Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma.

BACKGROUND: Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors. RESULTS: We tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations. CONCLUSION: Multiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.

Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach.

Effluents are a main source of direct and continuous input of pollutants to the aquatic environment, and can cause ecotoxicological effects at different levels of biological organization. Since gene expression responses represent the primary interaction site between environmental contaminants and biota, they provide essential clues to understand how chemical exposure can affect organismal health. The aim of the present study was to investigate the applicability of a microarray approach for unraveling modes of action of whole effluent toxicity and impact assessment. A chronic toxicity test with common carp (Cyprinus carpio) was conducted where fish were exposed to a control and 100% effluent for 21 days under flow-through conditions. Microarray analysis revealed that effluent treatment mainly affected molecular pathways associated with the energy balance of the fish, including changes in carbohydrate and lipid metabolism, as well as digestive enzyme activity. These gene expression responses were in clear agreement with, and provided additional mechanistic information on various cellular and higher level effects observed for the same effluent. Our results demonstrate the benefit of toxicogenomic tools in a "systems toxicology" approach, involving the integration of adverse effects of chemicals and stressors across multiple levels of biological complexity.