PYGO2 and breast carcinoma: We found that 17 PHF genes, including PYGO2, KDM5B, PHF20L1, and ZMYND8, had a higher frequency (>10%) of gain/amplification, and 9 PHF genes, including CHD3 and PHF23, had a higher frequency of deletion in the METABRIC breast cancer samples (Supplementary Table S6), although the frequency of gain/amplification identified in the METABRIC dataset is lower than that of TCGA dataset, possibly due to the different CNA analysis platforms and calling algorithms.