Genome sequencing reveals a deep intronic splicing <i>ACVRL1</i> mutation hotspot in Hereditary Haemorrhagic Telangiectasia.

Abstract

Hereditary haemorrhagic telangiectasia (HHT) is a genetically heterogeneous disorder caused by mutations in the genes <i>ENG</i>, <i>ACVRL1</i>, and <i>SMAD4.</i> Yet the genetic cause remains unknown for some families even after exhaustive exome analysis. We hypothesised that non-coding regions of the known HHT genes may harbour variants that disrupt splicing in these cases. DNA from 35 individuals with clinical findings of HHT and 2 healthy controls from 13 families underwent whole genome sequencing. Additionally, 87 unrelated cases suspected to have HHT were evaluated using a custom designed next-generation sequencing panel to capture the coding and non-coding regions of <i>ENG</i>, <i>ACVRL1</i> and <i>SMAD4</i>. Individuals from both groups had tested negative previously for a mutation in the coding region of known HHT genes. Samples were sequenced on a HiSeq2500 instrument and data were analysed to identify novel and rare variants. Eight cases had a novel non-coding <i>ACVRL1</i> variant that disrupted splicing. One family had an <i>ACVRL1</i>intron 9:chromosome 3 translocation, the first reported case of a translocation causing HHT. The other seven cases had a variant located within a ~300 bp CT-rich 'hotspot' region of <i>ACVRL1</i>intron 9 that disrupted splicing. Despite the difficulty of interpreting deep intronic variants, our study highlights the importance of non-coding regions in the disease mechanism of HHT, particularly the CT-rich hotspot region of <i>ACVRL1</i>intron 9. The addition of this region to HHT molecular diagnostic testing algorithms will improve clinical sensitivity.