Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma

ArrayCGH is commonly used for high-resolution detection of copy-number alterations in tumours, allowing identification of chromosomal aberrations with prognostic or diagnostic relevance. Currently available arrayCGH platforms are still very expensive for analysis of large sets of samples. For this purpose, we have constructed a dedicated mini-array that is enriched for BAC/PAC clones in the prognostic important regions for neuroblastoma and that only covers a small area on the slide, allowing down-scaling of the labelling and hybridisation reagents and hence reducing the price. The mini-arrays were validated on neuroblastoma samples and comparison with high-resolution whole-genome arrayCGH data yielded complete concordant results.