快速产前诊断13、X和Y染色体非整倍体的研究
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摘要
目的
1筛选出天津汉族群体13、X和Y染色体上遗传信息含量高的短串联重复序列(short tandem repeat, STR)基因座,建立快速诊断13、X和Y染色体非整倍体的技术,为用STR基因座产前诊断13、X和Y染色体非整倍体提供实验依据。
2建立快速产前诊断13、X和Y染色体非整倍体的技术,探讨定量荧光聚合酶链反应(quantitative fluorescence polymerase chain reaction, QF-PCR)扩增STR基因座在快速产前诊断中的临床应用价值。
方法
1根据文献报道选择13、X和Y染色体上30个基因座作为候选基因座,应用QF-PCR、毛细管电泳研究其在350例无亲缘关系天津汉族个体中的遗传多态性。ABI Prism GeneMapper v3.0软件分析数据,得出片段大小、峰面积、峰图等相关数据。直接计数法观察各基因座的等位基因频率和基因型频率,基因型频率的观察值和理论值用x2检验,验证是否符合Hardy-Weinberg平衡定律(P>0.05)。采用PowerStatsV12软件分析STR基因座的期望杂合度(expected heterozygosity, He)、观察杂合度(observed heterozygosity, Ho)、多态信息量(polymorphic information content, PIC)、个体识别率(power of discrimination, PD)、非父排除率(power of exclusion, PE)等群体遗传学数据。用SPSS17.0软件统计杂合子峰面积比值范围、峰面积比值均数±标准差(x±s)和95%可信区间(confidence interval, CI)。每个STR基因座测序2个纯合子样本,对比分析后确定其重复序列及重复次数。
2QF-PCR扩增筛选出的高遗传信息量STR基因座,对362例外周血样本和452例产前诊断样本(包括373例羊水、79例绒毛)进行检测,并将结果与染色体核型分析结果比较。
结果
113、X和Y染色体STR基因座遗传多态性结果
1.1根据易于扩增、结果稳定、重复性好、高信息量等标准,最终确定13号染色体D13S305、D13S631和D13S634基因座、X染色体HPRTB、DXS6803和DXS6809基因座、Y染色体DYS19、DYS390和DYS393基因座为本研究的基因座。
1.2350例天津汉族人群中13号染色体D13S305、D13S631和D13S634基因座的重复序列为CTTT、ATCT和AAGA,分别发现11、7和11个等位基因,42、22和29种基因型。基因型分布经x2检验,符合Hardy-Weinberg平衡定律(P>0.05)。3个基因座的He分别为0.833、0.754、0.796,Ho为0.809、0.714、0.757,PIC为0.810、0.714、0.765,PD为0.948、0.893、0.927,PE为0.615、0.451、0.522。
1.3150例天津汉族女性中X染色体HPRTB、DXS6803和DXS6809基因座的重复序列为TCTA、GATA和ATCT,分别发现10、6和10个等位基因,22、12和29种基因型。基因型分布经x2检验,符合Hardy-Weinberg平衡定律(P>0.05)。3个基因座的He分别为0.748、0.649、0.806,Ho为0.607、0.700、0.713,PIC为0.706、0.599、0.775,PD为0.894、0.814、0.931,PE为0.299、0.428、0.449。
1.4200例天津汉族男性中Y染色体DYS19、DYS390和DYS393基因座的重复序列为TAGA、TCTA和TATC,分别发现5、6和6个等位基因,基因多样性(gene diversity, GD)为0.743、0.731、0.634。
1.513号染色体D13S305、D13S631、D13S634基因座和X染色体HPRTB、 DXS6803、DXS6809基因座杂合子峰面积比值范围介于0.68～1.49之间,峰面积比值x±s为1.09±0.18,95%CI为1.08～1.10。
2基因诊断和产前基因诊断染色体非整倍体结果
2.1基因诊断结果
362例外周血样本QF-PCR均扩增成功。352例样本未见异常,3例47,XXY、4例45,X、1例47,XYY、1例46,XY女性和1例45,X/47,XYY (嵌合比例60%)得到诊断。与染色体核型分析结果相比,360例样本结果一致,2例嵌合体因为嵌合比例较低,分别为6%和5%,未能检出。
2.2产前基因诊断结果
2.2.1452例产前诊断样本,均成功检测出胎儿性别,包括219例男性胎儿和233例女性胎儿,与染色体核型分析结果相符。
2.2.2D13S305、D13S631、D13S634、HPRTB、DXS6803、DXS6809、DYS19、DYS390和DYS393基因座分别有20、12、12、37、13、35、35、19和18例样本扩增失败。统计数据发现共有415例样本9个基因座均扩增成功,扩增的成功率为91.81%(415/452)。
2.2.3D13S305、D13S631、D13S634、HPRTB、DXS6803和DXS6809基因座正常杂合子峰面积比值范围介于0.70-1.48之间,峰面积比值x±s为1.12±0.18,95%CI为1.10～1.14。
2.2.4扩增成功的样本中发现3例QF-PCR结果异常,包括1例13-三体、1例47,XXY和1例45,X,其余412例未见异常,QF-PCR结果与染色体核型分析相符。
2.3QF-PCR扩增STR基因座诊断13、X和Y染色体非整倍体的灵敏度为86.67%(13/15),特异度为100%(762/762)。
结论
1本研究显示D13S305、D13S631、D13S634、HPRTB、DXS6803、DXS6809、 DYS19、DYS390和DYS393基因座在天津汉族群体具有较高的杂合度和多态信息量,是13、X和Y染色体良好的遗传标记。
2应用QF-PCR扩增13、X和Y染色体上9个STR基因座基因诊断和产前基因诊断13、X和Y染色体非整倍体结果准确,方法简便、快速,在临床上有广阔的应用前景。
