Division of Genomic Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.
Department of Biomedical and Health Informatics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
J Mol Diagn. 2018 Sep;20(5):643-652. doi: 10.1016/j.jmoldx.2018.05.003. Epub 2018 Jun 22.
Exome-based panels are becoming the preferred diagnostic strategy in clinical laboratories. This approach enables dynamic gene content update and, if needed, cost-effective reflex to whole-exome sequencing. Currently, no guidelines or appropriate resources are available to support the clinical implementation of exome-based panels. Here, we highlight principles and important considerations for the clinical development and validation of exome-based panels. In addition, we developed ExomeSlicer, a novel, web-based resource, which uses empirical exon-level next-generation sequencing quality metrics to predict and visualize technically challenging exome-wide regions in any gene or genes of interest. Exome sequencing data from 100 clinical epilepsy cases were used to illustrate the clinical utility of ExomeSlicer in predicting poor-quality regions and its impact on streamlining the ad hoc Sanger sequencing fill in burden. With the use of ExomeSlicer, >2100 low complexity and/or high-homology regions affecting >1615 genes across the exome were also characterized. These regions can be a source of false-positive or false-negative variant calls, which can lead to misdiagnoses in tested patients and/or inaccurate functional annotations. We provide important considerations and a novel resource for the clinical development of exome-based panels.
基于外显子组的panel 正在成为临床实验室首选的诊断策略。这种方法能够实现动态的基因内容更新，如果需要，还可以进行具有成本效益的外显子组测序。目前，尚无指南或适当的资源可用于支持基于外显子组的panel 的临床实施。在这里，我们强调了基于外显子组的panel 的临床开发和验证的原则和重要考虑因素。此外，我们开发了 ExomeSlicer，这是一种新颖的基于网络的资源，它使用经验性的外显子水平下一代测序质量指标来预测和可视化任何感兴趣的基因中的技术上具有挑战性的外显子范围。使用 100 例临床癫痫病例的外显子组测序数据说明了 ExomeSlicer 在预测低质量区域方面的临床效用及其对简化特定 Sanger 测序填补负担的影响。使用 ExomeSlicer，还对影响外显子组中 1615 多个基因的 2100 多个低复杂度和/或高同源性区域进行了特征描述。这些区域可能是假阳性或假阴性变异呼叫的来源，这可能导致受测试患者的误诊和/或不准确的功能注释。我们为基于外显子组的panel 的临床开发提供了重要的考虑因素和新的资源。
