Abstract: Whole exon sequencing is a genomic analysis method that uses sequence capture technology to capture and enrich the whole genome exon region DNA for high-throughput sequencing. This technology has been applied to gene diagnosis and treatment of various complex diseases. At present, the pathogenesis of breast cancer has not been clearly elucidated, and the activation of oncogenes and the inactivation of tumor suppressor genes caused by gene mutation of somatic cells play a crucial role in the development of breast cancer. In recent years, numerous research groups have carried out a large number of whole exon sequencing researches, found and identified many genetic mutations associated with complex diseases/traits, which provide important clues for the study of the pathogenesis of complex diseases. This paper reviews the pathogenesis and diagnosis and treatment of breast cancer by whole exon sequencing.