应用全外显子组测序技术进行小耳畸形核心家系新生突变分析

Trio-based de novo mutation analysis by whole exome sequencing in congenital microtia

目的在中国汉族小耳畸形核心家系中评估基因新生突变模式在散发小耳畸形中的作用,寻找可能的致病性新生突变。方法选取2017年3月至2018年7月就诊于中国医学科学院整形外科医院的24个中国单纯小耳畸形核心家系。其中小耳畸形患者24例,年龄6~10岁,男15例,女9例,均为单侧小耳畸形,包括左侧15例,右侧9例。获知情同意后,抽取患者及其未患病双亲的外周血,对24个单纯小耳畸形患者及其未患病双亲进行全外显子组测序,筛选位于基因编码区及经典剪接位点的新生突变,观察每例患者外显子区的新生突变数量。对筛选到的新生突变依美国医学遗传学与基因组学会变异分类标准进行分类,使用ExAc数据库、VarCards数据库、Human Splicing Finder 3.1在线软件分别对丧失功能突变、错义突变和同义突变进行变异特征判断,结合小鼠基因组信息数据库查询同源基因在小鼠鳃弓部位的表达情况、使用David6.8生物信息数据库对候选基因进行通路富集分析,使用在线人类孟德尔疾病遗传数据库查询候选基因与人类疾病之间的对应关系,从而对不同变异进行变异功能和基因功能2方面的致病性评估。结果24个小耳畸形家系中共检测到23个新生突变,每个患者检测到0~3个外显子区新生突变,与正常人相比未见明显增加。突变类型包括错义突变12个、同义突变8个以及无义突变、起始密码子突变、整码插入突变各1个。其中LRP12基因无义突变依指南分类为致病变异。使用多种生物信息学软件及数据库对所有新生突变进行分析,未见明显的致病性特征。结论小耳畸形患者中并没有发现明显的新生突变负担加重,尽管致病基因可能通过新生突变模式在小耳畸形中致病,但新生突变模式可能不是小耳畸形致病的主要遗传模式。

Objective To evaluate the role of de novo mutations(DNMs)in Chinese patients with non-syndromic congenital microtia by using whole exome sequencing in patient-parent trios and to detect the pathogenic DNMs,if there are any.Methods Twenty-four Chinese trio families with congenital microtia were recruited from March 2017 to July 2018 at the Plastic Surgery Hospital of Chinese Academy of Medical Sciences.The patients,aged from 6 to 10 years old,15 males and 9 females,had unilateral microtia,including 15 on the left and 9 on the right.After informed consent,peripheral blood was collected from patients and their unaffected parents.Whole exome sequencing was performed on all patients and their parents.DNMs in the coding region and canonical splicing sites were detected,and the number of DNMs in each patient was obtained.Each DNM was classified according to the ACMG standards and guidelines for the interpretation of sequence variants.In-silico prediction was performed using different algorithms and databases considering both variant-and gene-level implications.ExAc database,VarCards,Human Splicing Finder 3.1 software were used to predict each variant’s pathogenicity,including loss of function variant,missense variant and nonsynonymous variant.Mouse genome information database was used to detect the expression of the homologous gene,and David 6.8 bioinformatics database was used for pathway enrichment analysis of candidate genes.The Online Mendelian Inheritance in Man database was used to query the correspondence between candidate genes and human diseases.Results Twenty-three DNMs were detected in 24 microtia trios.In each patient,there was 0-3 DNMs with no significant difference in population.Twelve missense variants,eight synonymous variants,one nonsense,one start codon variant,and one inframe indel were detected.Among them,a nonsense LRP12 mutation was classified as pathogenic according to ACMG guidelines.However,none of the variants were considered disease-causing according to in-silico predictions.Conclusions Increased number or mutational burden of DMNs are not observed in Chinese patients with microtia.DMNs is not the primary cause of microtia,although rare DNMs in responsible genes could occasionally lead to cases.