Data integration from two microarray platforms identifies bi-allelic genetic inactivation of RIC8A in a breast cancer cell line

Background: Using array comparative genomic hybridization (aCGH), a large number of deleted genomic regions have been identified in human cancers. However, subsequent efforts to identify target genes selected for inactivation in these regions have often been challenging. Methods: We integrated here genome-wide copy number data with gene expression data and non-sense mediated mRNA decay rates in breast cancer cell lines to prioritize gene candidates that are likely to be tumour suppressor genes inactivated by bi-allelic genetic events. The candidates were sequenced to identify potential mutations. Results: This integrated genomic approach led to the identification of RIC8A at 11p15 as a putative candidate target gene for the genomic deletion in the ZR-75-1 breast cancer cell line. We identified a truncating mutation in this cell line, leading to loss of expression and rapid decay of the transcript. We screened 127 breast cancers for RIC8A mutations, but did not find any pathogenic mutations. No promoter hypermethylation in these tumours was detected either. However, analysis of gene expression data from breast tumours identified a small group of aggressive tumours that displayed low levels of RIC8A transcripts. qRT-PCR analysis of 38 breast tumours showed a strong association between low RIC8A expression and the presence of TP53 mutations (P = 0.006). Conclusion: We demonstrate a data integration strategy leading to the identification of RIC8A as a gene undergoing a classical double-hit genetic inactivation in a breast cancer cell line, as well as in vivo evidence of loss of RIC8A expression in a subgroup of aggressive TP53 mutant breast cancers.Peer reviewe

Evaluation of MetriGenix custom 4D™ arrays applied for detection of breast cancer subtypes

BACKGROUND: Previously, a total of five breast cancer subtypes have been identified based on variation in gene expression patterns. These expression profiles were also shown to be associated with different prognostic value. In this study tumour samples from 27 breast cancer patients, previously subtyped by expression analysis using DNA microarrays, and four controls from normal breast tissue were included. A new MetriGenix 4D™ array proposed for diagnostic use was evaluated. METHODS: We applied MetriGenix custom 4D™ arrays for the detection of previously defined molecular subtypes of breast cancer. MetriGenix 4D™ arrays have special features including probe immobilization in microchannels with chemiluminescence detection that enable shorter hybridization time. RESULTS: The MetriGenix 4D™ array platform was evaluated with respect to both the accuracy in classifying the samples as well as the performance of the system itself. In a cross validation analysis using "Nearest Shrunken Centroid classifier" and the PAM software, 77% of the samples were classified correctly according to earlier classification results. CONCLUSION: The system shows potential for fast screening; however, improvements are needed

Evaluation of MetriGenix custom 4D™ arrays applied for detection of breast cancer subtypes-1

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of MetriGenix custom 4D™ arrays applied for detection of breast cancer subtypes"</p><p>BMC Cancer 2006;6():59-59.</p><p>Published online 15 Mar 2006</p><p>PMCID:PMC1421426.</p><p>Copyright © 2006 Muggerud et al; licensee BioMed Central Ltd.</p>luminal tumours (group 2, pink squares). Coloured samples names represent the different subtypes previously determined using different microarray technologies: Dark blue = luminal A, light blue = luminal B, green = normal-like, red = basal-like and purple = ERBB2+. M = early breast cancer, F = locally advanced breast cancer

Evaluation of MetriGenix custom 4D™ arrays applied for detection of breast cancer subtypes-2

<p><b>Copyright information:</b></p><p>Taken from "Evaluation of MetriGenix custom 4D™ arrays applied for detection of breast cancer subtypes"</p><p>BMC Cancer 2006;6():59-59.</p><p>Published online 15 Mar 2006</p><p>PMCID:PMC1421426.</p><p>Copyright © 2006 Muggerud et al; licensee BioMed Central Ltd.</p>and B, ERBB2+ and normal-like) and blue squares indicate control samples