First interchromosomal insertion in a patient with cerebral and spinal cavernous malformations

Robin A Pilz,Christian A Hübner,Thomas Liehr,Konrad Schwefel,Matthias Rath,Andreas Spuler,Anja Weise,Ute Felbor,Stefanie Spiegler,Philipp Demmer,Eberhard Gilberg

doi:10.1038/s41598-020-63337-5

Abstract

Autosomal dominant cerebral cavernous malformations (CCM) are leaky vascular lesions that can cause epileptic seizures and stroke-like symptoms. Germline mutations in either CCM1, CCM2 or CCM3 are found in the majority of patients with multiple CCMs or a positive family history. Recently, the first copy number neutral inversion in CCM2 has been identified by whole genome sequencing in an apparently mutation-negative CCM family. We here asked the question whether further structural genomic rearrangements can be detected within NGS gene panel data of unsolved CCM cases. Hybrid capture NGS data of eight index patients without a pathogenic single nucleotide, indel or copy number variant were analyzed using two bioinformatics pipelines. In a 58-year-old male with multiple CCMs in his brain and spinal cord, we identified a 294 kb insertion within the coding sequence of CCM2. Fine mapping of the breakpoints, molecular cytogenetic studies, and multiplex ligation-dependent probe amplification verified that the structural variation was an inverted unbalanced insertion that originated from 1p12-p11.2. As this rearrangement disrupts exon 6 of CCM2 on 7p13, it was classified as pathogenic. Our study demonstrates that efforts to detect structural variations in known disease genes increase the diagnostic sensitivity of genetic analyses for well-defined Mendelian disorders.

Highlights

Autosomal dominant cerebral cavernous malformations (CCM) are leaky vascular lesions that can cause epileptic seizures and stroke-like symptoms
The index patient reported an atrial septal defect and a traumatic L1 vertebral body fracture at the age of 55 years which had been treated with balloon kyphoplasty
We have identified the first interchromosomal insertion, sometimes referred to as interchromosomal insertional translocation (IT), in a CCM patient

Summary

Introduction

Autosomal dominant cerebral cavernous malformations (CCM) are leaky vascular lesions that can cause epileptic seizures and stroke-like symptoms. Fine mapping of the breakpoints, molecular cytogenetic studies, and multiplex ligation-dependent probe amplification verified that the structural variation was an inverted unbalanced insertion that originated from 1p12p11.2 As this rearrangement disrupts exon 6 of CCM2 on 7p13, it was classified as pathogenic. Pathogenic variants in a yet unknown CCM4 candidate gene have been discussed for unresolved cases[13], we recently were able to identify the first copy number neutral inversion in CCM2 in an apparently mutation-negative CCM family by whole genome sequencing (WGS)[14]. While deletions and duplications of exonic sequences can be reliably detected with qPCR, multiplex ligation-dependent probe amplification or NGS-based CNV detection algorithms, copy number neutral SVs or deletions and duplications in non-coding regions of known disease-associated genes may escape targeted genetic approaches. An interchromosomal insertion which led to an interruption of exon 6 of the CCM2 gene was identified in a sporadic CCM patient

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Conclusion