DataSheet1_Case Report: Decrypting an interchromosomal insertion associated with Marfan’s syndrome: how optical genome mapping emphasizes the morbid burden of copy-neutral variants.pdf

Optical genome mapping (OGM), which allows analysis of ultra-high molecular weight (UHMW) DNA molecules, represents a response to the restriction created by short-read next-generation-sequencing, even in cases where the causative variant is a neutral copy-number-variant insensitive to quantitative investigations. This study aimed to provide a molecular diagnosis to a boy with Marfan syndrome (MFS) and intellectual disability (ID) carrying a de novo translocation involving chromosomes 3, 4, and 13 and a 1.7 Mb deletion at the breakpoint of chromosome 3. No FBN1 alteration explaining his Marfan phenotype was highlighted. UHMW gDNA was isolated from both the patient and his parents and processed using OGM. Genome assembly was followed by variant calling and annotation. Multiple strategies confirmed the results. The 3p deletion, which disrupted ROBO2, (MIM*602431) included three copy-neutral insertions. Two came from chromosome 13; the third contained 15q21.1, including the FBN1 from intron-45 onwards, thus explaining the MFS phenotype. We could not attribute the ID to a specific gene variant nor to the reshuffling of topologically associating domains (TADs). Our patient did not have vesicular reflux-2, as reported by missense alterations of ROBO2 (VUR2, MIM#610878), implying that reduced expression of all or some isoforms has a different effect than some of the point mutations. Indeed, the ROBO2 expression pattern and its role as an axon-guide suggests that its partial deletion is responsible for the patient’s neurological phenotype. Conclusion: OGM testing 1) highlights copy-neutral variants that could remain invisible if no loss of heterozygosity is observed and 2) is mandatory before other molecular studies in the presence of any chromosomal rearrangement for an accurate genotype-phenotype relationship.

光学基因组图谱（OGM）技术，能够对超高分子量（UHMW）DNA分子进行解析，作为一种应对短读长下一代测序（NGS）所带来限制的手段，即便在致病变异为中性拷贝数变异且对定量研究不敏感的情况下亦然。本研究旨在对一位携带3号、4号和13号染色体新发易位及3号染色体断裂点1.7 Mb缺失的Marfan综合征（MFS）合并智力障碍（ID）的男孩进行分子诊断。未发现可解释其Marfan表型的FBN1突变。从患者及其父母中分离出超高分子量基因组DNA（gDNA），并采用OGM技术进行处理。随后进行基因组组装、变异检测和注释。多种策略验证了结果。3p缺失破坏了ROBO2基因（MIM*602431），包括三个拷贝中性的插入，其中两个来自13号染色体；第三个插入包含15q21.1，自内含子-45起包含FBN1，从而解释了MFS表型。我们无法将智力障碍归因于特定的基因变异，也无法归因于拓扑关联结构域（TADs）的重组。患者未出现囊性反流-2（VUR2，MIM#610878）的症状，这是由ROBO2错义突变所报告的，暗示着所有或某些异构体表达水平的降低与某些点突变的效果不同。事实上，ROBO2的表达模式和其在轴突导向中的作用表明，其部分缺失是该患者神经学表型的原因。结论：OGM检测1）突显了那些在未观察到杂合性丢失的情况下可能保持隐性的拷贝中性变异；2）在存在任何染色体结构变异的情况下，进行其他分子研究前进行OGM检测是必要的，以确保准确的基因型-表型关系。