Department of Ophthalmology, Shiley Eye Institute, University of California at San Diego, San Diego, California, United States of America.
Department of Ophthalmology, Mejora Vision MD, Merida, Yucatan, Mexico.
PLoS One. 2024 Oct 4;19(10):e0307266. doi: 10.1371/journal.pone.0307266. eCollection 2024.
Whole genome sequencing has been an effective tool in the discovery of variants that cause rare diseases. In this study, we determined the suitability of a novel avidity sequencing approach for rare disease applications. We built a sample to results workflow, combining this sequencing technology with standard library preparation kits, analysis workflows, and interpretation tools. We applied the workflow to ten pedigrees with inherited retinal degeneration (IRD) phenotype. Candidate variants of interest identified through whole genome sequencing were further evaluated using segregation analysis in the additional family members. Potentially causal variants in known IRD genes were detected in five of the ten cases. These high confidence variants were found in ABCA4, CERKL, MAK, PEX6 and RDH12 genes associated with retinal degeneration, that could be sufficient to cause pathology. Pending confirmatory clinical evaluation, we observed a 50% diagnostic yield, consistent with previously reported outcomes of IRD patient analysis. The study confirms that avidity sequencing is effective in detection of causal variants when used for whole genome sequencing in rare disease applications.
全基因组测序是发现罕见病致病变异的有效工具。本研究旨在评估新型亲和力测序方法在罕见病应用中的适用性。我们建立了一个从样本到结果的工作流程，将该测序技术与标准文库制备试剂盒、分析工作流程和解释工具相结合。我们将该工作流程应用于十个具有遗传性视网膜变性（IRD）表型的家系。通过全基因组测序鉴定出的候选变异，通过在其他家族成员中的分离分析进行进一步评估。在十个病例中的五个中检测到了已知 IRD 基因中的潜在致病变异。这些高可信度的变异存在于与视网膜变性相关的 ABCA4、CERKL、MAK、PEX6 和 RDH12 基因中，这些变异足以引起病变。在等待确认的临床评估中，我们观察到 50%的诊断率，与之前报道的 IRD 患者分析结果一致。本研究证实，亲和力测序在罕见病全基因组测序中用于检测致病变异是有效的。
