Supernumerary marker chromosomes (SMCs) are common, but their molecular content and mechanism of origin are often not precisely characterized. We analyzed all centromere regions to identify the junction between the unique chromosome arm and the pericentromeric repeats. A molecular-ruler clone panel for each chromosome arm was developed and used for the design of a custom oligonucleotide array. Of 27 nonsatellited SMCs analyzed by array comparative genomic hybridization (aCGH) and/or fluorescence in situ hybridization (FISH), seven (approximately 26%) were shown to be unique sequence negative. Of the 20 unique-sequence-positive SMCs, the average unique DNA content was approximately 6.5 Mb (range 0.3-22.2 Mb) and 33 known genes (range 0-149). Of the 14 informative nonacrocentric SMCs, five (approximately 36%) contained unique DNA from both the p and q arms, whereas nine (approximately 64%) contained unique DNA from only one arm. The latter cases are consistent with ring-chromosome formation by centromere misdivision, as first described by McClintock in maize. In one case, a r(4) containing approximately 4.4 Mb of unique DNA from 4p was also present in the proband's mother. However, FISH revealed a cryptic deletion in one chromosome 4 and reduced alpha satellite in the del(4) and r(4), indicating that the mother was a balanced ring and deletion carrier. Our data, and recent reports in the literature, suggest that this "McClintock mechanism" of small-ring formation might be the predominant mechanism of origin. Comprehensive analysis of SMCs by aCGH and FISH can distinguish unique-negative from unique-positive cases, determine the precise gene content, and provide information on mechanism of origin, inheritance, and recurrence risk.

Microarray-based comparative genomic hybridization (aCGH) can determine genome-wide copy number alterations at the kilobase (kb) level. We highlight the clinical utility of aCGH in determining tumor susceptibility in 3 patients with dysmorphic features and developmental delay, likely decreasing both morbidity and mortality in these patients.

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Subtelomeric imbalances have been implicated in developmental delay and mental retardation (MR) and described for most chromosomes. This study reports the first detailed description of two individuals with de novo 12q subtelomere deletions and high-resolution mapping of their deletion size with oligonucleotide array CGH for genotype/phenotype comparisons. Patient 1 is an 8-year-old male with borderline mild MR, food-seeking behavior, obesity, no significant dysmorphic facial features, abnormal hair whorl pattern, brachydactyly and mild clinodactyly. Patient 2 is a 12-year-old male with mild MR, food-seeking behavior, obesity, short stature, mild dysmorphic facial features, multicystic kidney and unilateral cryptorchidism. Both patients share a deleted region of approximately 1.6 Mb, including 14 known genes, which perhaps contributed to their similar phenotypes. However, Patient 2 has more severe MR and organ system involvement, possibly due to the larger deletion size ( approximately 4.5 Mb) including an additional eight genes, although it is difficult to make phenotype/genotype correlations based on only two patients. Due to the relatively mild presentation of both of our patients, we propose that a proportion of individuals with subtelomeric imbalances may go undetected and therefore, recommend subtelomeric studies be carried out for cases of unexplained mild MR or isolated learning disability (LD) with behavioral problems in the absence of major dysmorphic features or birth defects. In addition, 12q subtelomeric deletions should be considered in the differential diagnosis of patients presenting with food-seeking behavior and resultant obesity, as well as those referred to rule out Prader-Willi syndrome.

Submicroscopic telomere imbalances are a significant cause of mental retardation with or without other phenotypic abnormalities. We previously developed a set of unique telomere clones that identify imbalances in 3% to 5% of children with unexplained mental retardation and a normal karyotype. This targeted screening approach, however, does not provide information about the size or gene content of the imbalance. To enable such comprehensive characterization, a "molecular ruler" clone panel, extending up to 5 Mb proximal to the first telomere clone for each chromosome arm, was developed. This panel of clones was successfully used to delineate the size of unbalanced telomere aberrations in a fluorescence in situ hybridization assay. However, the fluorescence in situ hybridization analysis was quite labor-intensive, and for many cases, the imbalance extended beyond our 5-Mb coverage.Therefore, to develop a more efficient and comprehensive method for characterizing telomere imbalances, we developed a custom oligonucleotide microarray consisting of high-density coverage of all telomere regions as well as a whole-genome backbone. Overall, 44 pathogenic imbalances studied by fluorescence in situ hybridization or oligonucleotide array showed a size range of 400 kb to 13.5 Mb. In four of these, the array detected additional interstitial imbalances adjacent to the telomere imbalance, demonstrating the usefulness of added probe coverage. In 10 cases with benign imbalances inherited from a normal parent, the size ranged from 170 kb to 1.6 Mb.These results demonstrate that array comparative genomic hybridization will aid in more efficient and precise characterization of telomere imbalances leading to the development of gene dosage maps at human telomere regions for genotype/phenotype correlations. Genet Med 2007:9(9):566-573.