Association Of Gene Copy Number Research Articles

Determination of Beta-Defensin Genomic Copy Number in Different Populations: A Comparison of Three Methods

BackgroundThere have been conflicting reports in the literature on association of gene copy number with disease, including CCL3L1 and HIV susceptibility, and β-defensins and Crohn's disease. Quantification of precise gene copy numbers is important in order to define any association of gene copy number with disease. At present, real-time quantitative PCR (QPCR) is the most commonly used method to determine gene copy number, however the Paralogue Ratio Test (PRT) is being used in more and more laboratories.FindingsIn this study we compare a Pyrosequencing-based Paralogue Ratio Test (PPRT) for determining beta-defensin gene copy number with two currently used methods for gene copy number determination, QPCR and triplex PRT by typing five different cohorts (UK, Danish, Portuguese, Ghanaian and Czech) of DNA from a total of 576 healthy individuals. We found a systematic measurement bias between DNA cohorts revealed by QPCR, but not by the PRT-based methods. Using PRT, copy number ranged from 2 to 9 copies, with a modal copy number of 4 in all populations.ConclusionsQPCR is very sensitive to quality of the template DNA, generating systematic biases that could produce false-positive or negative disease associations. Both triplex PRT and PPRT do not show this systematic bias, and type copy number within the correct range, although triplex PRT appears to be a more precise and accurate method to type beta-defensin copy number.

Aurora-A gene is frequently amplified in basal-like breast cancer

Aurora-A is a serine-threonine kinase having vital cellular functions in mitosis and is a promising target for therapy in treating patients with cancer. This study assesses the clinicopathological associations of AURKA gene amplification in clinical breast tumors and association of gene copy number with its mRNA and protein expression in breast cancer cell lines. In this pilot study, we examined Aurora-A gene (AURKA) amplification in 126 clinical breast tumors by chromogenic in situ hybridisation (CISH). AURKA amplification (found in 21%) showed an association with basal-like tumor phenotype (p=0.046). A separate series of basal-like breast tumors (n=26) provided further evidence of the importance of AURKA in these tumors. AURKA amplification status was associated with immunohistochemically detectable Aurora-A protein expression (p<0.0001). In breast cancer cell lines, gene amplification was strongly associated with high mRNA expression (p<0.0001). JIMT-1 cell line was found as a possible in vitro model system for testing Aurora-A inhibitors, since it has been classified as basal-like breast cancer and here it showed both AURKA gene amplification and elevated mRNA expression. AURKA gene amplification is a common genetic aberration in breast cancer, especially in tumors displaying basal-like phenotype. Thus, these patients might be suitable candidates for future targeted therapies with Aurora-A inhibitors.

3019 POSTER Association of gene copy number (GCN) of the epidermal growth factor receptor (EGFr) and clinical outcome in patients (pts) with metastatic colorectal cancer (mCRC) treated with panitumumab monotherapy

3019 POSTER Association of gene copy number (GCN) of the epidermal growth factor receptor (EGFr) and clinical outcome in patients (pts) with metastatic colorectal cancer (mCRC) treated with panitumumab monotherapy