产前诊断中采用拷贝数变异测序技术检测胎儿DMD基因缺失或重复的效能  

Efficiency of CNV-seq in detecting fetal DMD gene deletion or duplication in prenatal diagnosis

作　　者：邱霞 郭晶晶 靳婵婵 贺静 王蕾 杨必成 章印红 朱宝生 唐新华 Qiu Xia;Guo Jingjing;Jin Chanchan;He Jing;Wang Lei;Yang Bicheng;Zhang Yinhong;Zhu Baosheng;Tang Xinhua(Department of Medical Genetics,NHC Key Laboratory of Health Birth and Birth Defect Prevention in Western China,Yunnan Provincial Key Laboratory for Birth Defects and Genetic Diseases,Affiliated Hospital of Kunming University of Science and Technology,the First People′s Hospital of Yunnan Province,Kunming 650032,China)

机构地区：[1]昆明理工大学附属医院,云南省第一人民医院医学遗传科,国家卫生健康委西部优生与出生缺陷防控重点实验室,云南省出生缺陷与遗传病研究重点实验室,昆明650032

出　　处：《中华妇产科杂志》2024年第4期279-287,共9页Chinese Journal of Obstetrics and Gynecology

基　　金：云南省卫生科技计划(2014NS281);云南省云岭学者项目(YNWR-YLXZ-2019-005);云南省生殖妇产疾病临床医学中心开放课题(2022LCZXKF-SZ02)。

摘　　要：目的评估产前诊断中采用低深度高通量全基因组拷贝数变异测序(CNV-seq)技术对胎儿DMD基因缺失或重复的诊断效能。方法对2018年1月至2023年7月于云南省第一人民医院行产前诊断的34544例胎儿的CNV-seq检测结果进行回顾性分析,共纳入156例胎儿,包括:有假性肥大型进行性肌营养不良[DMD;包括表型较轻的贝氏肌营养不良(BMD)]生育史或家族史的胎儿125例;无DMD/BMD生育史或家族史但因其他指征行产前诊断检出DMD基因缺失或重复的胎儿31例。采用多重连接依赖性探针扩增(MLPA)技术对胎儿样本进行检测验证,对CNV-seq和MLPA结果进行一致性检验,获得CNV-seq对胎儿DMD基因缺失或重复的检测效能。结果与MLPA相比,CNV-seq对胎儿DMD基因缺失或重复的检出总符合率为92.3%(144/156),敏感度和阳性预测值均为88.2%,特异度和阴性预测值均为94.3%,漏检率为3.8%,Kappa系数为0.839。有DMD/BMD生育史或家族史的胎儿中,MLPA共检出20例缺失和6例重复,其中4例缺失和2例重复因变异片段<100 Kb被CNV-seq漏检。无DMD/BMD生育史或家族史的胎儿中,CNV-seq检出缺失占42%(13/31),重复占58%(18/31),重复占比高于有DMD/BMD生育史或家族史的胎儿,其中3例位于第42~67号外显子(可能致病),9例覆盖DMD基因5’或3’末端,均包含第1或第79号外显子(临床意义未明),其余6例CNV-seq检出重复片段位于chrX:32650635_32910000(临床意义未明),但MLPA检测结果均为阴性。结论CNV-seq可有效检出胎儿DMD基因缺失或重复,但存在少量漏检风险,结果需MLPA验证。CNV-seq检测到chrX:32650635_32910000区域重复及检出覆盖DMD基因5′端或3′端重复的变异可能并不致病。Objective To evaluate the diagnostic efficiency of copy number variation sequencing(CNV-seq)to detect the deletion or duplication of DMD gene in prenatal diagnosis.Methods A retrospective analysis was carried out on the CNV-seq results of 34544 fetuses diagnosed in the First People′s Hospital of Yunnan Province from January 2018 to July 2023.A total of 156 cases of fetuses were collected,including Group 1:125 cases with family history of Duchenne muscular dystrophy or Becker muscular dystrophy(DMD/BMD),and Group 2:31 cases with no family history but a DMD gene deletion or duplication was detected unexpectedly by CNV-seq.Multiplex ligation-dependent probe amplification(MLPA)was used as a standard method to detect the deletion or duplication.Consistency test was carried out basing on the results of CNV-seq and MLPA of all 156 cases.Results Comparing to MLPA,CNV-seq had a coincidence rate of 92.3%(144/156)for DMD gene deletion or duplication,with a sensitivity and positive predictive value of 88.2%,with a specificity and negative predictive value of 94.3%,a missed detection rate of 3.8%,and a Kappa value of 0.839.CNV-seq missed 4 cases with deletions and 2 with duplications due to involved fragments less than 100 Kb,among 20 cases of deletions and 6 cases of duplications detected by MLPA in Group 1.In Group 2,the deletions and duplications detected by CNV-seq were 42%(13/31)and 58%(18/31),respectively,in which the percentage of duplication was higher than that in Group 1.Among those 18 cases with duplications,3 cases with duplication locating in exon 42~67 were likely pathogenic;while 9 cases with duplication covering the 5′or 3′end of the DMD gene,containing exon 1 or 79 and with only one breakpoint within the gene,along with the last 6 cases with duplications locating at chrX:32650635_32910000 detected only by CNV-seq,which might be judged as variants of uncertain significance.Conclusions CNV-seq has a good efficiency to detect fetal DMD gene deletion or duplication in prenatal diagnosis,while a further veri

关 键 词：肌营养不良 杜氏 基因缺失 基因复制 DNA拷贝数变异 多重聚合酶链式反应 产前诊断 

分 类 号：R714.5[医药卫生—妇产科学] R440[医药卫生—临床医学]