Radboud Center for Mitochondrial and Metabolic Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands.
University Children's Hospital, Paracelsus Medical University, Salzburg, Austria.
J Inherit Metab Dis. 2022 Jul;45(4):663-681. doi: 10.1002/jimd.12507. Epub 2022 May 22.
Exome sequencing (ES) in the clinical setting of inborn metabolic diseases (IMDs) has created tremendous improvement in achieving an accurate and timely molecular diagnosis for a greater number of patients, but it still leaves the majority of patients without a diagnosis. In parallel, (personalized) treatment strategies are increasingly available, but this requires the availability of a molecular diagnosis. IMDs comprise an expanding field with the ongoing identification of novel disease genes and the recognition of multiple inheritance patterns, mosaicism, variable penetrance, and expressivity for known disease genes. The analysis of trio ES is preferred over singleton ES as information on the allelic origin (paternal, maternal, "de novo") reduces the number of variants that require interpretation. All ES data and interpretation strategies should be exploited including CNV and mitochondrial DNA analysis. The constant advancements in available techniques and knowledge necessitate the close exchange of clinicians and molecular geneticists about genotypes and phenotypes, as well as knowledge of the challenges and pitfalls of ES to initiate proper further diagnostic steps. Functional analyses (transcriptomics, proteomics, and metabolomics) can be applied to characterize and validate the impact of identified variants, or to guide the genomic search for a diagnosis in unsolved cases. Future diagnostic techniques (genome sequencing [GS], optical genome mapping, long-read sequencing, and epigenetic profiling) will further enhance the diagnostic yield. We provide an overview of the challenges and limitations inherent to ES followed by an outline of solutions and a clinical checklist, focused on establishing a diagnosis to eventually achieve (personalized) treatment.
外显子组测序 (ES) 在先天性代谢疾病 (IMD) 的临床环境中，为更多患者实现准确和及时的分子诊断带来了巨大的进步，但仍有大多数患者无法得到诊断。与此同时，（个性化）治疗策略也越来越多，但这需要有分子诊断。IMD 是一个不断扩展的领域，新的疾病基因不断被发现，多个遗传模式、嵌合体、已知疾病基因的可变外显率和表现度也得到了认识。与单样本 ES 相比，三核苷酸 ES 分析更受欢迎，因为等位基因来源（父源、母源、“新生”）的信息可减少需要解释的变异数量。所有 ES 数据和解释策略都应加以利用，包括 CNV 和线粒体 DNA 分析。现有技术和知识的不断进步，需要临床医生和分子遗传学家密切交流基因型和表型，以及了解 ES 的挑战和陷阱，以启动适当的进一步诊断步骤。功能分析（转录组学、蛋白质组学和代谢组学）可用于描述和验证已识别变异的影响，或指导基因组搜索以解决未解决的病例。未来的诊断技术（基因组测序 [GS]、光学基因组图谱、长读测序和表观遗传分析）将进一步提高诊断的效果。我们提供了 ES 所固有的挑战和局限性的概述，随后介绍了解决方案和临床检查表，重点是建立诊断，最终实现（个性化）治疗。
