Genes with significant loss of genomic alterations after neoadjuvant treatment include ZFHX3, CDK12, and EP300, suggesting that, in addition to pro-proliferation (PIK3CA), genomic instability (TP53), cell cycle (CDK12), chromatin remodeling, and epigenetic modification (ARID1A, EP300) are also prevalent in breast cancer. The gene discussed is ZFHX3; the disease is breast cancer.