptors (TCRs) or CAR-T cells. This ensures enhanced specificity and functionality of adoptive T-cell therapies, improving their ability to recognize and eliminate cancer cells while reducing the risk of immune-related adverse events.

Checkpoint Inhibitor Combination Therapy

Explore how neoantigen profiling enables smarter combination therapies.

OncoNeoantigen profiling supports rational design of combination therapies by identifying immunogenic mutations that can synergize with checkpoint inhibitors. This approach enhances immune activation, helps overcome resistance mechanisms, and improves clinical outcomes in patients receiving immune checkpoint blockade.

Dendritic Cell Vaccines

Enhance T-cell priming by identifying biologically validated neoantigens ideal for dendritic cell presentation.

OncoNeoantigen helps you to identify with high-confidence, biologically validated neoantigens ideal for dendritic cell loading. These neoantigens optimize antigen presentation and T cell priming, enabling the development of potent dendritic cell-based vaccines that drive effective anti-tumor immunity in clinical settings.

Immune monitoring

Track neoantigen-specific immune responses over time with integrated genomic and transcriptomic profiling.

OncoNeoantigen enables longitudinal tracking of neoantigen-specific immune responses by integrating genomic and transcriptomic data over time. This dynamic profiling reveals how the immune system interacts with tumor mutations during treatment, offering insights into therapeutic efficacy, immune activation, and tumor evolution—supporting adaptive decisions in immunotherapy trials.

Service Specifications Sheet

We have summarized key information about our OncoNeoantigen service into a service specification sheet.

Download sheet

Explore our oncology portfolio

Whole Genome Sequencing

Whole Exome Sequencing

Ultra low input Transcriptomics

FFPE tissue RNA sequencing

Genetic QC

Long-read sequencing

Contact us today!

Fill out the form below or reach out directly to our Head of Oncology, Stefanie,at oncology@genomescan.nl— we’ll get back to you shortly to discuss how we can support your project.

GenomeScan^® OncoNeoantigen

What is OncoNeoantigen?