Telomeric chromosome abnormalities are a substantial cause of mental retardation and birth defects. Although subtelomeric fluorescence in situ hybridization (FISH) probes have been widely used to identify submicroscopic telomeric rearrangements, array-based comparative genomic hybridization (array CGH) has emerged as a more efficient and comprehensive detection method. Due to the clinical relevance of telomeric abnormalities, it has been proposed that array CGH using panels of BAC clones that map to regularly spaced intervals along the length of each telomere could be used to characterize subtelomeric aberrations more precisely in a single experiment. We have added 1,120 FISH-mapped BAC clones to our microarray to enhance the coverage of the 41 unique human subtelomeric regions. Contigs of clones were selected in increments of approximately 0.5 Mb beginning with the most distal unique sequence for each subtelomere and extending on average approximately 5.7 Mb toward the centromere. We have used this microarray to characterize 169 clinically significant subtelomeric abnormalities identified out of nearly 7,000 consecutive clinical cases analyzed by array CGH in our diagnostic laboratory. The expanded telomere coverage was sufficient to define the breakpoints of over half (56%) of the chromosome abnormalities. However, 44% of the subtelomeric aberrations extended beyond the size of this expanded coverage suggesting that many subtelomeric abnormalities are >5 Mb in size and that greater representation may be of even more value. In addition to identifying 6 cases of complex rearrangements, we have identified 42 cases of interstitial deletions that would have been missed by subtelomere FISH panels that use a single clone to the most distal unique sequence for each region. Microarrays designed to investigate regions known to be involved in chromosome abnormalities will enhance the detection of cytogenetic abnormalities at unprecedented resolution and frequency.

Objective To develop a novel, rapid prenatal assay for pregnancies with high likelihood of normal karyotypes, using BACs‐on‐Beads™ technology, a suspension array‐based multiplex assay that employs Luminex® xMAP® technology, for the detection of gains and losses in chromosomal DNA. Methods Fifteen relatively common microdeletions were selected that are not detectable, or may be missed, by karyotyping and usually do not present with abnormal ultrasound findings. Chromosomes 13, 18, 21, X, and Y were included. We validated the assay with 430 samples. Results All microdeletions and aneuploidies were correctly identified, except for a 69,XXX incorrectly identified as a normal female and a male with ∼20% maternal cell contamination (MCC) that could not be distinguished from 69,XXY. MCC became apparent at 20 to 30%. Mosaicism was identified at 30 to 35% abnormal cells. Conclusion We have developed an alternative to fluorescence in situ hybridization (FISH) aneuploidy screening and microarray analysis in otherwise normal pregnancies undergoing invasive testing. We demonstrated that the assay will detect all microdeletions and aneuploidies of regions covered on the assay. We developed analytical software that displays results for well‐characterized syndromes but not abnormalities of unclear clinical significance. This assay is likely to be preferred by women seeking testing beyond routine karyotyping but who desire more information than provided by aneuploidy FISH. Copyright © 2011 John Wiley & Sons, Ltd.

Purpose: Small supernumerary marker chromosomes are centric chromosomal segments that, by definition, cannot be characterized unambiguously by conventional chromosome banding. Marker chromosomes are of particular interest in clinical cytogenetics because they are nearly 10 times more frequent in individuals with mental retardation (0.426%) than in the normal population (0.043%). However, they are often found in only a small percentage of cells, making them difficult to detect and characterize in a diagnostic setting. We designed, constructed, and employed a bacterial artificial chromosome (BAC)-based microarray to demonstrate the utility of array-based comparative genomic hybridization (array CGH) for detecting and characterizing marker chromosomes in clinical diagnostic specimens. Methods: We constructed a high-density microarray using 974 BAC clones that were mapped by fluorescence in situ hybridization and cover approximately 5 Mb of the most proximal unique sequence adjacent to the centromere on all 43 unique pericentromeric regions of the human genome (excluding the acrocentric short arms). This array was used to further characterize 20 previously identified marker chromosomes that were originally found with either conventional chromosome analysis or a targeted microarray. Results: The enhanced coverage of this pericentromeric array not only identified the chromosomal origin of each marker in 15 cases, it also distinguished between the involvement of the short arm and/or the long arm of each chromosome, defined the sizes of many of the markers, and revealed complex rearrangements or multiple markers in single individuals. However, in five cases, the markers could not be identified by this assay, most likely because of very low levels of mosaicism and/or their small size and lack of detectable euchromatin. The expanded coverage of the pericentromeric regions represented on the array was adequate to refine the breakpoints in two-thirds of all cases in which a marker chromosome was identified by this assay. Conclusions: This study demonstrates the utility of array CGH in the detection and characterization of mosaic marker chromosomes. Because approximately one-third of the markers characterized in this study involved more unique sequence than that represented on this array, additional pericentromeric coverage may be even more valuable. We anticipate that this will allow detailed characterization of small supernumerary marker chromosomes that will greatly facilitate phenotype/genotype correlations and play a valuable role in the diagnosis and medical management of both pre-and postnatal cases in which marker chromosomes have been identified. Genet Med 2007:9(3):150-162.

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