Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome

Abstract

Background: Bardet-Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants.

Methods: Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review.

Results: We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7-kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements.

Conclusion: This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.

Keywords: BBS1; BBS; Bardet-Biedl syndrome; SVA; ciliopathy; human genome; mutation; repetitive element; transposable element.

Figure 1

(a) Pedigree of the affected family and BBS1 variant segregation; (b) retinal photography of the right eye centered on the optic nerve (ON, left image) and on the nasal retina (right image). Gray arrow locates the foveal area which shows atrophy (center of the retina), and a blunted reflex. Filled white arrow (right) points toward narrowed (very thin) vessels, p: bone spiculing pigmentary deposits typical of retinal degeneration. (c) Optical coherence tomography (OCT) of the right eye centered on the fovea (gray arrow) shows markedly disruption of outer retinal layers including the photoreceptor outer and inner segments, and the outer nuclear layer. rnfl: retinal nerve fiber layer, c: choroidal layer. Insert to the right shows the area scanned (green line). The quality of the images was limited due to the patient's ability to participate

Figure 2

Disease‐causing mutations in the proband with retrotransposon insertion detail. Pathogenic mutations are represented in purple, Target Site Duplication (TSD) is shown in cyan, and exon is represented in blue. (a) Schematic representation of the retrotransposon insertion in exon 13 of BBS1 in Integrative Genome Viewer using the whole exome and the whole genome sequence alignment maps, respectively (Robinson et al., 2011). Nucleotides matching the reference are gray; unmatched A, T, C, and G nucleotides to reference are color coded in green, red, blue, and orange, respectively. (b) Schematic diagram of the two alleles comprising both BBS1 mutations (Met390Arg and the exonic TE insertion in exon 13) observed in the proband and parents. (c) Detailed characterization of the novel SVAF insertion detected in this study and schematic representation of the results used to assemble the mutation map. Each PCR product is represented as a bar overlapping the region they comprise in the mutation map. Chromatograms from Sanger sequencing represent the BBS1‐SVAF junction