Deep whole genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias

Abstract

The diaphragm is a mammalian muscle critical for respiration and separation of the thoracic and abdominal cavities. Defects in the development of the diaphragm are the cause of congenital diaphragmatic hernia (CDH), a common birth defect. In CDH, weaknesses in the developing diaphragm allow abdominal contents to herniate into the thoracic cavity and impair lung development, leading to a high neonatal mortality. The genetic etiology of CDH is complex. Single nucleotide variants (SNVs), insertion/deletions (indels), and structural/copy number variants in more than 150 genes have been associated with CDH, although few genes are recurrently mutated in multiple patients and recurrently mutated genes can be incompletely penetrant. This suggests that multiple genetic variants in combination, other not yet investigated classes of variants, and/or nongenetic factors contribute to CDH susceptibility. However, to date no studies have comprehensively investigated the contribution of all possible classes of variants throughout the genome to the etiology of CDH. In our study, we used a unique cohort of four patients with isolated CDH with samples from blood, skin, and diaphragm connective tissue and parental blood samples and deep whole genome sequencing to assess germline and somatic de novo and inherited variants of various sizes (SNVs, indels, and structural variants) in exons, introns, UTRs, and intergenic regions. In each patient we found a different mutational landscape that included germline de novo, and inherited SNVs and indels in multiple genes. We also found in two patients an inherited 343 bp deletion interrupting an annotated enhancer of the CDH associated gene, GATA4, and we hypothesize that this common deletion (found in 1-2% of the population) acts as a sensitizing allele for CDH. Overall, our comprehensive reconstruction of the genetic architecture of four CDH individuals demonstrates that the etiology of CDH is heterogeneous and multifactorial.Bogenschutz et al. AUTHOR SUMMARYDeep whole genome sequencing of family trios shows that etiology of congenital diaphragmatic hernias is heterogeneous and multifactorial.

Unraveling the Genetics of Congenital Diaphragmatic Hernia: An Ongoing Challenge

“…In line with this, whole genome sequencing did not find causative somatic variants in diaphragm biopsies (96,97). In contrast, germline de novo variants are often present (33,(96)(97)(98). Females have a higher burden of de novo variants (98), suggesting a female protective model.…”

“…The mutated diaphragmatic cells might not have survived in sufficient quantities and, therefore, be undetectable with sequencing technologies (95). In line with this, whole genome sequencing did not find causative somatic variants in diaphragm biopsies (96,97). In contrast, germline de novo variants are often present (33,(96)(97)(98).…”

Genetic Diagnostic Strategies and Counseling for Families Affected by Congenital Diaphragmatic Hernia

“…Somatic mosaicism is not a major contributor. 54 55 In contrast, de novo variants in the germline can usually be detected in blood. 32 54 55 56 Constrained coding regions are enriched for de novo variants 57 and diagnostic yields of at least 20% are feasible depending on the technology used to determine the genetic variation.…”