Detection of low‐level mosaicism by array CGH in routine diagnostic specimens

Abstract

The advent of microarray-based comparative genomic hybridization (array CGH) promises to revolutionize clinical cytogenetics because of its ability to rapidly screen the genome at an unprecedented resolution. Yet, the ability of array CGH to detect and evaluate low-level mosaicism is not known. Our laboratory has analyzed over 3,600 clinical cases with the SignatureChip which we developed for the detection of microdeletions, microduplications, aneuploidy, unbalanced translocations, and subtelomeric and pericentromeric copy number alterations. Here, we report 18 cases of mosaicism detected by array CGH in a routine diagnostic setting, 14 of which were not known to us at the time of the analysis. These 14 cases represent approximately 8% of all abnormal cases identified in our laboratory. For each case, fluorescence in situ hybridization (FISH) analysis was performed on PHA-stimulated cultures after mosaic chromosome abnormalities were suspected by array CGH. In all cases, FISH confirmed the mosaic chromosome abnormalities which included a variety of marker chromosomes, autosomal trisomies, terminal and interstitial deletions, and derivative chromosomes. Interestingly, confirmatory FISH analyses on direct blood smears indicated that the percentage of abnormal cells in unstimulated cultures was in some cases different than that found in PHA-stimulated cells. We also report the detection of a previously unsuspected case of an isochromosome 12p (associated with Pallister-Killian syndrome) by array CGH using genomic DNA extracted from peripheral blood. These results support a growing body of data that suggests that stimulated peripheral blood cultures likely distort the percentage of abnormal cells and may, for some chromosome abnormalities, make their detection unlikely by conventional analysis. Thus, array CGH, which is based on genomic DNA extracted directly from uncultured peripheral blood, may be more likely to detect low-level mosaicism for unbalanced chromosome abnormalities than traditional cytogenetic techniques.

Array-CGH fine mapping of minor and cryptic HR-CGH detected genomic imbalances in 80 out of 590 patients with abnormal development

“…33 It illustrates that such mosaicism, similar to our three patients with mosaic trisomy 9 (cases 25-27; Table 1), can be detected by CGH using blood sample DNA even though metaphase studies of blood lymphocyte cultures are completely normal. 10,34 The lowest HR-CGH-detected mosaicism grade was 15%, and this was found in a patient with trisomy 9 (case 27). Previously, mosaicism grade as low as 8% has been detected by 1 Mb array-CGH analysis.…”

A new diagnostic workflow for patients with mental retardation and/or multiple congenital abnormalities: test arrays first

“…Although it was suspected that array analysis would not be able to detect mosaicisms, the aCGH and SNP array techniques actually appear to be more sensitive in detecting low-level mosaicism than conventional karyotyping. 43,44 If mosaicism is not suspected, the number of cells counted with conventional karyotyping may not be sufficient to detect the aberrant subset of cells, and a single abnormal cell might be interpreted as an artifact of cell culture. 45 Two such cases of low-level mosaicism were reported in this study.…”

Comparison of chromosome analysis and chromosomal microarray analysis: what is the value of chromosome analysis in today’s genomic array era?

“…Studies have demonstrated that CMA may be more sensitive when abnormal cells fail to respond to mitogens and/or abnormalities are rare or absent in T cells, such as in PallisterKillian syndrome. 5,6 Five cases of mosaic trisomy, involving chromosomes 8, 9, 14, and 22, were detected only by CMA.…”