Methylome remodeling in regional breast cancer metastasis [DNA methylation]

Genome-wide DNA methylation profiling of of 44 matched primary breast tumors and metastases. We sought to characterize methylome remodeling during regional metastasis. We profiled the DNA methylome (n=44) and transcriptome (n=36) of matched primary breast tumors and regional metastases. All paired samples (n = 88) were obtained following surgical resection at the MSKCC as part of routine clinical care. Tumors were obtained in accordance with Institutional Review Board policies at the MSKCC. Each sample was examined histologically by a breast pathologist and microdissected to achieve >70% tumor cell content. Genomic DNA was extracted using the DNeasy kit (Qiagen) as per the manufacturer’s instructions. Bisulphite converted DNA from the 44 primary breast tumors and matching metastases were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.