Somatic mutation detection from ER Chip-Seq

Since corresponding control tissues are not available for the ER ChIP-seq data, we used mutation sites that are identified from the 560 WGS BRCA-EU samples [4, 26] and are within 200 bps of ERBS summits as potential somatic mutation sites. Bam files for the 9 ER ChIP-seq samples with good outcome, and the 12 samples with poor or metastasis outcome were merged for mutation discovery [23]. Then, we used bam-readcount (https://github.com/genome/bam-readcount) to get the counts of different alleles covering the potential mutation sites in the two merged bam files. To increase the credibility of somatic mutations identified from the ChIP-seq data, only the sites covered with at least 10 reads and encompassing both the reference and alternative alleles in BRCA-EU were selected as potential somatic mutations. In the end, the percentage of outcome-associated ERBS that contain potential somatic mutations was calculated for samples with corresponding outcomes.