miRNA expression profiling of formalin-fixed paraffin-embedded (FFPE) hereditary breast tumors.
Hereditary breast cancer constitutes only 5-10% of all breast cancer cases and is characterized by strong family history of breast and/or other associated cancer types. Only ~ 25% of hereditary breast cancer cases carry a mutation in BRCA1 or BRCA2 gene, while mutations in other rare high and moderate-risk genes and common low penetrance variants may account for additional 20% of the cases. Thus the majority of cases are still unaccounted for and designated as BRCAX tumors. MicroRNAs are small non-coding RNAs that play important roles as regulators of gene expression and are deregulated in cancer. To characterize hereditary breast tumors based on their miRNA expression profiles we performed global microarray miRNA expression profiling on a retrospective cohort of 80 FFPE breast tissues, including 66 hereditary breast tumors (13 BRCA1, 10 BRCA2 and 43 BRCAX), 10 sporadic breast carcinomas and 4 normal breast tissues, using Exiqon miRCURY LNA™ microRNA Array v.11.0. Here we describe in detail the miRNA microarray expression data and tumor samples used for the study of BRCAX tumor heterogeneity (Tanic et al., 2013) and biomarkers associated with positive BRCA1/2 mutation status (Tanic et al., 2014). Additionally, we provide the R code for data preprocessing and quality control.
Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Miljana
M
Tanić
Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Kira
K
Yanowski
Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Eduardo
E
Andrés
Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Gonzalo
G
Gómez-López
Pathology Department, Fundación Jimenez Díaz, Madrid, Spain.
María Rodríguez-Pinilla
MR
Socorro
Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
David G
DG
Pisano
Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.
Beatriz
B
Martinez-Delgado
Human Genetics Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.
Javier
J
Benítez
Hereditary breast cancer; Microarray; miRNA