The detected large-scale imbalances were either recurrent or appeared only once in our samples.
In order to exclude any effect of large-scale imbalances (such as trisomies or monosomies), the gene-centered CGH/expression correlations were computed in the relevant genomic regions only for tumors without the large-scale imbalances.
Genomic regions involved in large-scale imbalances such as trisomies or monosomies were analyzed separately by removing data from trisomic or monosomic tumors.
Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose.
The contrasting dose of sex chromosomes in males and females potentially introduces a large-scale imbalance in levels of gene expression between sexes, and between sex chromosomes and autosomes.
Importantly, this report, together with a recent study of sex-biased expression in somatic tissue of chicken, demonstrates the first example of an organism with a lack of global dosage compensation, providing an unexpected case of a viable system with large-scale imbalance in gene expression between sexes.
A number of large scale chromosomal imbalances, including loss of either 1p or 11q or gain of 17q, are also associated with poor survival [3] [5].
In addition, large scale chromosomal imbalances such as gain of chromosomes 1q and 7, and losses of 10q and 13q, reported at high frequencies in primary tumours [24], are present within these cell lines.
These studies have revealed that large scale chromosomal imbalances result in dysregulated miRNAs which have a functional role in neuroblastoma pathogenesis and tumorigenicity.
It is also reassuring for future large scale detection of imbalanced allelic expression that the accuracy of our methods seemed to be similar for cDNA and genomic DNA.
The purpose of our study was to evaluate microarray based minisequencing for multiplexed detection and quantification of imbalanced expression of SNP alleles, as a prelude to further large scale screening for allelic imbalance.
