By default, significance of allelic imbalances is determined using a standard binomial test, but the AA-ALIGNER pipeline can be easily modified to incorporate alternative statistical methods of detecting imbalance.
AA-ALIGNER also attempts to correct other biases that can influence imbalance detection, such as incorrect heterozygous site annotations in reference genome sequences and incorrectly detected imbalances due to differences in mappability between reads containing each of the alleles or due to PCR duplications introduced during sequencing [ 25].
They proposed that the array detected imbalances accounting for the mental retardation and other phenotypic abnormalities observed.
Presence in dbSNP is not a requirement, thus in theory we can detect imbalances due to either de novo point mutation or altered expression of preexisting variants.
Thus, array CGH has the potential to detect imbalances in a considerable percentage of patients who have apparently balanced translocations based on routine cytogenetics, particularly in patients with abnormal phenotypes.
Moreover, most of the detected imbalances (70.6%) were subtelomeric defects (Tables 2 5), which are known to be difficult to characterize by G-banding due to their location in the distal G-negative staining regions of the chromosomes.
Cerebral oximetry is a non-invasive method to detect imbalances in the cerebral oxygen supply/demand-ratio.
Most of the detected imbalances have been repeatedly reported in non-bilharzial bladder carcinomas, suggesting that the cytogenetic profiles of chemical- and bilharzia-induced carcinomas are largely similar.
Of the imbalanced sites, 61 % (11/18) using partial genotypes and 42 % (8/19) using common variants were also imbalanced when using complete genotypes, underscoring the difficulty in using short reads to detect imbalances at predicted heterozygous sites.
Overall, total base coverage and signal dispersion across the genome most affected our ability to detect imbalances, while parameters such as imbalance significance, imputation quality thresholds, and alignment mismatches had little effect.
