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Neoantigen Detection Service

For personalized cancer therapies

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Neoantigen Detection Service - patient's hands holding a ribbon of hope, supported by a medical scientist's hands

Unlocking the Power of Precision Immunotherapy

Cancer originates from mutations and genomic instability that drives uncontrolled cell growth. When tumor cells mutate, they produce abnormal proteins — neoantigens — that the immune system can recognize as "foreign".

Identifying neoantigens involves identifying mutated peptides that are presented by cancer cells. Neoantigens are unique to tumor cells (i.e. they are absent in normal tissue). This means that they can be used to raise highly specific immune responses with minimal risk of damaging healthy tissue.

Neoantigens arise from somatic mutations and are highly immunogenic. This makes them ideal candidates for many therapeutic techniques, including:

  • Personalized cancer vaccines
  • Adoptive T-cell therapies (e.g., TCR-T, neoTILs)
  • Immune checkpoint inhibitor response prediction
  • Biomarker discovery for clinical trials
  • Tumor immunogenicity profiling in translational research

Our neoantigen detection service begins with high-throughput DNA and/or RNA sequencing data from tumor samples. Using advanced bioinformatics pipelines, we identify somatic mutations and predict the resulting mutant peptides or potential neoantigens that may be presented by MHC molecules on cancer cells. These computationally predicted, tumor-specific peptides enable the development of personalized immunotherapies.

 

Our Neoantigen Detection Service Overview

We offer an end-to-end neoantigen discovery platform tailored for immuno-oncology research, translational programs, and early-phase clinical development. Using matched tumor-normal samples, we apply:

Whole Exome Sequencing (WES) to Identify Somatic Mutations

Using cutting edge Next generation sequencing techniques, we use Whole Exome sequencing (WES) to sequence the protein coding regions of both tumor and matched normal samples. This enables accurate identification of somatic mutations the genetic changes found only in cancer cells. These mutations form the basis for neoantigen prediction.

Whole Exome Sequencing (WES) to Identify Somatic Mutations

RNA Sequencing (RNA-Seq) to Confirm Gene Expression

RNA- sequence or transcriptome sequencing provides insight into gene expression within the tumor. It confirms which somatic mutations are transcribed, helping prioritize neoantigen candidates that are actively expressed. This enhances the biological relevance and clinical potential of predicted neoantigens.

RNA Sequencing (RNA-Seq) to Confirm Gene Expression

Tailored Computational Methods/ Algorithms to Predict MHC-Binding Neoantigens

Using in house optimised computational algorithms and the patient's HLA genotype, we predict which mutated peptides show high affinity binding to MHC molecules. Only high-affinity binders are prioritized, ensuring that selected neoantigens are both tumor-specific and immunologically relevant.

Tailored Computational Methods/ Algorithms to Predict MHC-Binding Neoantigens

Our neoantigen detection service supports comprehensive tumor profiling and neoantigen identification, streamlining your path to precision cancer immunotherapy.

What Samples Can You Send Us?

Fresh Frozen Tumor
Fresh Frozen Tumor
≥100 mg, >50% tumor content, stored at -80°C,
shipped on dry ice
FFPE sample tray
FFPE

10 sections (5–10 μm), unstained,
>50% tumor content

Blood samples
Blood (germline DNA)

5 ml in EDTA tube,
shipped at 4°C

Genomic DNA double helix
gDNA

2–5 µg, high-quality

RNA single strand
RNA

≥50 ng, DV200 ≥30%, RIN ≥2.0,
shipped on dry ice

Our Neoantigen Detection Service Workflow

We offer an end-to-end solution that will take you all the way from raw tumor samples to neoantigen insights.

Our neoantigen discovery platform tailored for immuno-oncology research, translational programs, and early-phase clinical development. Using matched tumor-normal samples, we apply:

Sample QC and DNA/RNA Extraction
 
WES (tumor + normal) and RNA-seq
 
Somatic Mutation Calling and Expression Filtering
 
Neoantigen Prediction using computational algorithms
 
Prioritized set of neoantigen peptide candidates

Turnaround Time (TAT):
30 days from sample receipt

Custom TAT options available — contact us with your requirements

What You Can Expect From Our Neoantigen Detection Service

Whether you send us fresh frozen tumors and healthy tissue, FFPE, blood, or extracted DNA or RNA, once we have received your samples our expert scientists will get to work. If you haven't provided  DNA or RNA, we will extract it from the sample(s) you have provided.

Typically, we can get you your results in 30 days of receiving your sample. But we have the capacity to be flexible, so that we can sometimes do better than this in order to meet your preclinical or translational timeline. We are always working on ways to improve our process and expand our facility, so that we can reduce our turnaround time (TAT).

Our team has a rich experience of more than 10 years in Next Generation Sequencing (NGS), cancer diagnostics, and immunogenetics.

