Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that poss...Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.展开更多
Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease rem...Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease remains a challenge. Methods： In this study, we tested a three-generation Chinese family with autosomal dominant CCs by targeted sequencing of 45 CC genes on next generation sequencing and evaluated the pathogenicity of the detected mutation by protein structure, pedigree validation, and molecular dynamics （MD） simulation. Results： A novel 15 bp deletion on GJA8 （c.426_440delGCTGGAGGGGACCCT or p. 143147delLEGTL） was detected in the family. The deletion, concerned with an in-frame deletion of 5 amino acid residues in a highly evolutionarily conserved region within the cytoplasmic loop domain of the gap junction channel protein connexin 50 （CxS0）, was in full cosegregation with the cataract phenotypes in the family but not found in 1100 control exomes. MD simulation revealed that the introduction of the deletion destabilized the Cx50 gap junction channel, indicating the deletion as a dominant-negative mutation, Conclusions： The above results support the pathogenic role of the 15 bp deletion on GJA8 in the Chinese family and demonstrate targeted genes sequencing as a resolution to molecular diagnosis of CCs.展开更多
目的:利用目标基因捕获测序技术,对9例肺动脉高压(PAH)患者进行4个已知致病基因突变筛查,探讨利用目标基因捕获测序技术对PAH进行基因诊断的可行性。方法:抽取PAH患者外周血,提取全基因组DNA,制备文库。设计骨形成蛋白2型受体(BMPR2)、...目的:利用目标基因捕获测序技术,对9例肺动脉高压(PAH)患者进行4个已知致病基因突变筛查,探讨利用目标基因捕获测序技术对PAH进行基因诊断的可行性。方法:抽取PAH患者外周血,提取全基因组DNA,制备文库。设计骨形成蛋白2型受体(BMPR2)、激活素受体样激酶1(ACVR1)、细胞内皮糖蛋白(En G),信号蛋白SMAD4基因(SMAD4)外显子区域特异性捕获探计,利用目标基因捕获技术,进行杂交,富集目标基因组区域的DNA片段,利用Illumina Hi Seq 2000进行高通量测序,分析致病基因突变与PAH的相关性。结果:9例患者中,2例患者发现BMPR2基因突变,1例发现ACVRL1突变,BMPR2突变临床症状较重,ACVRL1突变发病年龄较小。结论:本研究利用目标基因捕获测序技术,在9例PAH患者中查出3个致病基因突变。该方法快速有效,可实现对PAH致病基因突变的初步筛查,对PAH的临床基因诊断具有重要价值。展开更多
目的建立目标基因捕获结合第二代测序技术对腹主动脉瘤患者原纤维蛋白1(FBN1)基因进行突变筛查,探讨腹主动脉瘤与FBN1基因突变的关系。方法提取4例腹主动脉瘤患者外周血全基因组DNA,利用Gen Cap目标基因捕获技术,设计FBN1的65个外显子...目的建立目标基因捕获结合第二代测序技术对腹主动脉瘤患者原纤维蛋白1(FBN1)基因进行突变筛查,探讨腹主动脉瘤与FBN1基因突变的关系。方法提取4例腹主动脉瘤患者外周血全基因组DNA,利用Gen Cap目标基因捕获技术,设计FBN1的65个外显子区域特异性捕获探针,与基因组DNA文库进行杂交,将目标基因组区域的DNA片段进行富集后,再利用Illumina Hi Seq2000第二代测序仪进行测序,通过数据分析,确定突变位点,用Sanger测序法对突变位点进行验证。结果设计合成的目标基因特异性捕获探针可有效地捕捉并富集基因组DNA的目标靶片段。4例患者目标区域平均测序深度为448.15~536.61,99.5%~99.7%目标区域覆盖度。经过数据分析及Sanger测序验证发现1个新的错义突变c.2753 C>G(p.Pro918Arg),db SNP137数据库、千人基因组及内部800名正常汉族人数据库均无此突变。经SIFT预测为有害突变。结论本研究所建立的Gen Cap目标基因捕获技术结合Illumina Hi Seq2000第二代测序技术成功地发现了FBN1的新突变。该方法快速而有效,对腹主动脉瘤分子病因学有更好的认识。展开更多
文摘为建立一种高同源区段的单核苷酸多态性(SNP)基因分型技术,通过构建本地Blast对SNP所在的200和400 bp区段进行同源性评估,并筛选出高同源区段的SNP。利用第一轮多重长PCR(polymerase chain reaction)捕获329个样本的9个高同源区段SNP所在的长片段,使用纯化后的第一轮PCR产物作为模板进行扩增子建库测序,检测样本共得2 928个SNP位点信息,测序成功率高达98.885 6%。利用Hardy-Weinberg(HWE)法则计算试验研究的9个高同源区段SNP位点的基因频率(p值均大于0.05,符合HWE法则),并与NCBI(national center for biotechnology information)中千人基因组数据库中获取的基因频率相比对,发现二者单碱基基因频率一致(误差限<0.15)。研究表明,利用多重长PCR靶向捕获技术结合二代测序技术为高同源区段的SNP分型提供一个准确、快速、大样本检测方案。
基金This research is supported by the National Key Research and Development Program of China(2016YFD0101803 and 2017YFD0101201)the Central Public-interest Scientific Institution Basal Research Fund(Y2020PT20)+4 种基金the Agricultural Science and Technology Innovation Program(ASTIP)of the Chinese Academy of Agricultural Sciences(CAAS)(CAAS-XTCX2016009)the Key Research Area and Development Program of Guangdong Province(2018B020202008)the Shijiazhuang Science and Technology Incubation Program(191540089A)the Hebei Innovation Capability Enhancement Project(19962911D)Research activities at CIMMYT were supported by the Bill and Melinda Gates Foundation and the CGIAR Research Program MAIZE.
