Targeted FAIRE-sequencing of breast cancer risk regions in two breast cancer cell lines

Purpose: The goal of this study was to identify allele-specific open chromatin regions in breast cancer cell lines, focusing on the fraction of the genome that has been previously associated to breast-cancer risk. Methods: DNA obtained from Angilent SureSelect solution-based sequence capture was subjected to Illumina HiSeq 2500 paired-end sequencing (Illumina). We performed targeted sequencing of 3 replicated FAIRE samples per cell-line and the correspondent genomic DNA controls in two breast cancer cell lines (T47D and MDAMB134). Allele-specific analysis was performed with BaalChIP R package (version 0.1.9) with the default parameters and options. Results: Using targeted sequencing, we investigated 69 genomic loci that have been previously associated to breast cancer risk. We identified a total of 21 allele-specific SNPs in MDAMB134 and allele-specific 9 SNPs in T-47D cell lines (see processed files). Targeted FAIRE sequencing of breast cancer risk regions. FAIRE-seq and the correspondent genomic DNA control samples were obtained in two breast cancer cell lines (T47D and MDAMB134). Three replicates per experiment.