Autism spectrum disorder(ASD)is a neurodevelopmental disorder with high genetic heritability but heterogeneity.Fully understanding its genetics requires whole-genome sequencing(WGS),but the ASD studies utilizing WGS d...Autism spectrum disorder(ASD)is a neurodevelopmental disorder with high genetic heritability but heterogeneity.Fully understanding its genetics requires whole-genome sequencing(WGS),but the ASD studies utilizing WGS data in Chinese population are limited.In this study,we present a WGS study for 334 individuals,including 112 ASD patients and their non-ASD parents.We identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding regions.By integrating these variants with an association model,we identified 33 potential risk genes(P<0.001)enriched in neuron and regulation related biological process.Besides the well-known ASD genes(SCN2A,NF1,SHANK3,CHD8 etc.),several high confidence genes were highlighted by a series of functional analyses,including CTNND1,DGKZ,LRP1,DDN,ZNF483,NR4A2,SMAD6,INTS1,and MRPL12,with more supported evidence from GO enrichment,expression and network analysis.We also integrated RNA-seq data to analyze the effect of the variants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased expression.We further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on phenotype.Regarding variants in noncoding regions,a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence,which were mapped to specific genes or regulatory features.The number of de novo variants found in patient was significantly associated with the parents’ages at the birth of the child,and gender with trend.We also identified small de novo structural variants in ASD trios.The results in this study provided important evidence for understanding the genetic mechanism of ASD.展开更多
目的探讨极体测序技术在Van der Woude综合征患者胚胎植入前单基因遗传病检测中的应用价值。方法对1例因IRF6基因新发变异导致的Van der Woude综合征女性患者,应用极体测序技术进行胚胎植入前遗传学检测。6枚卵经卵胞质内单精子注射(int...目的探讨极体测序技术在Van der Woude综合征患者胚胎植入前单基因遗传病检测中的应用价值。方法对1例因IRF6基因新发变异导致的Van der Woude综合征女性患者,应用极体测序技术进行胚胎植入前遗传学检测。6枚卵经卵胞质内单精子注射(intracytoplasmic sperm injection,ICSI)受精后,分别顺序活检第一极体、第二极体和囊胚滋养外胚层细胞。活检细胞经全基因组扩增后,利用PCR联合Sanger测序的方法检测极体和胚胎的致病变异携带状态,推断对应胚胎的致病性。为预防因囊胚培养失败造成无可移植胚胎的情况,在囊胚形成前对1枚致病性低的优质胚胎进行玻璃化冷冻。此外,通过在夫妇双方以及特定基因型的极体和胚胎样本中对变异位点及其上下游1M区域内的175个单核苷酸多态性(single nucleotide polymorphism,SNP)位点进行靶向捕获高通量测序,连锁分析构建单体型。选择致病性低的胚胎移植,成功妊娠后进行产前诊断以及跟踪随访。结果成功获得第一极体和第二极体各6枚,其中11枚极体的变异位点检测成功。6枚胚胎中,1枚预测致病性低的胚胎在患者知情同意后于第4日(day 4,D4)玻璃化冷冻;1枚胚胎成功发育至囊胚,但致病性高;4枚胚胎囊胚培养失败。连锁分析成功构建出与致病变异紧密连锁的SNP单体型,胚胎单体型分析与Sanger测序结果吻合。移植致病性低的D4期冷冻胚胎,成功妊娠后,患者夫妇拒绝有创产前诊断。出生后新生儿随访未发现唇腭裂,脐血基因检测不携带致病变异。结论本研究利用卵母细胞极体测序的检测方法,为1例因IRF6基因新发变异导致的Van der Woude综合征女性患者进行胚胎植入前单基因遗传病检测,成功阻断了该病向子代传递。展开更多
目的分析1例重型Cornelia de Lange综合征(Cornelia de Lange syndrome,CdLS)患儿的NIPBL基因变异,明确其遗传学病因。方法提取患儿及其父母外周血中DNA物质,应用全外显子基因组测序法检测相关基因变异,应用Sanger测序法验证变异。对可...目的分析1例重型Cornelia de Lange综合征(Cornelia de Lange syndrome,CdLS)患儿的NIPBL基因变异,明确其遗传学病因。方法提取患儿及其父母外周血中DNA物质,应用全外显子基因组测序法检测相关基因变异,应用Sanger测序法验证变异。对可疑变异进行生物信息学预测。结果经全外显子基因组测序分析并经Sanger测序验证,发现患儿NIPBL基因第9外显子存在c.1507A>G(p.Lys503Glu)杂合错义变异,该变异为新发变异,且为未报道过的新变异。经PolyPhen-2、Mutation Taster、SIFT预测软件预测c.1507A>G(p.Lys503Glu)变异为可能有害变异,并经HomoloGene系统分析NIPBL蛋白第503位Lys在各种属间均高度保守,该位点氨基酸改变可导致编码的NIPBL原有蛋白功能发生障碍。而经过PubMed BLAST系统进一步分析发现该位点氨基酸的改变可通过影响Neuromodulin_N superfamily结构域的形成来导致NIPBL蛋白功能发生障碍的。结论NIPBL基因c.1507A>G(p.Lys503Glu)错义变异可能为该患儿罹患重型CdLS的致病原因,基因变异检测结果可以为家系的遗传咨询和产前诊断提供依据。展开更多
