Conclusions
Copy number variation can be a good indicator of immune infiltration and immunotherapy efficacy, and with its low cost, it is expected to become a substitute for TMB.
Methods
In this study, 50 samples (23 of which were from patients who received immunotherapy) were subjected to low-depth (10X) chromosome sequencing on the MGI platform. CNVA was calculated by the formula avg (abs (copy number-2)). In addition, CNVA and TMB were compared with regard to their ability to predict immune infiltration in 509 patients from TCGA.
Results
The high-CNVA group had higher expression levels of PD-L1, CD39 and CD19 and a higher degree of infiltration of CD8+ T cells and CD3 + T cells. Among the 23 patients treated with immunotherapy, the average CNVA value of the stable disease/partial response group was higher than that of the progressive disease group (P < 0.05). Whole-genome sequencing data of 509 patients from TCGA and RT-PCR results of 22 frozen specimens showed that CNVA is more effective than TMB in indicating infiltration of CD8+ T cells and expression of PD-L1, and CNVA also showed a specific positive correlation with TMB (r = 0.2728, P < 0.0001). Conclusions: Copy number variation can be a good indicator of immune infiltration and immunotherapy efficacy, and with its low cost, it is expected to become a substitute for TMB.