Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Roberts Individualized Medical Genetics Center, Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.
Genet Med. 2018 Dec;20(12):1600-1608. doi: 10.1038/gim.2018.48. Epub 2018 Mar 29.
Hereditary hearing loss is highly heterogeneous. To keep up with rapidly emerging disease-causing genes, we developed the AUDIOME test for nonsyndromic hearing loss (NSHL) using an exome sequencing (ES) platform and targeted analysis for the curated genes.
A tiered strategy was implemented for this test. Tier 1 includes combined Sanger and targeted deletion analyses of the two most common NSHL genes and two mitochondrial genes. Nondiagnostic tier 1 cases are subjected to ES and array followed by targeted analysis of the remaining AUDIOME genes.
ES resulted in good coverage of the selected genes with 98.24% of targeted bases at >15 ×. A fill-in strategy was developed for the poorly covered regions, which generally fell within GC-rich or highly homologous regions. Prospective testing of 33 patients with NSHL revealed a diagnosis in 11 (33%) and a possible diagnosis in 8 cases (24.2%). Among those, 10 individuals had variants in tier 1 genes. The ES data in the remaining nondiagnostic cases are readily available for further analysis.
The tiered and ES-based test provides an efficient and cost-effective diagnostic strategy for NSHL, with the potential to reflex to full exome to identify causal changes outside of the AUDIOME test.
遗传性听力损失具有高度异质性。为了跟上不断涌现的致病基因，我们使用外显子组测序（ES）平台和针对已审定基因的靶向分析，为非综合征性听力损失（NSHL）开发了 AUDIOME 测试。
该测试采用分层策略。第 1 层包括对两种最常见的 NSHL 基因和两种线粒体基因进行联合 Sanger 和靶向缺失分析。未诊断出第 1 层的病例将进行 ES 和阵列分析，然后对其余的 AUDIOME 基因进行靶向分析。
ES 实现了所选基因的良好覆盖，靶向碱基的覆盖率为 >15 ×，达 98.24%。针对覆盖不佳的区域开发了填充策略，这些区域通常位于 GC 丰富或高度同源区域内。对 33 名 NSHL 患者的前瞻性测试显示，11 例（33%）有诊断结果，8 例（24.2%）有疑似诊断结果。其中，10 名个体在第 1 层基因中存在变异。剩余非诊断病例的 ES 数据可随时用于进一步分析。
分层和基于 ES 的测试为 NSHL 提供了一种高效且具有成本效益的诊断策略，具有通过全外显子组分析来确定 AUDIOME 测试之外的因果变化的潜力。
