The use of array-based comparative genomic hybridization to identify chromosome abnormalities
Comparative Genomic Hybridization by microarray (array-CGH) is a relatively new technology that is used to identify microscopic and submicroscopic cytogenetic abnormalities. In our laboratory, we use the SignatureChip® which has BAC contigs that represent 140 clinical loci and 164 control loci. The clinical loci include common and rare microdeletion syndromes, 41 subtelomeres, and 43 pericentromeric regions. To date, Signature Genomic Laboratories has processed over 3,000 cases for microarray analysis. The indications for study were comparable to those normally encountered by a clinical cytogenetics laboratory. Evaluation of the abnormalities revealed that ~6% had clinically relevant DNA copy number changes. Among these cases, ~40% of abnormal cases had a subtelomeric abnormality including terminal deletions, unbalanced translocations and interstitial deletions, the latter of which would not be identified by subtelomeric FISH. The most common altered telomere was 1p36, comprising nearly 10% of all abnormalities identified. Among these cases, deletions, duplications, and unbalanced translocations were identified. Additionally, ~46% of abnormalities were of regions other than the subtelomeres, indicating that these regions are also of great clinical diagnostic importance in the populations studied and would not be identified by a subtelomere FISH assay. Finally, ~14% of abnormalities were mosaic aneuploidies and marker chromosomes. Confirmatory FISH analyses on direct blood smears indicate that the percentage of abnormal cells in unstimulated cultures was up to twice that of PHA-stimulated cells. This suggests that there may be a selection bias introduced in the culturing process as compared to array-CGH, which is based on genomic DNA extracted directly from uncultured cells. Thus, chromosomal mosaicism is likely under-ascertained and much more frequent than currently estimated by routine cytogenetic analysis and that stimulated peripheral blood cultures likely distort the percentage of abnormal cells, and for some abnormalities, may make the detection unlikely by chromosome analysis. Overall, the detection rate of cytogenetic abnormalities by array-CGH is nearly twice that of conventional chromosome analysis.