title: Genome-wide oligonucleotide-based array comparative genome hybridization analysis of non-isolated congenital diaphragmatic hernia.
abstract: 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.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Daryl A
authors.initials: DA
authors.lastname: Scott
authors.forename: Merel
authors.initials: M
authors.lastname: Klaassens
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Holder
authors.forename: Kevin P
authors.initials: KP
authors.lastname: Lally
authors.forename: Caraciolo J
authors.initials: CJ
authors.lastname: Fernandes
authors.forename: Robert-Jan
authors.initials: RJ
authors.lastname: Galjaard
authors.forename: Dick
authors.initials: D
authors.lastname: Tibboel
authors.forename: Annelies
authors.initials: A
authors.lastname: de Klein
authors.forename: Brendan
authors.initials: B
authors.lastname: Lee
mesh_terms: 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