X-linked genetic disorders typically affect females less severely than males owing to the presence of a second X Chromosome not carrying the deleterious variant. However, the phenotypic expression in females is highly variable, which may be explained by an allelic skew in X-Chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions. We propose a novel approach using nanopore sequencing to quantify skewed X inactivation accurately. By phasing sequence variants and methylation patterns, this single assay reveals the disease variant, X inactivation skew, and its directionality and is applicable to all patients and X-linked variants. Enrichment of X Chromosome reads through adaptive sampling enhances cost-efficiency. Our study includes a cohort of 16 X-linked variant carrier females affected by two X-linked inherited retinal diseases: choroideremia and RPGR-associated retinitis pigmentosa. As retinal DNA cannot be readily obtained, we instead determine the skew from peripheral samples (blood, saliva, and buccal mucosa) and correlate it to phenotypic outcomes. This reveals a strong correlation between X inactivation skew and disease presentation, confirming the value in performing this assay and its potential as a way to prioritize patients for early intervention, such as gene therapy currently in clinical trials for these conditions. Our method of assessing skewed X inactivation is applicable to all long-read genomic data sets, providing insights into disease risk and severity and aiding in the development of individualized strategies for X-linked variant carrier females.

中文翻译：

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使用自适应纳米孔测序测量 X 连锁疾病的 X 染色体失活偏斜


X 连锁遗传病对女性的影响通常比男性轻，因为存在第二条 X 染色体不携带有害变异。然而，女性的表型表达高度可变，这可能是由 X 染色体失活的等位基因偏斜来解释的。准确测量 X 失活偏斜对于理解和预测女性携带者的疾病表型至关重要，其中预测尤其与退行性疾病相关。我们提出了一种使用纳米孔测序来准确量化偏斜 X 失活的新方法。通过对序列变异和甲基化模式进行分阶段，这种单一检测揭示了疾病变异、X 失活偏斜及其方向性，适用于所有患者和 X 连锁变异。通过自适应采样富集 X 染色体读数可提高成本效益。我们的研究包括 16 名 X 连锁变异携带者女性队列，这些女性受两种 X 连锁遗传性视网膜疾病的影响：脉络膜血症和 RPGR 相关的视网膜色素变性。由于视网膜 DNA 不容易获得，我们改为确定外周样本 （血液、唾液和口腔粘膜） 的偏斜，并将其与表型结果相关联。这揭示了 X 失活偏斜与疾病表现之间的强相关性，证实了进行该检测的价值及其作为优先为患者进行早期干预的一种方式的潜力，例如目前正在针对这些情况进行临床试验的基因治疗。我们评估偏斜 X 失活的方法适用于所有长读长基因组数据集，提供对疾病风险和严重程度的见解，并有助于为 X 连锁变异携带者女性制定个体化策略。