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

Autor:	Bogenschutz EL; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Fox ZD; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Farrell A; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.; USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Wynn J; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA., Moore B; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.; USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Yu L; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA., Aspelund G; Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032, USA., Marth G; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.; USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Yandell M; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.; USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT 84112, USA., Shen Y; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.; Department of Biomedical Informatics, Columbia University Irving Medical Center, New York, NY 10032, USA.; JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Chung WK; Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032, USA.; Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA.; Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA., Kardon G; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
Jazyk:	angličtina
Zdroj:	HGG advances [HGG Adv] 2020 Oct 22; Vol. 1 (1). Date of Electronic Publication: 2020 Aug 25.
DOI:	10.1016/j.xhgg.2020.100008
Abstrakt:	The diaphragm is critical for respiration and separation of the thoracic and abdominal cavities, and defects in diaphragm development are the cause of congenital diaphragmatic hernias (CDH), a common and often lethal birth defect. The genetic etiology of CDH is complex. Single-nucleotide variants (SNVs), insertions/deletions (indels), and structural variants (SVs) in more than 150 genes have been associated with CDH, although few genes are recurrently mutated in multiple individuals and mutated genes are incompletely penetrant. This suggests that multiple genetic variants in combination, other not-yet-investigated classes of variants, and/or nongenetic factors contribute to CDH etiology. However, no studies have comprehensively investigated in affected individuals the contribution of all possible classes of variants throughout the genome to CDH etiology. In our study, we used a unique cohort of four individuals with isolated CDH with samples from blood, skin, and diaphragm connective tissue and parental blood and deep whole-genome sequencing to assess germline and somatic de novo and inherited SNVs, indels, and SVs. In each individual we found a different mutational landscape that included germline de novo and inherited SNVs and indels in multiple genes. We also found in two individuals a 343 bp deletion interrupting an annotated enhancer of the CDH-associated gene GATA4 , and we hypothesize that this common SV (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. Competing Interests: Declaration of Interests The authors declare no competing interests.
Databáze:	MEDLINE
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