Illumina HiSeq 2500 paired end sequencing; DNA sequencing of endocrine resistant breast cancer
DNA sequencing of endocrine resistant breast cancer
Surgical specimens were collected and either (i) snap-frozen and stored at -70oC or (ii) fixed in formalin and embedded in paraffin. For fresh frozen tissues, RNA and DNA were isolated using QIAGEN RNAeasy and DNAeasy kits, respectively, according to the manufacturer's protocols. For FFPE tissues, RNA and DNA were isolated with QIAGEN AllPrep FFPE Kit, according to the manufacturer's protocols.   DNA was prepared for sequencing using the Agilent Technologies SureSelect XT library protocol. Fresh-frozen tumors were processed according to the manufacturer's protocol for 3 μg input, while FFPE tumors were processed with the low-volume input according to the manufacturer's protocol for 200 ng input. DNA libraries were captured and amplified with Agilent Technologies SureSelect Human All Exon, version 5 for fresh frozen tissues or version 6 for FFPE tissues, according to the manufacturer's protocol. The quality of both the DNA libraries and DNA exome capture and concentration were quantified with Agilent TapeStation DNA 1000 and High Sensitivity D1000, respectively.