上海交通大学学报（医学版）

上海交通大学学报（医学版） ›› 2017, Vol. 37 ›› Issue (11): 1535-.doi: 10.3969/j.issn.1674-8115.2017.11.015

• 论著（临床研究） • 上一篇    下一篇

运用耳聋基因隐性突变携带者重测序策略纠正假阳性变异的致病性误判#br#

施俊，何龙霞，杨涛   

  1. 上海交通大学 医学院附属第九人民医院耳鼻咽喉 - 头颈外科，上海交通大学 医学院耳科学研究所，上海市耳鼻疾病转化医学重点实验室， 上海  200011
  • 出版日期:2017-11-28 发布日期:2018-01-10
  • 通讯作者: 杨涛，电子信箱：yangtfxl@sina.com
  • 作者简介:施俊（1969—），女，副主任医师，硕士；电子信箱：shijun6898@163.com
  • 基金资助:
    上海市教育委员会高峰高原学科建设计划（20152519）

Correcting false-positive pathogenic categorization of benign variants by re-sequencing of the recessive deafness genes in carriers#br#

SHI Jun, HE Long-xia, YANG Tao   

  1. Department of Otolaryngology-Head and Neck Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine; Ear Institute, Shanghai Jiao Tong University School of Medicine; Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai 200011, China
  • Online:2017-11-28 Published:2018-01-10
  • Supported by:
    Shanghai Municipal Education Commission—Gaofeng Clinical Medicine Grant Support，20152519

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摘要：  目的 · 运用隐性突变携带者重测序策略发现并归类耳聋致病基因罕见良性变异，为遗传性耳聋的高通量二代测序结果解读提 供良性多态参考数据库。方法 · 在已明确隐性耳聋基因双等位基因致病突变的耳聋患者的正常听力亲属中进行相应突变筛查，发现 单杂合致病突变的携带者。运用靶向捕获二代测序技术在这些携带者中对相应耳聋基因进行外显子重测序，对所发现的对侧等位基 因变异进行非致病性推断。结果 · 共 30 位正常听力的耳聋病例亲属被明确为某一已知耳聋基因隐性致病突变的杂合携带者。通过相 应基因的靶向二代测序，在对侧等位基因上共发现32 个非同义变异，在隐性完全外显的遗传模式下可被归类为良性非致病变异。其 中 SLC26A4 基因p.A434T 变异、LOXHD1 基因p.R266Q 变异、MYO15A 基因p.K96Q 变异、GJB2 基因p.T123N 变异及CDH23 基因 p.V1299I 变异，共 5 个罕见变异等位基因频率小于 0.005，部分变异被 Polyphen-2、PROVEAN、SIFT 或 MutationTaster 软件预测为致 病突变，或被耳聋变异数据库或人类基因组突变数据库记载为致病突变。结论 · 运用隐性突变携带者重测序策略可有效纠正部分被误 判为致病的罕见良性变异，提高二代测序在单基因隐性遗传病病因诊断中的准确性和有效性。

关键词: 外显子测序, 耳聋, 常染色体隐性遗传, 携带者, 致病性

Abstract:

 Objective · To correct the false-positive categorization of the rare and benign variants by re-sequencing of the recessive deafness genes in carriers.  Methods · Heterozygous carriers of known causative mutations in recessive deafness genes were identified from normal hearing relatives of the deaf probands. Targeted next-generation sequencing was performed in those carriers to identify additional variants in trans, which was presumed to be benign.  Results · A total of 30 normal-hearing carriers of heterozygous and known pathogenic mutations were identified. By targeted nextgeneration sequencing of corresponding genes, 32 non-synonymous variants in trans were identified, which were categorized to benign mutations under the recessive and full-penetrant mode. Among those variants p.A434T in SLC26A4, p.R266Q in LOXHD1, p.K96Q in MYO15A, p.T123N in GJB2 and pV1299I in CDH23 were five rare variants with minor allele frequency of less than 0.005. Some of the 5 variants were predicted to be pathogenic by prediction programs including Polyphen-2, PROVEAN, SIFT and MutationTaster, or documented to be pathogenic by Deafness Variation Database or Human Genome Mutation Database.  Conclusion · Re-sequencing of the recessive deafness genes in carriers may efficiently correct the false-positive categorization of some rare and benign variants to improve the accuracy and efficiency of the next-generation sequencing in diagnosis of monogenic recessive hereditary disorders.

Key words:  exome sequencing, deafness, autosomal recessive inheritance, carrier, pathogenesis