Cancer immunotherapy has been proven in recent years to be a promising strategy to enhance the strengths of the immune system of cancer patients to fight cancer. Neoantigens are the key to distinguishing cancer cells from normal cells and to stimulate the immune system to fight against cancer. Neoantigen identification is the most critical step in the development of effective antitumor vaccines for cancer immunotherapy.

Neoantigen detection is challenging. Mass Spectrometry-based neoantigen detection is an unbiased method, but requires highly sensitive and high throughput MS systems as well as large amounts of fresh patient tissue. Current NGS-based methods present advantages with outstanding performance for mutation detection, while still challenged to accurately detect somatic mutations of low allele frequency from FFPE or limited clinical biopsy samples. Lastly, the computational prediction of neoantigens remains a daunting problem.

BGI has developed a comprehensive service package for neoantigen detection, combining a highly accurate neoantigen prediction algorithm with whole paired tumor/normal exome and transcriptome sequencing protocols that are optimized for challenging FFPE or biopsy samples.

We provide a one-stop solution for neoantigen identification and tumor mutation landscape profiling for immuno-oncology research.

Service Description

<ul><li>One-stop&nbsp;solution&nbsp;from sample processing to candidate neoantigen identification. Optional functional validation is available.</li></ul> <ul><li>Patented&nbsp;PSSMHCpan algorithm[1]&nbsp;for accurate, sensitive and efficient in-silico neoantigen</li></ul> <ul><li>Comprehensive&nbsp;training&nbsp;data&nbsp;set&nbsp;containing over 210,000 allele specific binders across 128 HLA</li></ul> <ul><li>Extensive&nbsp;experience&nbsp;with sample processing and sequencing from more than 50,000 FFPE samples.</li></ul> <ul><li>Quality:&nbsp;Services will be performed in laboratories that operate under CLIA/CAP quality systems.</li></ul>

Why Choose BGI for Neoantigen Detection

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

Project Workflow

How to order

Exome and Transcriptome Sequencing for Neoantigen prediction services will be performed with DNBSEQ or Illumina platforms.

<ul><li>Tumor and normal whole exome sequencing</li><li>Tumor whole transcriptome sequencing</li><li>Tumor mutation landscape and expression profiling</li><li>Bioinformatics analysis for Neoantigen prediction</li><li>Optional Bioinformatics analysis for functional validation of Neoantigens</li></ul>

The BGI Neoantigen prediction package includes

<ul><li>Guaranteed 30Gb of tumor whole exome data; 10Gb of tumor whole transcriptome data; 10Gb of normal whole exome data</li><li>Guaranteed ≥ 80% of bases with quality score of ≥ Q30</li></ul>

Sequencing Quality Standard

<ul><li>Typical 25 working days from sample QC acceptance to neoantigen prediction result</li><li>Expedited services are available, contact your local BGI specialist for details</li></ul>

Turn Around Time

Service Specification

<ul><li>Data Filtering</li><li>Alignment to reference genome</li><li>SNV calling and annotation</li><li>Somatic InDel calling and annotation</li><li>Gene expression profiling</li><li>Gene fusion detection and annotation</li><li>Cross validation of WES and Transcriptome</li><li>Tumor mutation burden (TMB) calculation</li><li>Neoantigen prediction</li><li>Tumor Neoantigen burden (TNB) calculation</li></ul>

STANDARD ANALYSIS

With our patented PSSMHCpan neoantigen prediction algorithm following standard data processing and tumor variants calling, we provide highly accurate neoantigen prediction result as well as tumor mutation landscape and expression profile analysis to support your cancer research needs.
Reports and output data files are delivered in industry standard file formats: FASTQ, BAM, VCF, CNS and Excel.

Data Analysis

Further customization of Bioinformatics analysis to suit your unique project is available: Please contact your BGI technical representative

GenoImmune Neoantigen Prediction