Project description:This set of experiments includes 38 IDCs, 21 ILCs, 2 lymphnode metastases, and 3 normal breast samples. It is designed to compare gene expression profiles of IDCs and ILCs. Total RNAs from all samples were isolated using TRIzol, amplified using optimized T7 linear amplification protocol, and labeled with Cy5. Stratagen Universal Human Reference RNA was amplified the same way and labeled with Cy3. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
Project description:Invasive ductal carcinomas (IDCs) and invasive lobular carcinomas (ILCs) are the two major pathological types of breast cancer. Epidemiological and histoclinical data suggest biological differences, but little is known about the molecular alterations involved in ILCs. We undertook a comparative large-scale study by both array-compared genomic hybridization and cDNA microarray of a set of 50 breast tumors (21 classic ILCs and 29 IDCs) selected on homogeneous histoclinical criteria. Results were validated on independent tumor sets, as well as by quantitative RT-PCR. ILCs and IDCs presented differences at both the genomic and expression levels with ILCs being less rearranged and heterogeneous than IDCs. Supervised analysis defined a 75-BACs signature discriminating accurately ILCs from IDCs. Expression profiles identified two subgroups of ILCs: typical ILCs ( approximately 50%), which were homogeneous and displayed a normal-like molecular pattern, and atypical ILCs, more heterogeneous with features intermediate between ILCs and IDCs. Supervised analysis identified a 75-gene expression signature that discriminated ILCs from IDCs, with many genes involved in cell adhesion, motility, apoptosis, protein folding, extracellular matrix and protein phosphorylation. Although ILCs and IDCs share common alterations, our data show that ILCs and IDCs could be distinguished on the basis of their genomic and expression profiles suggesting that they evolve along distinct genetic pathways.
Project description:This SuperSeries is composed of the SubSeries listed below. Description of samples employed for the subseries NGS analyses including age, race, ER/PR immunohistochemistry results, ITIL/STIL scores and PAM50 classification is provided in the 'Supplementary Data1_Samples data.xlsx'. Refer to individual Series
Project description:This set of experiments includes 38 IDCs, 21 ILCs, 2 lymphnode metastases, and 3 normal breast samples. It is designed to compare gene expression profiles of IDCs and ILCs. Total RNAs from all samples were isolated using TRIzol, amplified using optimized T7 linear amplification protocol, and labeled with Cy5. Stratagen Universal Human Reference RNA was amplified the same way and labeled with Cy3. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
Project description:We examined a set of human breast cancers that were laser-microdissected from archived formalin fixed paraffin embedded (FFPE) tissue. These samples represent an important resource; however, they also represent a challenging aCGH application, as they tend to have significant amounts of noise. Our goal was to use known aberrations within these samples as a benchmark for determining the ability to differentiate between sample noise and real signal. Keywords: CGH