Review of molecular mechanisms at distal Xq28 leading to balanced or unbalanced genomic rearrangements and their phenotypic impacts on hemophilia

Abstract

The distal Xq28 region is very gene-rich, comprising a relatively large number of low-copy repeats (LCRs) predisposing to genomic rearrangements. The best-known rearrangement at this locus is the F8 intron 22 inversion, responsible for up to 45% of severe hemophilia A (HA) cases. An additional inversion of intron 1 of F8 has more recently been described, affecting 2%-5% of patients with severe HA. These "balanced" rearrangements are mediated by intrachromosomal homologous recombination between inversely oriented LCRs located in intron 1 or 22 and other extragenic copies positioned more telomerically outside the F8 gene. The successive innovations of semi-quantitative technologies like multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (array CGH) have rendered it possible to highlight a significant number of "unbalanced" rearrangements associated or not with these inversions. Some rearrangements are generated by the non-allelic homologous recombination (NAHR) pathway between directly oriented LCRs. Others are probably the result of unequal crossing-over or U-loop exchanges during female meiosis. This review sought to provide an overview of the mechanisms underlying rearrangements at the distal Xq28 locus and discuss their clinical impacts other than HA, such as risks of developing high inhibitor levels and spontaneous abortion, as well as other pathologies like cardiovascular disease or potentially X-linked intellectual disease.

Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

“…Because of the large number of repetitive elements such as Alu elements and LINE present in its sequence and its Xq28 location, the F8 appears to be extremely susceptible to genetic rearrangements . Whole F8 sequencing approaches previously reported were not able to detect F8 structural variant .…”

Tandem and inverted duplications in haemophilia A: Breakpoint characterisation provides insight into possible rearrangement mechanisms

“…Meanwhile, a small part of tandem duplications shares the same breakpoints, which could be explained by another dominant DSBs repair pathway: NAHR 19,21 . In principle, reversely oriented repetitive element mediated NAHR mainly contributes to recurrent inversion, while directly oriented repetitive element mediated NAHR is responsible for recurrent deletion or tandem duplication 37 . Taking int22h copies as an example, int22h‐1 and int22h‐2 are in the same orientation, while int22h‐3 is in the opposite orientation 5 .…”

“…19,21 In principle, reversely oriented repetitive element mediated NAHR mainly contributes to recurrent inversion, while directly oriented repetitive element mediated NAHR is responsible for recurrent deletion or tandem duplication. 37 Taking int22h copies as an example, int22h-1 and int22h-2 are in the same orientation, while int22h-3 is in the opposite orientation. 5 Correspondingly, int22h-1/int22h-3-mediated recurrent inversion makes up 34.7% of the defects of severe HA patients, 2 while int22h-1/int22h-2mediated 0.5 Mb tandem duplication has been described in almost 40 int22h1/Int22h2-mediated Xq28 duplication syndrome individuals.…”

Deciphering a novel complex inversion affecting F8 in a family with severe haemophilia A by optical genome mapping

“…Georges-Etienne Rivard 1,4 Mira Gandhi 5 Patrick Scott 1 Alexandre Montpetit 6 Shu-Huang Chen 3 KyungHee Park 5…”

“…Around 50% of severe HA is caused by recurrent inversions disrupting F8 either in intron 22 (Inv22) or intron 1 (Inv1). 1 Inverse-shifting PCR (IS-PCR 2 ) is one of the standard molecular diagnostic (Dx) assay for detecting Inv22. It sometimes reveals aberrantly sized fragments, which complicates the interpretation of results, leading to the suspicion that more complex genomic rearrangements (CGRs) could be involved.…”