Objective
1To screen out polymorphic short tandem repeat (STR) loci on chromosome13, X and Y in Tianjin Han population of China and set up a method to diagnose chromosome aneuploidies and provide basic data for using STR loci in prenatal diagnosis of aneuploidies accurately and rapidly.
2To establish a method for prenatal diagnosis of aneuploidies involving chromosome13, X and Y and discuss the clinical value of quantitative fluorescence polymerase chain reaction (QF-PCR) in rapid prenatal diagnosis.
Methods
1According to the literature we chose30loci on chromosome13, X and Y as candidate loci. QF-PCR and capillary electrophoresis was applied to350unrelated individuals of Tianjin Han population of China. The relevant data were analyzed by ABI Prism GeneMapper v3.0software. Allelic frequencies and genotype frequencies were calculated by direct counting. The frequencies of the genotypes were checked using Chi-square test to verify Hardy-Weinberg Equilibrium (P>0.05). Genetic polymorphisms data were calculated by PowerStatsV12software. The ratio scopes of heterozygote peak areas, the average peak areas ratio and95%confidence interval (CI) were calculated using SPSS17.0software. Two alleles of each locus were sequenced for confirmation of repeat sequence and repeat number.
2Polymorphic loci located on chromosome13, X and Y were used to examine362peripheral blood samples and452prenatal diagnosis samples (including373cases of amniotic fluid and79cases of villi) by QF-PCR. The results were compared with karyotype analysis.
Results
1The polymorphisms of STR loci on chromosome13, X and Y
1.1Based on preliminary experiments we finally chose D13S305, D13S631and D13S634markers on chromosome13, HPRTB, DXS6803and DXS6809markers on chromosome X, DYS19, DYS390and DYS393markers on chromosome Y for the loci of the present study.
1.2The repeat sequence of D13S305, D13S631and D13S634locus was CTTT, ATCT and AAGA.11,7and11alleles were found for each locus. No significant deviations from the Hardy-Weinberg equilibrium were observed in these three STR markers (P>0.05). The He of these three STR loci was0.833,0.754,0.796. The Ho was0.809,0.714,0.757. The PIC was0.810,0.714,0.765. The PD was0.948,0.893,0.927. The PE was0.615,0.451,0.522.
1.3The repeat sequence of HPRTB, DXS6803and DXS6809locus was TCTA, GATA and ATCT.10,6and10alleles were found for each locus. No significant deviations from the Hardy-Weinberg equilibrium were observed in these three STR markers (P>0.05). The He of these three STR loci was0.748,0.649,0.806. The Ho was0.607,0.700,0.713. The PIC was0.706,0.599,0.775. The PD was0.894,0.814,0.931. The PE was0.299,0.428,0.449.
