NovoNeoantigen 2.0

Service Overview

Neoantigens are newly formed antigens that have not been previously recognized by the immune system. It is a key element of cancer immunotherapies. NovoNeoantigen 2.0 is a robust and comprehensive bioinformatics analysis service developed by Novogene for discovering tumor-specific neoantigens using whole exome sequencing (WES) and mRNA sequencing (mRNA-Seq) data from paired tumor-normal samples.

Advantages

Comprehensive Results NovoNeoantigen 2.0 interrogates WES and mRNA-Seq data from paired tumor-normal samples for three types of genomic abnormalities (SNV, InDel, and Fusion) at DNA and RNA levels. From these data, it further generates results on tumor mutation burden (TMB), SNV Phasing, HLA typing and antigen affinity, eventually identify tumor-specific neoantigens.
Reliable Performance NovoNeoantigen 2.0 has demonstrated reliable performance when tested on data sets with known neoantigens caused by somatic mutations.
Short Turnaround Time With leading-edge sequencing solutions, superior wet-lab process efficiency and widely known bioinformatics capabilities, we can complete NovoNeoantigen 2.0 within 27 business days after sample QC result or 7 business days after raw data is available.

NovoNeoantigen 2.0 Service Overview

Testing Workflow

Sample Requirements

Sample Type	Sample Requirement	Sample
FFPE	≥ 10 sections (4-μm), each with tissue area ≥ 50 mm²;	Tumor DNA and RNA
FFPE Block	≥ 1 Block	Tumor DNA and RNA
Fresh Tissue	≥ 300 mg	Tumor DNA and RNA

Sequencing Strategy

HiSeq X Ten or NovaSeq 6000, PE150

Data Quality Guarantee

We guarantee that ≥ 80% of bases have a sequencing quality score ≥ Q30, which exceeds Illumina’s official guarantee of ≥ 75%.

Recommended Sequencing Depth

WES: Sequencing depth ≥ 200× for tumor DNA and ≥ 100× for normal DNA
RNA-Seq: TruSeq RNA Exome Seq with ≥ 40M Reads for FFPE samples or PolyA mRNA-Seq with ≥ 20M Reads for fresh tissue samples

NovoNeoantigen 2.0 Bioinformatics Analysis Workflow

Predicts all types of HLA-I and six types of HLA-II (including DQA1, DQB1, DPA1, DPB1, DRB1 and DRB5) with WES data from the DNA of normal tissue samples.
Identifies somatic mutations (SNV, InDel and Fusion) and their gene expression level with WES and mRNA-Seq data. It also generates other important results including TMB and SNV Phasing.
Predicts tumor-specific neoantigens based on the analysis above and antigen affinity analysis.

Novogene Data

HLA Typing

NovoNeoantigen 2.0 was applied to the HLA typing of 10 samples involving 100 HLA alleles from the 1,000 Genomes database. The overall coincidence rate was 91%.

Neoantigen Prediction

To evaluate the performance of the pipeline in predicting immunogenic neoantigens, we assembled 9 known and experimentally-validated immunogenic neoantigens from the literature^{[1, 2, 3]}.

We spiked in these neoepitopes into a BAM file. The results showed that NovoNeoantigen 2.0 is able to accurately identify 8 immunogenic peptides, including 5 HLA-I binding peptides and 3 HLA-II binding peptides.

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