Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA) S. A, Avda. Richard Grandío s/n, 33193, Oviedo, Spain.
Disease Research And Medicine (DREAMgenics) S. L., Oviedo, Spain.
BMC Med Genomics. 2018 Jul 9;11(1):58. doi: 10.1186/s12920-018-0375-5.
Sensorineural hearing loss (SNHL) is the most common sensory impairment. Comprehensive next-generation sequencing (NGS) has become the standard for the etiological diagnosis of early-onset SNHL. However, accurate selection of target genomic regions (gene panel/exome/genome), analytical performance and variant interpretation remain relevant difficulties for its clinical implementation.
We developed a novel NGS panel with 199 genes associated with non-syndromic and/or syndromic SNHL. We evaluated the analytical sensitivity and specificity of the panel on 1624 known single nucleotide variants (SNVs) and indels on a mixture of genomic DNA from 10 previously characterized lymphoblastoid cell lines, and analyzed 50 Spanish patients with presumed hereditary SNHL not caused by GJB2/GJB6, OTOF nor MT-RNR1 mutations.
The analytical sensitivity of the test to detect SNVs and indels on the DNA mixture from the cell lines was > 99.5%, with a specificity > 99.9%. The diagnostic yield on the SNHL patients was 42% (21/50): 47.6% (10/21) with autosomal recessive inheritance pattern (BSND, CDH23, MYO15A, STRC [n = 2], USH2A [n = 3], RDX, SLC26A4); 38.1% (8/21) autosomal dominant (ACTG1 [n = 3; 2 de novo], CHD7, GATA3 [de novo], MITF, P2RX2, SOX10), and 14.3% (3/21) X-linked (COL4A5 [de novo], POU3F4, PRPS1). 46.9% of causative variants (15/32) were not in the databases. 28.6% of genetically diagnosed cases (6/21) had previously undetected syndromes (Barakat, Usher type 2A [n = 3] and Waardenburg [n = 2]). 19% of genetic diagnoses (4/21) were attributable to large deletions/duplications (STRC deletion [n = 2]; partial CDH23 duplication; RDX exon 2 deletion).
In the era of precision medicine, obtaining an etiologic diagnosis of SNHL is imperative. Here, we contribute to show that, with the right methodology, NGS can be transferred to the clinical practice, boosting the yield of SNHL genetic diagnosis to 50-60% (including GJB2/GJB6 alterations), improving diagnostic/prognostic accuracy, refining genetic and reproductive counseling and revealing clinically relevant undiagnosed syndromes.
感音神经性听力损失（SNHL）是最常见的感觉障碍。综合下一代测序（NGS）已成为早期 SNHL 病因诊断的标准。然而，目标基因组区域（基因panel/外显子/基因组）的准确选择、分析性能和变异解释仍然是其临床实施的相关难点。
我们开发了一个新的 NGS 面板，包含 199 个与非综合征和/或综合征 SNHL 相关的基因。我们在由 10 个先前特征明确的淋巴母细胞系的混合基因组 DNA 上的 1624 个已知单核苷酸变异（SNVs）和插入缺失上评估了该面板的分析灵敏度和特异性，并分析了 50 名西班牙假定遗传性 SNHL 患者，这些患者不伴有 GJB2/GJB6、OTOF 或 MT-RNR1 突变。
该测试对细胞系 DNA 混合物上 SNVs 和插入缺失的分析灵敏度>99.5%，特异性>99.9%。在 SNHL 患者中的诊断率为 42%（21/50）：47.6%（10/21）为常染色体隐性遗传模式（BSND、CDH23、MYO15A、STRC [n=2]、USH2A [n=3]、RDX、SLC26A4）；38.1%（8/21）为常染色体显性遗传（ACTG1 [n=3；2 个新发]、CHD7、GATA3 [新发]、MITF、P2RX2、SOX10），14.3%（3/21）为 X 连锁（COL4A5 [新发]、POU3F4、PRPS1）。46.9%的致病变异（15/32）不在数据库中。28.6%的基因诊断病例（6/21）有先前未检测到的综合征（Barakat、Usher 2A 型[n=3]和 Waardenburg[n=2]）。19%的基因诊断（4/21）归因于大片段缺失/重复（STRC 缺失[n=2]；部分 CDH23 重复；RDX 外显子 2 缺失）。
在精准医学时代，获得 SNHL 的病因诊断至关重要。在这里，我们证明了通过正确的方法，NGS 可以转化为临床实践，将 SNHL 遗传诊断的检出率提高到 50-60%（包括 GJB2/GJB6 改变），提高诊断/预后准确性，完善遗传和生殖咨询，并揭示临床上相关的未确诊综合征。