基金supported by the National Program for Brain Science and Brain-like Intelligence Technology of China (2021ZD0200800)Beijing Municipal Science and Technology Commission (Z181100001518005)+1 种基金the National Natural Science Foundation of China (31401139, 32170613, 81671358, 81873803)the Natural Science Foundation of Beijing Municipality (7232225)
文摘Autism spectrum disorder(ASD)is a neurodevelopmental disorder with high genetic heritability but heterogeneity.Fully understanding its genetics requires whole-genome sequencing(WGS),but the ASD studies utilizing WGS data in Chinese population are limited.In this study,we present a WGS study for 334 individuals,including 112 ASD patients and their non-ASD parents.We identified 146 de novo variants in coding regions in 85 cases and 60 inherited variants in coding regions.By integrating these variants with an association model,we identified 33 potential risk genes(P<0.001)enriched in neuron and regulation related biological process.Besides the well-known ASD genes(SCN2A,NF1,SHANK3,CHD8 etc.),several high confidence genes were highlighted by a series of functional analyses,including CTNND1,DGKZ,LRP1,DDN,ZNF483,NR4A2,SMAD6,INTS1,and MRPL12,with more supported evidence from GO enrichment,expression and network analysis.We also integrated RNA-seq data to analyze the effect of the variants on the gene expression and found 12 genes in the individuals with the related variants had relatively biased expression.We further presented the clinical phenotypes of the proband carrying the risk genes in both our samples and Caucasian samples to show the effect of the risk genes on phenotype.Regarding variants in noncoding regions,a total of 74 de novo variants and 30 inherited variants were predicted as pathogenic with high confidence,which were mapped to specific genes or regulatory features.The number of de novo variants found in patient was significantly associated with the parents’ages at the birth of the child,and gender with trend.We also identified small de novo structural variants in ASD trios.The results in this study provided important evidence for understanding the genetic mechanism of ASD.
文摘目的探讨极体测序技术在Van der Woude综合征患者胚胎植入前单基因遗传病检测中的应用价值。方法对1例因IRF6基因新发变异导致的Van der Woude综合征女性患者,应用极体测序技术进行胚胎植入前遗传学检测。6枚卵经卵胞质内单精子注射(intracytoplasmic sperm injection,ICSI)受精后,分别顺序活检第一极体、第二极体和囊胚滋养外胚层细胞。活检细胞经全基因组扩增后,利用PCR联合Sanger测序的方法检测极体和胚胎的致病变异携带状态,推断对应胚胎的致病性。为预防因囊胚培养失败造成无可移植胚胎的情况,在囊胚形成前对1枚致病性低的优质胚胎进行玻璃化冷冻。此外,通过在夫妇双方以及特定基因型的极体和胚胎样本中对变异位点及其上下游1M区域内的175个单核苷酸多态性(single nucleotide polymorphism,SNP)位点进行靶向捕获高通量测序,连锁分析构建单体型。选择致病性低的胚胎移植,成功妊娠后进行产前诊断以及跟踪随访。结果成功获得第一极体和第二极体各6枚,其中11枚极体的变异位点检测成功。6枚胚胎中,1枚预测致病性低的胚胎在患者知情同意后于第4日(day 4,D4)玻璃化冷冻;1枚胚胎成功发育至囊胚,但致病性高;4枚胚胎囊胚培养失败。连锁分析成功构建出与致病变异紧密连锁的SNP单体型,胚胎单体型分析与Sanger测序结果吻合。移植致病性低的D4期冷冻胚胎,成功妊娠后,患者夫妇拒绝有创产前诊断。出生后新生儿随访未发现唇腭裂,脐血基因检测不携带致病变异。结论本研究利用卵母细胞极体测序的检测方法,为1例因IRF6基因新发变异导致的Van der Woude综合征女性患者进行胚胎植入前单基因遗传病检测,成功阻断了该病向子代传递。
文摘目的分析1例重型Cornelia de Lange综合征(Cornelia de Lange syndrome,CdLS)患儿的NIPBL基因变异,明确其遗传学病因。方法提取患儿及其父母外周血中DNA物质,应用全外显子基因组测序法检测相关基因变异,应用Sanger测序法验证变异。对可疑变异进行生物信息学预测。结果经全外显子基因组测序分析并经Sanger测序验证,发现患儿NIPBL基因第9外显子存在c.1507A>G(p.Lys503Glu)杂合错义变异,该变异为新发变异,且为未报道过的新变异。经PolyPhen-2、Mutation Taster、SIFT预测软件预测c.1507A>G(p.Lys503Glu)变异为可能有害变异,并经HomoloGene系统分析NIPBL蛋白第503位Lys在各种属间均高度保守,该位点氨基酸改变可导致编码的NIPBL原有蛋白功能发生障碍。而经过PubMed BLAST系统进一步分析发现该位点氨基酸的改变可通过影响Neuromodulin_N superfamily结构域的形成来导致NIPBL蛋白功能发生障碍的。结论NIPBL基因c.1507A>G(p.Lys503Glu)错义变异可能为该患儿罹患重型CdLS的致病原因,基因变异检测结果可以为家系的遗传咨询和产前诊断提供依据。
