【8.5.1.1】MuPeXI

The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides.

从概念上讲，基于NGS数据的新表位预测可分为三个步骤:(

1. 将基因组突变列表转换为蛋白质序列，并保留所有可能包含突变的适当长度的“新肽”;
2. 预测与患者特异性HLA等位基因的结合;
3. 根据预测结合、表达水平和与未突变自身蛋白的序列相似性等特征评估每个肽的免疫原性。一些研究利用这些或类似的考虑预测了各种癌症类型的新表位

参考资料

• https://github.com/ambj/MuPeXI 。
• Bjerregaard, A.-M., Nielsen, M., Hadrup, S. R., Szallasi, Z., & Eklund, A. C. (2017). MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunology, Immunotherapy 2017 66:9, 66(9), 1123–1130. https://doi.org/10.1007/S00262-017-2001-3