The clinical utility of enhanced subtelomeric coverage in array CGH

Abstract

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.

Cryptic Chromosomal Abnormalities Identified in Children With Congenital Heart Disease

“…However, a single test, array CGH, detected all of the chromosomal copy number changes and simultaneously defined the chromosome breakpoints. In addition, high resolution oligonucleotide array CGH can detect complex subtelomeric rearrangements, such as the deletion of chromosome 7 in Subject A20, which may be missed by subtelomeric FISH panels that use single large clones to the most distal unique sequences (26).…”

Telomere healing following DNA polymerase arrest-induced breakages is likely the main mechanism generating chromosome 4p terminal deletions

“…There are two lines of evidence that imply that all chromosome 4p telomeres analyzed were healed by telomerase [Ballif et al, 2007]. In vitro studies have demonstrated that telomerase preferably adds a segment of the telomeric hexamer repeat unit onto a DNA fragment at its 3' end.…”

“…Terminal chromosomal deletions are the most common class of subtelomeric abnormalities and are often associated with mental retardation and multiple congenital anomalies [Ballif et al, 2007]. The most frequent terminal deletion syndromes include the 1p36 deletion syndrome (MIM 607872), the 4p terminal deletion leading to Wolf-Hirschhorn syndrome (MIM 194190), the 5p terminal deletions causing Cri-du-chat syndrome (MIM 123450), the 16p terminal deletion leading to alpha thalassaemia (MIM 141750), 9q34 deletion syndrome (MIM 610253) and the 22q terminal deletion syndrome (MIM 606232).…”

“…In a recent study on chromosome 9q deletions, only 2 out of 14 apparently pure terminal deletions could be sequenced [Yatsenko et al, 2009] . The inability to analyze the breakpoints may relate to the complexity of the genomic sequence at the breakpoint such as inverted and tandem duplications or intervening sequence of unknown or ectopic origin Ballif et al, 2007;Rooms et al, 2007;Gajecka et al, 2007]. Another reason for the inability to identify precisely the genomic location of the telomeric breakpoint is its location within repetitive sequences [D'Angelo et al, 2009].…”

Genomics, Intellectual Disability, and Autism

“…Another assay that FISH permitted was the investigation of subtelomeric deletions and duplications, which were found to cause 2.5 to 5% of previously unexplained intellectual disability. [16][17][18] The more recent introduction of genomewide techniques to identify submicroscopic copynumber changes has revolutionized both the approach used in the laboratory to identify chromosome abnormalities that are responsible for intellectual disability and the diagnostic approach used in the clinic for patients with developmental delays or intellectual disability. The two techniques that are routinely used for discovery of copy-number changes are array CGH and SNP genotyping arrays, collectively referred to as chromosome microarrays (see text box).…”