Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet–Biedl Syndrome 9 (BBS9) deletion

Abstract

Bardet–Biedl syndrome (BBS) is a recessive disorder characterized by heterogeneous clinical manifestations, including truncal obesity, rod-cone dystrophy, renal anomalies, postaxial polydactyly, and variable developmental delays. At least 20 genes have been implicated in BBS, and all are involved in primary cilia function. We report a 1-year-old male child from Guyana with obesity, postaxial polydactyly on his right foot, hypotonia, ophthalmologic abnormalities, and developmental delay, which together indicated a clinical diagnosis of BBS. Clinical chromosomal microarray (CMA) testing and high-throughput BBS gene panel sequencing detected a homozygous 7p14.3 deletion of exons 1–4 of BBS9 that was encompassed by a 17.5 Mb region of homozygosity at chromosome 7p14.2–p21.1. The precise breakpoints of the deletion were delineated to a 72.8 kb region in the proband and carrier parents by third-generation long-read single molecule real-time (SMRT) sequencing (Pacific Biosciences), which suggested non-homologous end joining as a likely mechanism of formation. Long-read SMRT sequencing of the deletion breakpoints also determined that the aberration included the neighboring RP9 gene implicated in retinitis pigmentosa; however, the clinical significance of this was considered uncertain given the paucity of reported cases with unambiguous RP9 mutations. Taken together, our study characterized a BBS9 deletion, and the identification of this shared haplotype in the parents suggests that this pathogenic aberration may be a BBS founder mutation in the Guyanese population. Importantly, this informative case also highlights the utility of long-read SMRT sequencing to map nucleotide breakpoints of clinically relevant structural variants.

Complete genome sequence unveiled cellulose degradation enzymes and secondary metabolic potentials in Streptomyces sp. CC0208

“…Sequence reads were generated from 10 kb SMRT Bell library and 350 bp library. After sub‐read filtering of raw data from the PacBio RS II and Illumina PE150 sequencer, the low quality reads were filtered by the SMRT Link 5.0.1 and the filtered reads were assembled.…”

Long-Read Sequencing Emerging in Medical Genetics

“…The fine-mapping of SVs at single-nucleotide resolution is important for patients in which translocation or inversion breakpoints disrupt disease causing genes (Chen et al, 2010). For this, long reads are highly beneficial and may render mapping by laborious amplicon-based Sanger sequencing obsolete, as demonstrated by Reiner et al (2018) who used SMRT to fine-map BBS9 deletion in a patient with Bardet–Biedl syndrome. In another diagnostic case-study, ONT-WGS was able to track down the exact breakpoints of a reciprocal translocation, which led to the identification of disrupted ARHGEF9 gene in a girl with intellectual disability (Dutta et al, 2018).…”

Maternal effects shape the alternative splicing of parental alleles in reciprocal cross hybrids of Megalobrama amblycephala × Culter alburnus

“…After obtaining the sequencing data, adaptors were deleted using SMRTLINK (v 5.0.1) [43,44]. Low-quality data (such as adaptor sequences, subreads < 50 bp, and reads with accuracy rates < 0.75) were deleted from the raw data.…”