文摘Genotyping platforms,as critical supports for genomics,genetics,and molecular breeding,have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput,automatic,large-scale,and shared facilities.In this study,we integrated an improved genotyping by target sequencing(GBTS)system with capture-in-solution(liquid chip)technology to develop a multiple single-nucleotide polymorphism(mSNP)approach in which mSNPs can be captured from a single amplicon.From one 40K maize mSNP panel,we developed three types of markers(40K mSNPs,251K SNPs,and 690K haplotypes),and generated multiple panels with various marker densities(1K–40K mSNPs)by sequencing at different depths.Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs.Compared with the one-amplicon-one-SNP system,mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection,linkage disequilibrium decay analysis,and genome-wide association studies.The technologies,protocols,and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals,plants,and microorganisms.
文摘Background： Congenital cataract （CC） is the leading cause of visual impairment or blindness in children worldwide. Because of highly genetic and clinical heterogeneity, a molecular diagnosis of the lens disease remains a challenge. Methods： In this study, we tested a three-generation Chinese family with autosomal dominant CCs by targeted sequencing of 45 CC genes on next generation sequencing and evaluated the pathogenicity of the detected mutation by protein structure, pedigree validation, and molecular dynamics （MD） simulation. Results： A novel 15 bp deletion on GJA8 （c.426_440delGCTGGAGGGGACCCT or p. 143147delLEGTL） was detected in the family. The deletion, concerned with an in-frame deletion of 5 amino acid residues in a highly evolutionarily conserved region within the cytoplasmic loop domain of the gap junction channel protein connexin 50 （CxS0）, was in full cosegregation with the cataract phenotypes in the family but not found in 1100 control exomes. MD simulation revealed that the introduction of the deletion destabilized the Cx50 gap junction channel, indicating the deletion as a dominant-negative mutation, Conclusions： The above results support the pathogenic role of the 15 bp deletion on GJA8 in the Chinese family and demonstrate targeted genes sequencing as a resolution to molecular diagnosis of CCs.
文摘目的:利用目标基因捕获测序技术,对9例肺动脉高压(PAH)患者进行4个已知致病基因突变筛查,探讨利用目标基因捕获测序技术对PAH进行基因诊断的可行性。方法:抽取PAH患者外周血,提取全基因组DNA,制备文库。设计骨形成蛋白2型受体(BMPR2)、激活素受体样激酶1(ACVR1)、细胞内皮糖蛋白(En G),信号蛋白SMAD4基因(SMAD4)外显子区域特异性捕获探计,利用目标基因捕获技术,进行杂交,富集目标基因组区域的DNA片段,利用Illumina Hi Seq 2000进行高通量测序,分析致病基因突变与PAH的相关性。结果:9例患者中,2例患者发现BMPR2基因突变,1例发现ACVRL1突变,BMPR2突变临床症状较重,ACVRL1突变发病年龄较小。结论:本研究利用目标基因捕获测序技术,在9例PAH患者中查出3个致病基因突变。该方法快速有效,可实现对PAH致病基因突变的初步筛查,对PAH的临床基因诊断具有重要价值。
文摘目的建立目标基因捕获结合第二代测序技术对腹主动脉瘤患者原纤维蛋白1(FBN1)基因进行突变筛查,探讨腹主动脉瘤与FBN1基因突变的关系。方法提取4例腹主动脉瘤患者外周血全基因组DNA,利用Gen Cap目标基因捕获技术,设计FBN1的65个外显子区域特异性捕获探针,与基因组DNA文库进行杂交,将目标基因组区域的DNA片段进行富集后,再利用Illumina Hi Seq2000第二代测序仪进行测序,通过数据分析,确定突变位点,用Sanger测序法对突变位点进行验证。结果设计合成的目标基因特异性捕获探针可有效地捕捉并富集基因组DNA的目标靶片段。4例患者目标区域平均测序深度为448.15~536.61,99.5%~99.7%目标区域覆盖度。经过数据分析及Sanger测序验证发现1个新的错义突变c.2753 C>G(p.Pro918Arg),db SNP137数据库、千人基因组及内部800名正常汉族人数据库均无此突变。经SIFT预测为有害突变。结论本研究所建立的Gen Cap目标基因捕获技术结合Illumina Hi Seq2000第二代测序技术成功地发现了FBN1的新突变。该方法快速而有效,对腹主动脉瘤分子病因学有更好的认识。
