二代测序法用于先天性长QT综合征临床基因检测的假阴性分析

发布时间：2018-06-02 14:30

  本文选题：QT延长综合征 + 高通量核苷酸测序　； 参考：《中国循环杂志》2017年08期

【摘要】：目的:探讨二代测序法在先天性长QT综合征(LQTS)临床基因检测中的假阴性问题。方法:选取2个商业医学检验实验室(Lab1和Lab2,Hi Seq2000测序平台)、1个商业科研服务实验室(Lab3,Ion Torrnet测序平台)和1个学术机构实验室(Lab 4,Hi Seq2000测序平台)产生的共28例样本数据(Lab1:6例;Lab2:8例;Lab3:8例;Lab4:6例),定量分析LQTS的三个主要致病基因KCNQ1、KCNH2和SCN5A外显子区域测序覆盖度以及可能漏检的致病变异数目。结果:采用Hi Seq2000测序平台的3个实验室(Lab1、Lab2和Lab4)中,三个致病基因外显子区域覆盖度10倍的比例均高于98%,覆盖度30倍的区域介于90%~95%。KCNQ1在两个商业医学检验实验室的14例样本中,低于10倍和30倍覆盖的外显子区域比例平均为3.63%和9.84%;低于10倍覆盖区域集中在第一外显子,平均包含约2%的已知致病或疑似致病变异。KCNH2在两个商业医学检验实验室14个样本中,低于10倍和30倍覆盖的区域分别为2.64%和15.76%,低覆盖区分布在多个外显子中。Lab1的数据中,KCNH2低于30倍覆盖区域最高达28.56%,其内包含已知致病或疑似致病变异113个(19.79%)。SCN5A的整体覆盖度最好,四个实验室的数据都不存在低于10倍覆盖的区域,其中两个商业医学检验实验室也不存在低于30倍覆盖的区域。结论:当前的LQTS基因二代测序检测中,KCNQ1和KCNH2都存在一定程度的低覆盖区,因此普遍存在漏检致病变异的可能,假阴性问题值得高度重视。
[Abstract]:Objective: to investigate the false negative of second generation sequencing in clinical gene detection of congenital long QT syndrome (LQTS). Methods: a total of 28 samples were collected from two commercial medical laboratory laboratories: Lab1 and Lab2Hi Seq2000 sequencing platform, 1 commercial research service laboratory Lab3 + Ion Torrnet sequencing platform, and 1 academic laboratory lab, Lab4Hi Seq2000 sequencing platform. Six cases of Lab1: 8 cases of Lab3: 8 cases of Lab4: 6 cases of LQTS quantitative analysis of the three main pathogenic genes KCNQ1KCNH2 and SCN5A exon region sequencing coverage and the number of possible misdetected pathogenic variation. Results: in the three laboratories using the Hi Seq2000 sequencing platform, the proportion of the three pathogenic gene exon region coverage was 10 times higher than that of 98%, and the area with 30 times coverage was between 90%~95%.KCNQ1 in 14 samples from two commercial medical laboratory. The proportion of exon regions less than 10 times and 30 times of coverage averaged 3.63% and 9.84% respectively, and the areas below 10 times coverage were concentrated in the first exon, containing on average about 2% of known pathogenic or suspected pathogenic variations .KCNH2 in 14 samples from two commercial medical laboratory laboratories. The areas covered by less than 10 times and 30 times were 2.64% and 15.76%, respectively. In the data of .Lab1 of multiple exons, the coverage area of KCNH _ 2 was lower than 30 times, the highest was 28.566.The overall coverage of the area containing 113 known pathogenic or suspected pathogenic variations was the best, and the overall coverage of SCN5A was the best. No area of less than 10 times coverage exists in all four laboratories, and no area less than 30 times coverage exists in two of the commercial medical laboratories. Conclusion: in the second generation sequencing of LQTS gene, both KCNQ1 and KCNH2 have low coverage to some extent. Therefore, the possibility of missing the pathogenic variation is common, and the false negative problem should be paid more attention to.
【作者单位】： 首都医科大学附属北京安贞医院心内科国家心血管病临床医学研究中心;
【基金】：国家自然科学基金(81500246,81470465) 北京市自然科学基金(7161003) 北京市医管局临床医学发展专项(ZYLX201302)
【分类号】：R541.7
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本文编号：1969098