High-Throughput Analysis of Subtelomeric Chromosome Rearrangements by Use of Array-Based Comparative Genomic Hybridization

Abstract

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome-specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure.

12p-Amplicon structure analysis in testicular germ cell tumors of adolescents and adults by array CGH

“…DOP-PCR was performed on DNA from all clones essentially as described before (Telenius et al, 1992) with minor modifications (Veltman et al, 2002). The DOP-PCR products were robotically spotted in triplicate onto CMT-GAPS-coated glass slides (Corning, Schiphol-Rijk, The Netherlands) using a Cartesian 5510 Prosys arrayer (Genomic Solutions, Cambridgeshire, UK).…”

A tiling resolution DNA microarray with complete coverage of the human genome

“…These arrays are sensitive enough to detect singlecopy changes, but the technique is limited by the small number of BAC markers representing the genome on the slide, rather than the methodology. Even at this resolution, array CGH is useful for detecting chromosomal aberrations associated with congenital abnormalities and somatic malignancies [9][10][11][12] .Recent studies focused on higher-density regional arrays for fine mapping and identifying new genes in specific chromosomal regions [13][14][15][16][17][18] . For example, a candidate oncogene for association with…”

“…These arrays are sensitive enough to detect singlecopy changes, but the technique is limited by the small number of BAC markers representing the genome on the slide, rather than the methodology. Even at this resolution, array CGH is useful for detecting chromosomal aberrations associated with congenital abnormalities and somatic malignancies [9][10][11][12] .…”

Comprehensive analysis of human subtelomeres with combined binary ratio labelling fluorescence in situ hybridisation

“…Among the methods used for the detection of unbalanced subtelomeric chromosome abnormalities are variable number of tandem repeat (VNTR) typing, 5 modified comparative genomic hybridisation (CGH) 6 and array-based CGH, 7 short tandem repeat (STRP) typing, 8 recently also in the form of automated fluorescent genotyping, 9 as well as multiplex amplifiable probe hybridisation (MAPH). 10 However, the most widely used method is fluorescence in situ hybridisation (FISH) which, in contrast to the techniques mentioned above, is additionally able to detect balanced aberrations.…”