1.4The repeat sequence of DYS19, DYS390and DYS393locus was TAGA, TCTA and TATC.5,6and6alleles were found for each locus. The gene diversity (GD) values for each locus were0.743,0.731,0.634.
1.5Combined six markers on chromosome13and X, the ratio scope of heterozygote peak areas was0.68～1.49. The average peak area ratio was1.09±0.18. The95%CI was1.08-1.10.
2Genetic diagnosis and prenatal gene diagnosis of chromosome aneuploidy
2.1The genetic diagnosis results
362peripheral blood samples were successfully amplified.352samples gave a normal QF-PCR results and3cases of47,XXY,4cases of45,X,1case of47,XYY,1female with karyotype46,XY and1mosaic case were diagnosed correctly. Two mosaic cases failed to diagnose because of the low percentage of mosaicism.
2.2The prenatal gene diagnosis results
2.2.1Fetal sexing was successfully achieved in all cases and the results were in consistent with the chromosome karyotype. There were219male fetuses and233female fetuses.
2.2.2There were20,12,12,13,35,35,37,19and18cases failed to amplify for each nine locus. The overall success rate was91.81%(415/452).
2.2.3Combined six markers on chromosome13and X, the ratio scope of heterozygote peak areas was0.70～1.48. The average peak area ratio was1.12±0.18. The95%CI was1.10-1.14.
2.2.41cases of trisomy13,1case of47,XXY and1case of45.X were detected by QF-PCR. Other412samples were normal and the results were in accordance with karyotype analysis.
2.3The sensitivity and specificity of QF-PCR were86.67%(13/15) and100%(762/762).
Conelusions
1This research showed that D13S305, D13S631and D13S634markers on chromosome13, HPRTB, DXS6803and DXS6809markers on chromosome X, DYS19, DYS390and DYS393markers on chromosome Y were highly polymorphic in Tianjin Han population of China. They are good genetic markers on chromosome13,X and Y.
2QF-PCR amplifying STR loci is a sensitive, specific, simple and rapid method for prenatal diagnosis of chromosome aneuploidies. It has a broad application prospect in clinic.
1筛选出天津汉族群体13、X和Y染色体上遗传信息含量高的短串联重复序列(short tandem repeat, STR)基因座,建立快速诊断13、X和Y染色体非整倍体的技术,为用STR基因座产前诊断13、X和Y染色体非整倍体提供实验依据。
2建立快速产前诊断13、X和Y染色体非整倍体的技术,探讨定量荧光聚合酶链反应(quantitative fluorescence polymerase chain reaction, QF-PCR)扩增STR基因座在快速产前诊断中的临床应用价值。
方法
1根据文献报道选择13、X和Y染色体上30个基因座作为候选基因座,应用QF-PCR、毛细管电泳研究其在350例无亲缘关系天津汉族个体中的遗传多态性。ABI Prism GeneMapper v3.0软件分析数据,得出片段大小、峰面积、峰图等相关数据。直接计数法观察各基因座的等位基因频率和基因型频率,基因型频率的观察值和理论值用x2检验,验证是否符合Hardy-Weinberg平衡定律(P>0.05)。采用PowerStatsV12软件分析STR基因座的期望杂合度(expected heterozygosity, He)、观察杂合度(observed heterozygosity, Ho)、多态信息量(polymorphic information content, PIC)、个体识别率(power of discrimination, PD)、非父排除率(power of exclusion, PE)等群体遗传学数据。用SPSS17.0软件统计杂合子峰面积比值范围、峰面积比值均数±标准差(x±s)和95%可信区间(confidence interval, CI)。每个STR基因座测序2个纯合子样本,对比分析后确定其重复序列及重复次数。
