Custom oligonucleotide array-based CGH: a reliable diagnostic tool for detection of exonic copy-number changes in multiple targeted genes

Abstract

The frequency of disease-related large rearrangements (referred to as copy-number mutations, CNMs) varies among genes, and search for these mutations has an important place in diagnostic strategies. In recent years, CGH method using custom-designed high-density oligonucleotide-based arrays allowed the development of a powerful tool for detection of alterations at the level of exons and made it possible to provide flexibility through the possibility of modeling chips. The aim of our study was to test custom-designed oligonucleotide CGH array in a diagnostic laboratory setting that analyses several genes involved in various genetic diseases, and to compare it with conventional strategies. To this end, we designed a 12-plex CGH array (135k; 135 000 probes/subarray) (Roche Nimblegen) with exonic and intronic oligonucleotide probes covering 26 genes routinely analyzed in the laboratory. We tested control samples with known CNMs and patients for whom genetic causes underlying their disorders were unknown. The contribution of this technique is undeniable. Indeed, it appeared reproducible, reliable and sensitive enough to detect heterozygous single-exon deletions or duplications, complex rearrangements and somatic mosaicism. In addition, it improves reliability of CNM detection and allows determination of boundaries precisely enough to direct targeted sequencing of breakpoints. All of these points, associated with the possibility of a simultaneous analysis of several genes and scalability ‘homemade' make it a valuable tool as a new diagnostic approach of CNMs.

European Consensus Statement on congenital hypogonadotropic hypogonadism—pathogenesis, diagnosis and treatment

“…21,28,104,157 CHH accompanied by other syndromic features such as congenital ichthyosis 158 or spherocytosis 159 is suggestive of a contiguous gene syndrome for which a karyotype or comparative genomic hybridization array analysis might be useful for identifying underlying chromosomal abnormalities. [159][160][161] Genetic counselling A legitimate question often raised by patients with CHH relates to the risk of passing on the disease to their offspring. 26,127,162 When autosomal dominant transmission is suspected, the patient and partner should receive genetic counselling before fertility-inducing treatment.…”

Detection of TRIM32 deletions in LGMD patients analyzed by a combined strategy of CGH array and massively parallel sequencing

“…CGH normalized data were analyzed using the CGHweb online analysis (http:// compbio.med.harvard.edu/CGHweb) 16 and SignalMap software (Roche-NimbleGen) as previously described. 17 …”

Microdeletion and Microduplication Analysis of Chinese Conotruncal Defects Patients with Targeted Array Comparative Genomic Hybridization

“…It was first used for detecting large CNVs at the scale of multiple contiguous genes in whole genome analysis [15]. But now, more and more studies have applied targeted oligonucleotide CGH arrays because of the high-resolution and flexibility provided by these target designs [16]. We developed a targeted aCGH that permits a high-resolution analysis on Agilent platform for detecting 11 common congenital diseases, such as DiGeorge syndrome, cri du chat syndrome, Prader-Willi syndrome and so on (Table 1).…”