Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost ef...Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.展开更多
目的:对1例X连锁隐性遗传鱼鳞病合并隐睾的患儿及其家系成员进行遗传学分析,探讨其致病原因。方法:对患儿及其家庭成员进行常规染色体G显带核型分析和低深度全基因组拷贝数变异测序分析(CNV-seq)。结果:染色体核型分析未见明显异常。CNV...目的:对1例X连锁隐性遗传鱼鳞病合并隐睾的患儿及其家系成员进行遗传学分析,探讨其致病原因。方法:对患儿及其家庭成员进行常规染色体G显带核型分析和低深度全基因组拷贝数变异测序分析(CNV-seq)。结果:染色体核型分析未见明显异常。CNV-seq检测发现患儿及哥哥和母亲的X染色体p22.33-p22.31处缺失5.28Mb区域,该片段包含Xp22.31 recurrent region (includes STS)全部。结论:患儿X染色体拷贝数变异遗传自其母亲,Xp22.31缺失是该患儿异常表型的遗传学病因。展开更多
目的探索在孕早期利用子宫颈胎儿滋养层细胞进行无创产前诊断的可行性。方法用宫颈刷收集10例自然受孕的孕妇孕早期的子宫颈脱落细胞,利用免疫磁珠分离法(trophoblast retrieval and isolation from the cervix,TRIC),从脱落宫颈细胞中...目的探索在孕早期利用子宫颈胎儿滋养层细胞进行无创产前诊断的可行性。方法用宫颈刷收集10例自然受孕的孕妇孕早期的子宫颈脱落细胞,利用免疫磁珠分离法(trophoblast retrieval and isolation from the cervix,TRIC),从脱落宫颈细胞中分离出胎儿滋养层细胞,从分离出的阳性细胞中获得胎儿全基因组DNA,利用单细胞基因组扩增技术和低覆盖度全基因组测序检测染色体非整倍体及染色体微缺失/微重复。结果宫颈刷法收集的样本中有3例观察到β-HCG信号表达。3例样本经TRIC法分选后,β-hCG阳性细胞比例增加,利用荧光原位杂交技术可以进行准确的胎儿性别鉴定。选取TRIC法分选的男性胎儿阳性细胞进行高通量测序,结果显示利用TRIC法分选的阳性细胞中有20%为胎儿细胞,说明其捕获的特异性较低。结论利用脱落的子宫颈胎儿滋养层细胞有可能进行胎儿性别和染色体数目异常的检测,但其捕获的特异性需要进一步提高。展开更多
文摘Background Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome.It requires a low sequencing depth to be cost effective,which may increase the error at the genotype assigment.Third generation nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation,which provides added value to genotype-by-sequencing.The aim of this study was to evaluate the performance of genotype-by-low pass nanopore sequencing for estimating the direct genomic value in dairy cattle,and the possibility to obtain methylation marks simultaneously.Results Latest nanopore chemistry(LSK14 and Q20)achieved a modal base calling accuracy of 99.55%,whereas previous kit(LSK109)achieved slightly lower accuracy(99.1%).The direct genomic value accuracy from genotype-by-low pass sequencing ranged between 0.79 and 0.99,depending on the trait(milk,fat or protein yield),with a sequencing depth as low as 2×and using the latest chemistry(LSK114).Lower sequencing depth led to biased estimates,yet with high rank correlations.The LSK109 and Q20 achieved lower accuracies(0.57-0.93).More than one million high reliable methylated sites were obtained,even at low sequencing depth,located mainly in distal intergenic(87%)and promoter(5%)regions.Conclusions This study showed that the latest nanopore technology in useful in a LowPass sequencing framework to estimate direct genomic values with high reliability.It may provide advantages in populations with no available SNP chip,or when a large density of markers with a wide range of allele frequencies is needed.In addition,low pass sequencing provided nucleotide methylation status of>1 million nucleotides at≥10×,which is an added value for epigenetic studies.
文摘目的:对1例X连锁隐性遗传鱼鳞病合并隐睾的患儿及其家系成员进行遗传学分析,探讨其致病原因。方法:对患儿及其家庭成员进行常规染色体G显带核型分析和低深度全基因组拷贝数变异测序分析(CNV-seq)。结果:染色体核型分析未见明显异常。CNV-seq检测发现患儿及哥哥和母亲的X染色体p22.33-p22.31处缺失5.28Mb区域,该片段包含Xp22.31 recurrent region (includes STS)全部。结论:患儿X染色体拷贝数变异遗传自其母亲,Xp22.31缺失是该患儿异常表型的遗传学病因。
文摘目的探索在孕早期利用子宫颈胎儿滋养层细胞进行无创产前诊断的可行性。方法用宫颈刷收集10例自然受孕的孕妇孕早期的子宫颈脱落细胞,利用免疫磁珠分离法(trophoblast retrieval and isolation from the cervix,TRIC),从脱落宫颈细胞中分离出胎儿滋养层细胞,从分离出的阳性细胞中获得胎儿全基因组DNA,利用单细胞基因组扩增技术和低覆盖度全基因组测序检测染色体非整倍体及染色体微缺失/微重复。结果宫颈刷法收集的样本中有3例观察到β-HCG信号表达。3例样本经TRIC法分选后,β-hCG阳性细胞比例增加,利用荧光原位杂交技术可以进行准确的胎儿性别鉴定。选取TRIC法分选的男性胎儿阳性细胞进行高通量测序,结果显示利用TRIC法分选的阳性细胞中有20%为胎儿细胞,说明其捕获的特异性较低。结论利用脱落的子宫颈胎儿滋养层细胞有可能进行胎儿性别和染色体数目异常的检测,但其捕获的特异性需要进一步提高。
