Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method

Abstract

For the Focus Section on Array-CGHGenomic copy-number variations (CNVs) involving large DNA segments are known to cause many genetic disorders. Depending on the changes, they are predicted to lead either to decreased or an increased gene expression. However, the ability to detect smaller exonic copy-number changes has not been explored. Here we describe a new oligonucleotide-based comparative genomic hybridization (CGH)-array approach for highthroughput detection of exonic deletions or duplications and its application to deletion/duplication analyses of the genes encoding CFTR, six sarcoglycans (SGCA, SGCB, SGCG, SGCD, SGCE, and SGCZ), and DMD. In this work we show the successful development of an array format containing 158 exons that collectively span eight genes and its clinical application for the rapid screening of deletions and duplications in a diagnostic setting. We have analyzed a series of 35 DNA samples from patients affected with cystic fibrosis (CF), Duchenne and Becker muscular dystrophies (DMD/BMD), or sarcoglycanopathies, and have characterized exonic copy-number changes that have been validated with other methods. Interestingly, even heterozygous deletions and duplications of only one exon, as well as mosaic deletions, were detected by this CGH approach. Our results showed that the resolution is very high, as abnormalities of about 1.5-2 kb could be detected. Since this approach is completely scalable, this new molecular tool will allow the screening of combinations of genes involved in a particular group of clinically and genetically heterogeneous disorders such as mental retardation, muscular dystrophies and brain malformations. Hum Mutat 29(9), [1083][1084][1085][1086][1087][1088][1089][1090] 2008.

Comprehensive oligonucleotide array-comparative genomic hybridization analysis: new insights into the molecular pathology of the DMD gene

“…In conclusion, this large survey of 50 patients confirmed the previous observations [10][11][12][13] that array-CGH is a reliable and effective tool in detecting simple and complex DMD rearrangements. This approach offers some advantages over exon-based detection methods as it can identify pure intronic pathogenic events and it allows precise delineation of rearrangements, some of which may affect the splicing process.…”

Genetic and clinical specificity of 26 symptomatic carriers for dystrophinopathies at pediatric age

“…Currently, other diagnostic approaches, such as semi-quantitative fluorescent PCR (MLPA) and use of CGHgene-specific array represent reliable alternatives. 10 The widely proposed explanation for the occurrence of clinical manifestations in heterozygous females is preferential skewed inactivation of the X chromosome bearing the non-mutated DMD allele. [11][12][13][14][15][16] Female carriers with manifesting muscle weakness usually have a mosaic expression of dystrophin in muscle shown by immunostaining, but the question of a correlation between dystrophin expression and clinical weakness remains debatable.…”

Single exon-resolution targeted chromosomal microarray analysis of known and candidate intellectual disability genes

“…6 Although the power of next-generation sequencing has opened up the potential to screen all exons or the whole genome for sequence mutations, the analysis algorithms are not, as yet, robust for routine identification of losses or gains of sequence involving a single or a few exons. As the probe capacity on microarrays increases, there is the potential to screen a large number of genes at the exonic level using microarrays [7][8][9][10] providing the means to identify CNVs that are currently missed with whole-genome clinical arrays and nextgeneration sequencing.…”