Analysis of Mutant-Allele Isoform Expression of TP53 in Breast Cancer

Exonic mutations of TP53 in breast cancer can be detected and analyzed using RNA-sequencing (RNA-seq) data. However, the analysis often neglects their impacts at isoform level of transcriptome. In this study, we quantify mutant-allele isoform expression of TP53 from the RNA-seq samples for breast cancer patients and investigate their association with the patient's outcomes. The approach is applied to two datasets including n=400 breast cancer patients from The Cancer Genome Atlas cohort and n=28 breast cancer cell lines from the Cancer Cell Line Encyclopedia project. The results show that mutant-allele isoform expression is highly expressed in the breast cancer samples. In addition, the low mutant expression of the NM_001276761 isoform of TP53 is associated with better patient survival. We also identify 12 drugs that their sensitivities are highly correlated with the mutant expression ratio of the isoform.