The abnormal peptides (neoantigens) identified will bind to the major histocompatibility complex (MHC) molecules on cell outer membranes and be presented to antibodies on lymphocytes in the acquired immune system.

The end-goal of our neoantigen detection service is to provide you with an annotated somatic variant profile of your tumor sample, generated by our computational methods/ algorithms comparing the tumor against a healthy sample. 

Your Prioritized Neoantigen Panel will include:

  • Annotated variant files (VCF, TSV)
  • HLA typing and binding affinity scores for MHC Class I and II neoepitopes
  • A prioritized neo-antigen list with binding affinity predictions
  • A Tumor Mutation Burden (TMB) report and mutation spectrum
  • And a report summary

All this provides you with a high-confidence list of neoantigens for you to go forward with in your own specialist therapeutic area.

Applications

  • Immunotherapy development
    Our neoantigen discovery pipeline identifies tumor-specific, immunogenic peptides that serve as ideal targets for next-generation immunotherapies. By enabling precise antigen selection, we accelerate the design of effective T-cell–based therapies like TCR-T and neoTILs.
  • Personalized vaccine design
    We help design patient-specific cancer vaccines by predicting and prioritizing neoantigens that are both tumor-exclusive and highly immunogenic. This enables the development of custom-tailored vaccines to elicit strong, targeted immune responses.
  • Companion diagnostic biomarker studies
    Our neoantigen data supports the development of biomarkers that predict immunotherapy response. By profiling tumor immunogenicity and mutation-derived epitopes, we help identify patients most likely to benefit from immune checkpoint inhibitors or personalized approaches.
  • Immune-oncology research and clinical trials
    Our comprehensive neoantigen profiling aids in translational research and supports stratified clinical trial design. We provide actionable insights into tumor immune landscapes, helping researchers link neoantigen burden with therapeutic efficacy.
  • Patient stratification and response prediction
    We enable precision oncology by stratifying patients based on tumor-specific neoantigen load, expression, and MHC presentation potential. This allows better prediction of who may respond to immunotherapies, helping optimize treatment plans and trial enrollment.

Get Started Today

Ready to harness the full power of your tumor’s mutational profile? Contact us to explore how our Neoantigen Detection Service can accelerate your path to personalized cancer immunotherapy.

Contact our experts

Frequently Asked Questions (FAQ)

 

What types of cancers can be analyzed using your neoantigen detection platform?

Our pipeline is designed to work with all solid tumors, including lung, colorectal, breast, ovarian, melanoma, and gastrointestinal cancers. If sufficient tumor material and matched normal DNA are available, we can process nearly any cancer type.

 

What is the minimum sample quantity required for tumor DNA?

For FFPE, 10 × 5–10 µm sections; for fresh tissue, ≥100 mg with >50% tumor content.

 

Can I send only tumor samples without matched normal?

Yes, but tumor-only analysis has limitations for somatic variant calling.

 

Do you offer HLA typing if not already available?

Yes, we do.

 

Can this data be used to design personalized cancer vaccines or T-cell therapies?

Yes. Our neoantigen prediction report includes high-confidence peptide sequences suitable for downstream applications like vaccine synthesis or immune cell assays.

 

What quality control measures are applied to my samples?

We perform RNA integrity and DNA QC (concentration, purity) checks before sequencing. Low-quality samples are flagged, and the client is notified prior to proceeding.

 

What output files and reports will I receive?

You will receive:

  • Annotated variant files (VCF, TSV)
  • HLA typing results
  • Prioritized neo-antigen list with binding affinity predictions
  • Tumor Mutation Burden (TMB) report
  • Summary report (PDF)

References

  1. Ott, P. A., Hu, Z., Keskin, D. B., Shukla, S. A., Sun, J., Bozym, D. J., ... & Wu, C. J. (2017). 
    An immunogenic personal neoantigen vaccine for patients with melanoma. 
    Nature, 547(7662), 217–221.
  2. Schumacher, T. N., & Schreiber, R. D. (2015).Neoantigens in cancer immunotherapy. 
    Science, 348(6230), 69–74.
  3. Chan, T. A., Yarchoan, M., Jaffee, E., Swanton, C., Quezada, S. A., Stenzinger, A., & Peters, S. (2019).
    Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic. Annals of Oncology, 30(1), 44–56.
  4. Tran, E., Turcotte, S., Gros, A., Robbins, P. F., Lu, Y. C., Dudley, M. E., ... & Rosenberg, S. A. (2014). Cancer immunotherapy based on mutation-specific CD4+ T cells in a patient with epithelial cancer. Science, 344(6184), 641–645.

Contact Our Experts

Have questions or need help getting started? Our team is here to support you.

Whether you're exploring neoantigen profiling for research, clinical application, or therapy development, we’re happy to guide you through the process. Simply fill out the form below — and we’ll be in touch shortly.

Let’s take the next step together.