Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction
Abstract
:1. Introduction
2. Results and Discussion
2.1. Neoantigen Feature Prediction
2.2. Selection of the Best HLA-I Binding Affinity Prediction Algorithms
2.3. Data Used for Seq2Neo-CNN Model Training
2.4. Features Associated with Peptide Immunogenicity
2.5. Seq2Neo-CNN Model for Immunogenicity Prediction
2.6. Seq2Neo Validation
2.7. Seq2Neo Implementation
3. Materials and Methods
3.1. Data Preprocessing
3.2. Somatic Mutation Detection
3.3. HLA Genotyping
3.4. Gene Expression Detection
3.5. Neoepitope Features
3.6. Immunogenicity Prediction (Seq2Neo-CNN Model)
3.6.1. Dataset Selection
3.6.2. Allele Representation
3.6.3. Encoding Strategy
3.6.4. Feature Normalization
3.6.5. Prediction Model
3.7. Other Machine Learning-Based Immunogenicity Prediction Models
3.8. Seq2Neo Implementation in Cancer Patient Samples
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Method | Neoantigen Types | Input Data | Neoantigen Class | HLA Typing | Immunogenicity Score | TAP Score | Language | Publish Year |
---|---|---|---|---|---|---|---|---|
Seq2Neo | SNVs, indels, gene fusions | WES/WGS, RNA-seq | Class I | Yes | Yes | Yes | Python | This study |
pVACseq | SNVs, indels, gene fusions | VCF | Class I and II | No | No | No | Python | 2019 |
TSNAD 2 | SNVs, indels, gene fusions | WES/WGS, RNA-seq | Class I | Yes | Yes | No | Python | 2021 |
NeoPredPipe | SNVs, indels | VCF, HLA types | Class I and II | No | No | No | Python | 2019 |
Neopepsee | SNVs | VCF, RNA-seq, HLA types | Class I | Yes | Yes | No | Java | 2018 |
nextNEOpi | SNVs, indels, gene fusions | WES/WGS, RNA-seq | Class I and II | Yes | No | No | Nextflow | 2021 |
ProTECT | SNVs | WES/WGS, RNA-seq | Class I and II | Yes | No | No | Python | 2020 |
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Diao, K.; Chen, J.; Wu, T.; Wang, X.; Wang, G.; Sun, X.; Zhao, X.; Wu, C.; Wang, J.; Yao, H.; et al. Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction. Int. J. Mol. Sci. 2022, 23, 11624. https://doi.org/10.3390/ijms231911624
Diao K, Chen J, Wu T, Wang X, Wang G, Sun X, Zhao X, Wu C, Wang J, Yao H, et al. Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction. International Journal of Molecular Sciences. 2022; 23(19):11624. https://doi.org/10.3390/ijms231911624
Chicago/Turabian StyleDiao, Kaixuan, Jing Chen, Tao Wu, Xuan Wang, Guangshuai Wang, Xiaoqin Sun, Xiangyu Zhao, Chenxu Wu, Jinyu Wang, Huizi Yao, and et al. 2022. "Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction" International Journal of Molecular Sciences 23, no. 19: 11624. https://doi.org/10.3390/ijms231911624
APA StyleDiao, K., Chen, J., Wu, T., Wang, X., Wang, G., Sun, X., Zhao, X., Wu, C., Wang, J., Yao, H., Gerarduzzi, C., & Liu, X. -S. (2022). Seq2Neo: A Comprehensive Pipeline for Cancer Neoantigen Immunogenicity Prediction. International Journal of Molecular Sciences, 23(19), 11624. https://doi.org/10.3390/ijms231911624