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Am J Hum Genet. 2016 Aug 4;99(2):318-36. doi: 10.1016/j.ajhg.2015.04.023.

Copy-Number Variation Contributes to the Mutational Load of Bardet-Biedl Syndrome.

Author information

  • 1Center for Human Disease Modeling, Duke University School of Medicine, Durham, NC 27701, USA.
  • 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Centro de Pesquisas René Rachou - FIOCRUZ, Belo Horizonte, MG 30190-002, Brazil.
  • 3Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • 4Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
  • 5Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Ophthalmology, Baylor College of Medicine, Houston, TX 77030, USA.
  • 6Center for Retinal and Macular Degenerations, Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel.
  • 7Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
  • 8Center for Human Disease Modeling, Duke University School of Medicine, Durham, NC 27701, USA. Electronic address: erica.davis@duke.edu.
  • 9Center for Human Disease Modeling, Duke University School of Medicine, Durham, NC 27701, USA. Electronic address: katsanis@cellbio.duke.edu.

Abstract

Bardet-Biedl syndrome (BBS) is a defining ciliopathy, notable for extensive allelic and genetic heterogeneity, almost all of which has been identified through sequencing. Recent data have suggested that copy-number variants (CNVs) also contribute to BBS. We used a custom oligonucleotide array comparative genomic hybridization (aCGH) covering 20 genes that encode intraflagellar transport (IFT) components and 74 ciliopathy loci to screen 92 unrelated individuals with BBS, irrespective of their known mutational burden. We identified 17 individuals with exon-disruptive CNVs (18.5%), including 13 different deletions in eight BBS genes (BBS1, BBS2, ARL6/BBS3, BBS4, BBS5, BBS7, BBS9, and NPHP1) and a deletion and a duplication in other ciliopathy-associated genes (ALMS1 and NPHP4, respectively). By contrast, we found a single heterozygous exon-disruptive event in a BBS-associated gene (BBS9) in 229 control subjects. Superimposing these data with resequencing revealed CNVs to (1) be sufficient to cause disease, (2) Mendelize heterozygous deleterious alleles, and (3) contribute oligogenic alleles by combining point mutations and exonic CNVs in multiple genes. Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessive paradigm, defining a candidate BBS locus. Our data suggest that CNVs contribute pathogenic alleles to a substantial fraction of BBS-affected individuals and highlight how either deletions or point mutations in discrete splice isoforms can induce hypomorphic mutations in genes otherwise intolerant to deleterious variation. Our data also suggest that CNV analyses and resequencing studies unbiased for previous mutational burden is necessary to delineate the complexity of disease architecture.

KEYWORDS:

ciliopathy; mechanism of rearrangements; oligogenic disease; zebrafish model

PMID:
27486776
PMCID:
PMC4974085
DOI:
10.1016/j.ajhg.2015.04.023
[PubMed - in process]
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