Comprehensive Tumor Mutational Analysis

TMB is defined as the total number of base substitutions, insertions, and deletions per million bases in the coding region [24 (link)]. The TMB of each sample was calculated by the “tmb” function in the maftools package [21 (link)]. In addition, we recruited multiple measures, including neoantigens, SNV neoantigens, nonsilent mutation rate, and TCR Shannon from Thorsson V et al., to assess differences in overall genomic instability and immune status between the two groups [25 (link)].

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Wang L., Chen K., Weng S., Xu H., Ren Y., Cheng Q., Luo P., Zhang J., Liu Z, & Han X. (2023). PI3K pathway mutation predicts an activated immune microenvironment and better immunotherapeutic efficacy in head and neck squamous cell carcinoma. World Journal of Surgical Oncology, 21, 72.

Publication 2023

Deletions Genomic instability Insertions

Corresponding Organization :

Other organizations : First Affiliated Hospital of Zhengzhou University, Central South University, Xiangya Hospital Central South University, Zhujiang Hospital, Southern Medical University, Zhengzhou University

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Variable analysis

independent variables

Not explicitly mentioned

dependent variables

TMB (total number of base substitutions, insertions, and deletions per million bases in the coding region)
Neoantigens
SNV neoantigens
Nonsilent mutation rate
TCR Shannon

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the input protocol.

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