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分子进行分析，是对短读长下一代测序技术所受限制的一种回应，即便在致病变异为对定量研究不敏感的中性拷贝数变异的情况下。本研究旨在为一位携带3号、4号和13号染色体新发易位以及3号染色体断裂点1.7Mb缺失的Marfan综合征（MFS）和智力障碍（ID）的男孩提供分子诊断。未发现解释其Marfan表型的FBN1基因变异。从患者及其父母中分离出超高分子量gDNA，并使用OGM技术进行处理。基因组组装后进行变异检测和注释。多种策略证实了结果。3p区域的缺失破坏了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；第三个包含15q21.1区域，从内含子45开始包括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，也不能归因于拓扑关联域（TADs）的重排。患者没有像ROBO2错义突变（VUR2，MIM#610878）所报道的囊性反流-2，这意味着所有或某些等位基因表达水平的降低与某些点突变的影响不同。实际上，ROBO2的表达模式和其作为轴突引导者的作用表明，其部分缺失是患者神经表型的原因。结论：OGM检测1）突显了在未观察到杂合性丢失的情况下可能无法发现的拷贝中性变异，2）在存在任何染色体重排的情况下，在进行其他分子研究之前进行基因型-表型关系的准确分析是强制性的。