Abstract
BackgroundCancer 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.ResultsWe 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.ConclusionMultiplex 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.
Highlights
Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance
Construction of the Multiplex Amplicon Quantification (MAQ) neuroblastoma assay The MAQ technique consists of the quantification of fluorescently labelled test and control amplicons, obtained by a single multiplex PCR amplification
As a first step in the construction of the MAQ neuroblastoma assay, primers were designed in the critical regions of loss (1p, 3p and 11q) and gain (2p - the MYCN locus- and 17q) for NB and their respective opposite chromosome arm [12,13,15]
Summary
Cancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. 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. We evaluated the performance of a new method for relative quantification of specific DNA sequences in routine laboratory practice, called Multiplex Amplicon Quantification (MAQ) [5,6,7,8,9]. For this purpose, a MAQ assay was designed for neuroblastoma (NB), the most common solid extra-cranial pediatric malignancy [10]. MAQ results were compared to copy number changes detected with MLPA on a series of 52 NB for which detailed array CGH profiles were available
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