Fine Breakpoint Mapping by Genome Sequencing Reveals the First Large X Inversion Disrupting the NHS Gene in a Patient with Syndromic Cataracts

Abstract

Inversions are structural variants that are generally balanced. However, they could lead to gene disruptions or have positional effects leading to diseases. Mutations in the NHS gene cause Nance-Horan syndrome, an X-linked disorder characterised by congenital cataracts and dental anomalies. Here, we aimed to characterise a balanced pericentric inversion X(p22q27), maternally inherited, in a child with syndromic bilateral cataracts by breakpoint mapping using whole-genome sequencing (WGS). 30× Illumina paired-end WGS was performed in the proband, and breakpoints were confirmed by Sanger sequencing. EdU assays and FISH analysis were used to assess skewed X-inactivation patterns. RNA expression of involved genes in the breakpoint boundaries was evaluated by droplet-digital PCR. We defined the breakpoint position of the inversion at Xp22.13, with a 15 bp deletion, disrupting the unusually large intron 1 of the canonical NHS isoform, and also perturbing topologically-associated domains (TADs). Moreover, a microhomology region of 5 bp was found on both sides. RNA analysis confirmed null and reduced NHS expression in the proband and his unaffected mother, respectively. In conclusion, we report the first chromosomal inversion disrupting NHS, fine-mapped by WGS. Our data expand the clinical spectrum and the pathogenic mechanisms underlying the NHS defects.

Whole‐genome sequencing analysis in fetal structural anomalies: novel phenotype–genotype discoveries

“…Although simultaneous CMA and ES could reduce the turnaround time to 10-14 days 28,29 , there is a risk of misdiagnosis in complex cases due to separate analyses. Moreover, WGS refines breakpoints at a nucleotide-level resolution, which is crucial for identifying involved genes or regulatory elements and interpreting genotype-phenotype associations 30 . However, its utilization and clinical implementation is limited currently, due to high cost 31 and challenges in interpreting a great number of variants of uncertain significance and intronic variants because of the lack of referable databases and sophisticated professional multidisciplinary systems.…”

A novel Nance-Horan syndrome mutation identified by next-generation sequencing in a Chinese family

“…N ance-Horan syndrome (NHS; MIM 302350), a rare X-linked syndrome characterized by congenital bilateral cataracts and dental abnormity, was first reported in 1974 by two studies independently [1][2] . So far, this syndrome has been reported in different ethnic groups and reveal variable clinical features [3][4][5][6] . Male patients manifest severe bilateral congenital nuclear cataracts, including opacity in the fetal nucleus and posterior Y-suture; thus, surgical intervention should be performed at an early age [7] .…”