2QF-PCR扩增筛选出的高遗传信息量STR基因座,对362例外周血样本和452例产前诊断样本(包括373例羊水、79例绒毛)进行检测,并将结果与染色体核型分析结果比较。
结果
113、X和Y染色体STR基因座遗传多态性结果
1.1根据易于扩增、结果稳定、重复性好、高信息量等标准,最终确定13号染色体D13S305、D13S631和D13S634基因座、X染色体HPRTB、DXS6803和DXS6809基因座、Y染色体DYS19、DYS390和DYS393基因座为本研究的基因座。
1.2350例天津汉族人群中13号染色体D13S305、D13S631和D13S634基因座的重复序列为CTTT、ATCT和AAGA,分别发现11、7和11个等位基因,42、22和29种基因型。基因型分布经x2检验,符合Hardy-Weinberg平衡定律(P>0.05)。3个基因座的He分别为0.833、0.754、0.796,Ho为0.809、0.714、0.757,PIC为0.810、0.714、0.765,PD为0.948、0.893、0.927,PE为0.615、0.451、0.522。
1.3150例天津汉族女性中X染色体HPRTB、DXS6803和DXS6809基因座的重复序列为TCTA、GATA和ATCT,分别发现10、6和10个等位基因,22、12和29种基因型。基因型分布经x2检验,符合Hardy-Weinberg平衡定律(P>0.05)。3个基因座的He分别为0.748、0.649、0.806,Ho为0.607、0.700、0.713,PIC为0.706、0.599、0.775,PD为0.894、0.814、0.931,PE为0.299、0.428、0.449。
1.4200例天津汉族男性中Y染色体DYS19、DYS390和DYS393基因座的重复序列为TAGA、TCTA和TATC,分别发现5、6和6个等位基因,基因多样性(gene diversity, GD)为0.743、0.731、0.634。
1.513号染色体D13S305、D13S631、D13S634基因座和X染色体HPRTB、 DXS6803、DXS6809基因座杂合子峰面积比值范围介于0.68～1.49之间,峰面积比值x±s为1.09±0.18,95%CI为1.08～1.10。
2基因诊断和产前基因诊断染色体非整倍体结果
2.1基因诊断结果
362例外周血样本QF-PCR均扩增成功。352例样本未见异常,3例47,XXY、4例45,X、1例47,XYY、1例46,XY女性和1例45,X/47,XYY (嵌合比例60%)得到诊断。与染色体核型分析结果相比,360例样本结果一致,2例嵌合体因为嵌合比例较低,分别为6%和5%,未能检出。
2.2产前基因诊断结果
2.2.1452例产前诊断样本,均成功检测出胎儿性别,包括219例男性胎儿和233例女性胎儿,与染色体核型分析结果相符。
2.2.2D13S305、D13S631、D13S634、HPRTB、DXS6803、DXS6809、DYS19、DYS390和DYS393基因座分别有20、12、12、37、13、35、35、19和18例样本扩增失败。统计数据发现共有415例样本9个基因座均扩增成功,扩增的成功率为91.81%(415/452)。
2.2.3D13S305、D13S631、D13S634、HPRTB、DXS6803和DXS6809基因座正常杂合子峰面积比值范围介于0.70-1.48之间,峰面积比值x±s为1.12±0.18,95%CI为1.10～1.14。
2.2.4扩增成功的样本中发现3例QF-PCR结果异常,包括1例13-三体、1例47,XXY和1例45,X,其余412例未见异常,QF-PCR结果与染色体核型分析相符。
2.3QF-PCR扩增STR基因座诊断13、X和Y染色体非整倍体的灵敏度为86.67%(13/15),特异度为100%(762/762)。
结论
1本研究显示D13S305、D13S631、D13S634、HPRTB、DXS6803、DXS6809、 DYS19、DYS390和DYS393基因座在天津汉族群体具有较高的杂合度和多态信息量,是13、X和Y染色体良好的遗传标记。
2应用QF-PCR扩增13、X和Y染色体上9个STR基因座基因诊断和产前基因诊断13、X和Y染色体非整倍体结果准确,方法简便、快速,在临床上有广阔的应用前景。
Objective
1To screen out polymorphic short tandem repeat (STR) loci on chromosome13, X and Y in Tianjin Han population of China and set up a method to diagnose chromosome aneuploidies and provide basic data for using STR loci in prenatal diagnosis of aneuploidies accurately and rapidly.
2To establish a method for prenatal diagnosis of aneuploidies involving chromosome13, X and Y and discuss the clinical value of quantitative fluorescence polymerase chain reaction (QF-PCR) in rapid prenatal diagnosis.
