Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia

Abstract

Background: Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified.

Objective: To identify genomic alterations that contribute to the development of diaphragmatic defects.

Methods: A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis.

Results: Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype.

Conclusions: Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.

Figure 1

A) Array comparative genomic hybridization data from Patient 1 showing an 8q22.3q23.1 single gene deletion of ZFPM2. B) The relative location of the ZFPM2 gene in relation to aCGH data from the deletion region in Patient 1 is represented by a gray bar. C) A chest radiograph of Patient 1 demonstrating a severe diaphragmatic eventration containing loops of bowel. D) The same radiograph shown in panel C with the limits of the diaphragmatic eventration outlined in yellow. E) Quantitative PCR analysis demonstrates a normal copy number for ZFPM2 Exon 6 but a reduced copy number for Exons 7 and 8 in DNA from Patient 2 (Pt2) and his mother (M). Normal copy number values are seen in DNA from Patient 2’s father (F) and DNA from two unrelated controls (C1, C2).

Figure 2

Array comparative genomic hybridization data from Patient 4 is shown above a schematic representation of a portion of the 1q41–1q42 region. Genes in this region are represented by block arrows. Red vertical bars mark the limits of the deletion in Patient 4 and delineate the minimal deleted region for congenital diaphragmatic hernia (CDH) in this region of the genome. Genes with all or a portion of their coding sequence inside the minimal deleted region are shown in green.