GenoImmune Neoantigen Prediction

GenoImmune Neoantigen Prediction

Service Description

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.

 

Why Choose BGI for Neoantigen Detection

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

 

Project Workflow

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.

BGI Neoantigen workflow

 

Reference:
[1] PSSMHCpan: a novel PSSM-based software for predicting class I peptide-HLA binding affinity
Giga Science, 6, 2017, 1–11
https://www.ncbi.nlm.nih.gov/pubmed/28327987

Service Specification

Exome and Transcriptome Sequencing for Neoantigen prediction services will be performed with the Illumina HiSeq.

  • The BGI Neoantigen prediction package includes

    The BGI Neoantigen prediction package includes

    • Tumor and normal whole exome sequencing
    • Tumor whole transcriptome sequencing
    • Tumor mutation landscape and expression profiling
    • Bioinformatics analysis for Neoantigen prediction
    • Optional Bioinformatics analysis for functional validation of Neoantigens
  • Sequencing Quality Standard

    Sequencing Quality Standard

    • Guaranteed 30Gb of tumor whole exome data; 10Gb of tumor whole transcriptome data; 10Gb of normal whole exome data
    • Guaranteed ≥ 80% of bases with quality score of ≥ Q30
  • Turn Around Time

    Turn Around Time

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

Data 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.

Standard Analysis

  • Data Filtering

  • Alignment to reference genome

  • SNV calling and annotation

  • Somatic InDel calling and annotation

  • Gene expression profiling

  • Gene fusion detection and annotation

  • Cross validation of WES and Transcriptome

  • Tumor mutation burden (TMB) calculation

  • Neoantigen prediction

  • Tumor Neoantigen burden (TNB) calculation

Customised Analysis

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

Sample Requirements

We can process your FFPE, Fresh frozen tissue, Needle biopsy, Blood, gDNA, and Total RNA, with the following general requirements:

Sample Type

Requirement

Sample

FFPE

≥ 10 sections, unstained, (50 - 100 mm2, 5 - 10 μm thickness). Tumor content >70%.

Tumor RNA and DNA

Fresh Frozen Tissue

≥ 100 mg, Tumor content >70%. Snap frozen with liquid nitrogen followed by -80℃ cryopreservation.
Transport on dry ice.

Tumor RNA and DNA

Needle Biopsy

≥ 3 cores. Snap frozen with liquid nitrogen followed by -80℃ cryopreservation.
Transport on dry ice.

Tumor RNA and DNA

Blood

≥ 2ml whole blood in EDTA anticoagulation tube. -80℃ cryopreservation.
Transport on dry ice.

Normal DNA

gDNA

>400ng gDNA, concentration ≥5 ng/µl, main band >250bp.
Transport on dry ice.

Tumor RNA and DNA

Total RNA

>40ng, DV200 ≥30%; RIN ≥2.0.
Transport on dry ice.

Tumor RNA