Methods
1According to the literature we chose30loci on chromosome13, X and Y as candidate loci. QF-PCR and capillary electrophoresis was applied to350unrelated individuals of Tianjin Han population of China. The relevant data were analyzed by ABI Prism GeneMapper v3.0software. Allelic frequencies and genotype frequencies were calculated by direct counting. The frequencies of the genotypes were checked using Chi-square test to verify Hardy-Weinberg Equilibrium (P>0.05). Genetic polymorphisms data were calculated by PowerStatsV12software. The ratio scopes of heterozygote peak areas, the average peak areas ratio and95%confidence interval (CI) were calculated using SPSS17.0software. Two alleles of each locus were sequenced for confirmation of repeat sequence and repeat number.
2Polymorphic loci located on chromosome13, X and Y were used to examine362peripheral blood samples and452prenatal diagnosis samples (including373cases of amniotic fluid and79cases of villi) by QF-PCR. The results were compared with karyotype analysis.
Results
1The polymorphisms of STR loci on chromosome13, X and Y
1.1Based on preliminary experiments we finally chose D13S305, D13S631and D13S634markers on chromosome13, HPRTB, DXS6803and DXS6809markers on chromosome X, DYS19, DYS390and DYS393markers on chromosome Y for the loci of the present study.
1.2The repeat sequence of D13S305, D13S631and D13S634locus was CTTT, ATCT and AAGA.11,7and11alleles were found for each locus. No significant deviations from the Hardy-Weinberg equilibrium were observed in these three STR markers (P>0.05). The He of these three STR loci was0.833,0.754,0.796. The Ho was0.809,0.714,0.757. The PIC was0.810,0.714,0.765. The PD was0.948,0.893,0.927. The PE was0.615,0.451,0.522.
1.3The repeat sequence of HPRTB, DXS6803and DXS6809locus was TCTA, GATA and ATCT.10,6and10alleles were found for each locus. No significant deviations from the Hardy-Weinberg equilibrium were observed in these three STR markers (P>0.05). The He of these three STR loci was0.748,0.649,0.806. The Ho was0.607,0.700,0.713. The PIC was0.706,0.599,0.775. The PD was0.894,0.814,0.931. The PE was0.299,0.428,0.449.
1.4The repeat sequence of DYS19, DYS390and DYS393locus was TAGA, TCTA and TATC.5,6and6alleles were found for each locus. The gene diversity (GD) values for each locus were0.743,0.731,0.634.
1.5Combined six markers on chromosome13and X, the ratio scope of heterozygote peak areas was0.68～1.49. The average peak area ratio was1.09±0.18. The95%CI was1.08-1.10.
2Genetic diagnosis and prenatal gene diagnosis of chromosome aneuploidy
2.1The genetic diagnosis results
362peripheral blood samples were successfully amplified.352samples gave a normal QF-PCR results and3cases of47,XXY,4cases of45,X,1case of47,XYY,1female with karyotype46,XY and1mosaic case were diagnosed correctly. Two mosaic cases failed to diagnose because of the low percentage of mosaicism.
2.2The prenatal gene diagnosis results
2.2.1Fetal sexing was successfully achieved in all cases and the results were in consistent with the chromosome karyotype. There were219male fetuses and233female fetuses.
2.2.2There were20,12,12,13,35,35,37,19and18cases failed to amplify for each nine locus. The overall success rate was91.81%(415/452).
2.2.3Combined six markers on chromosome13and X, the ratio scope of heterozygote peak areas was0.70～1.48. The average peak area ratio was1.12±0.18. The95%CI was1.10-1.14.
2.2.41cases of trisomy13,1case of47,XXY and1case of45.X were detected by QF-PCR. Other412samples were normal and the results were in accordance with karyotype analysis.
2.3The sensitivity and specificity of QF-PCR were86.67%(13/15) and100%(762/762).
Conelusions
1This research showed that D13S305, D13S631and D13S634markers on chromosome13, HPRTB, DXS6803and DXS6809markers on chromosome X, DYS19, DYS390and DYS393markers on chromosome Y were highly polymorphic in Tianjin Han population of China. They are good genetic markers on chromosome13,X and Y.
2QF-PCR amplifying STR loci is a sensitive, specific, simple and rapid method for prenatal diagnosis of chromosome aneuploidies. It has a broad application prospect in clinic.
引文
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