Detection and characterization of supernumerary marker chromosomes by array CGH. S.A. Horner¹, S.G. Sulpizio², R.M. Lloyd², B.A. Bejjani^1,2, L.G. Shaffer^1,2, B.C. Ballif². 1) Health Research and Education Center, Washington State University, Spokane, WA; 2) Signature Genomic Laboratories, LLC, Spokane, WA.
   Small supernumerary marker chromosomes are found in ~0.04% of live births. However, the frequency of marker chromosomes is nearly ten times as high (0.41%) in individuals with mental retardation (Liehr et al., 2004). By definition, the characterization of small marker chromosomes can not be done unambiguously by conventional chromosome banding techniques. Furthermore, marker chromosomes are often found in only a small percentage of the cells which can make them difficult to detect without screening large numbers of cells. Array-based comparative genomic hybridization (array-CGH) is a powerful platform which offers high resolution analysis using genomic DNA extracted from uncultured peripheral blood. We have constructed a high-density microarray using 974 FISH-mapped BAC clones covering ~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 characterize the chromosomal content of 11 marker chromosomes found in routine diagnostic specimens. The enhanced coverage of this array over the pericentromeric regions not only uncovered the chromosomal origin of each marker but also distinguished between the involvement of the short arm and/or the long arm of each chromosome, and uncovered complex rearrangements or multiple markers in a single individual. Furthermore, the expanded coverage of the pericentromeric regions was adequate to refine the breakpoints in over half (56%) of the markers. However, 44% of the markers contained 5 Mb of unique sequence suggesting that additional coverage in the pericentromeric regions may be even more valuable in characterizing these rearrangements. Finally, most of these marker chromosomes were mosaic suggesting that array CGH is a powerful tool for the detection and characterization of low-level mosaicism in a clinical diagnostic setting.