Detection of exonic copy-number changes using a highly efficient oligonucleotide-based comparative genomic hybridization-array method.
Genomic 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 high-throughput 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.
Saillour
Yoann
Y
Institut Cochin, Université Paris Descartes, Paris, France.
Cossée
Mireille
M
Leturcq
France
F
Vasson
Aurélie
A
Beugnet
Caroline
C
Poirier
Karine
K
Commere
Virginie
V
Sublemontier
Sébastien
S
Viel
Marion
M
Letourneur
Franck
F
Barbot
Jean Claude
JC
Deburgrave
Nathalie
N
Chelly
Jamel
J
Bienvenu
Thierry
T
D003550:Cystic Fibrosis / Q000175:diagnosis / Q000235:genetics; D019005:Cystic Fibrosis Transmembrane Conductance Regulator / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods; D016189:Dystrophin / Q000235:genetics; D005091:Exons / Q000235:genetics*; D005260:Female; D018628:Gene Dosage / Q000235:genetics*; D030342:Genetic Diseases, Inborn / Q000175:diagnosis / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D008722:Methods; D020388:Muscular Dystrophy, Duchenne / Q000175:diagnosis / Q000235:genetics; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D049031:Sarcoglycans / Q000235:genetics
C484258:DMD protein, human; D016189:Dystrophin; D049031:Sarcoglycans; D019005:Cystic Fibrosis Transmembrane Conductance Regulator