DNA methylation and hormone receptor status in breast cancer, the BCCC study

ABSTRACT: Genome wide DNA methylation profiling of invasive breast cancer samples isolated from an ethnically diverse group of 80 patients in the Breast Cancer Care in Chicago (BCCC) study. DNA was extracted from formalin fixed, paraffin-embedded samples on 80 patients (21 White, 31 African-American, 23 Hispanic and 5 not reported) (training dataset) enrolled in the BCCC. Hormone receptor status was defined as negative if tumors were negative for both estrogen and progesterone (ER/PR) receptors (N=22/75). Formalin-fixed, paraffin-embedded (FFPE) tumor samples came from the Breast Cancer Care in Chicago (BCCC) study (Dookeran KA, Silva A, Warnecke RB, Rauscher GH: Race/ethnicity and disparities in mastectomy practice in the Breast Cancer Care in Chicago study. Ann Surg Oncol 2015, 22:66–74). Copies of pathology reports and the corresponding set of Hematoxylin and Eosin (H&E) stained slides were requested from the pathology department at each diagnosing institution, and a single pathologist selected tumor blocks representative of the tumor. Two recuts (at 4 µm each) were made from each selected block for H&E staining. The recuts were then examined in order to identify invasive components of the sample, and areas were marked according to tissue component. Cores of invasive tissue (2 mm in diameter) were obtained from the marked areas and DNA was extracted for the DNA methylation study.

ORGANISM(S): Homo sapiens

PROVIDER: GSE72110 | GEO | 2016/02/12

SECONDARY ACCESSION(S): PRJNA292997

REPOSITORIES: GEO