Genome-wide oligonucleotide-based array comparative genome hybridization analysis of non-isolated congenital diaphragmatic hernia.
Non-isolated congenital diaphragmatic hernia (CDH+) is a severe birth defect that is often caused by de novo chromosomal anomalies. In this report, we use genome-wide oligonucleotide-based array comparative genome hybridization (aCGH) followed by rapid real-time quantitative PCR analysis to identify, confirm and map chromosomal anomalies in a cohort of 26 CDH+ patients. One hundred and five putative copy number changes were identified by aCGH in our cohort of CDH+ patients. Sixty-one of these changes (58%) had been previously described in normal controls. Twenty of the remaining 44 changes (45%) were confirmed by quantitative real-time PCR or standard cytogenetic techniques. These changes included de novo chromosomal abnormalities in five of the 26 patients (19%), two of whom had previously normal G-banded chromosome analyses. Data from these patients provide evidence for the existence of CDH-related genes on chromosomes 2q37, 6p22-25 and 14q, and refine the CDH minimal deleted region on 15q26 to an interval that contains COUP-TFII and only eight other known genes. Although COUP-TFII is likely to play a role in the development of CDH in patients with 15q26 deletions, we did not find COUP-TFII mutations in 73 CDH samples. We conclude that the combination of oligonucleotide-based aCGH and quantitative real-time PCR is an effective method of identifying, confirming and mapping clinically relevant copy number changes in patients with CDH+. This method is more sensitive than G-banded chromosome analysis and may find wide application in screening patients with congenital anomalies.
Scott
Daryl A
DA
Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
Klaassens
Merel
M
Holder
Ashley M
AM
Lally
Kevin P
KP
Fernandes
Caraciolo J
CJ
Galjaard
Robert-Jan
RJ
Tibboel
Dick
D
de Klein
Annelies
A
Lee
Brendan
B
D002869:Chromosome Aberrations; D002871:Chromosome Banding; D002883:Chromosomes, Human, Pair 14; D002889:Chromosomes, Human, Pair 2; D002896:Chromosomes, Human, Pair 6; D005260:Female; D018628:Gene Dosage; D020869:Gene Expression Profiling; D005820:Genetic Testing; D015894:Genome, Human; D006548:Hernia, Diaphragmatic / Q000235:genetics*; D065630:Hernias, Diaphragmatic, Congenital; D006801:Humans; D008297:Male; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis