One of the many commercial technologies for genotyping single nucleotide polymorphisms (SNPs) is template direct dye-terminator incorporation with fluorescence-polarization (TDI-FP assay). It is a single-base extension assay followed by reading the fluorescence polarization values in an appropriate instrument. We have evaluated the suitability of the TDI-FP technique to detect haploid uniparentally inherited DNA polymorphisms on the nonrecombining portion of the Y chromosome. A sample of 47 individuals has been genotyped for 8 Y chromosome biallelic markers. The SNP typing was blindly duplicated by the denaturing high-performance liquid chromatography (DHPLC) technique for comparison. In the cases under examination the TDI-FP assay was able to resolve an allelic state fully. Such a result showed 100% concordance indicating how efficiently the TDI assay can be used to genotype Y chromosome DNA SNPs. However, a percentage of indeterminate genotypes remained unresolved by simple visual inspection: it varied from 0% to 11% depending on the SNP locus and on the success of amplification. This is consistent with previous findings. A maximum likelihood classificatory analysis allowed some of the indeterminate genotypes to be assigned and some potentially misclassified samples to be identified. Their percentage remains relatively high despite retyping and therefore alternative techniques for these noncompliant situations are required.

译文

用于单核苷酸多态性 (snp) 基因分型的许多商业技术之一是模板直接染料-终止剂与荧光偏振结合 (tdi-fp测定)。这是一种单碱基延伸测定法,然后在适当的仪器中读取荧光偏振值。我们已经评估了tdi-fp技术在Y染色体非重组部分上检测单倍体单亲遗传DNA多态性的适用性。已对47个个体的样本进行了8个Y染色体双等位基因标记的基因分型。通过变性高效液相色谱 (DHPLC) 技术盲目复制SNP分型,以进行比较。在接受检查的情况下,tdi-fp测定能够完全解析等位基因状态。这样的结果显示出100% 一致性,表明TDI测定可有效地用于基因型Y染色体DNA snp。然而,通过简单的目视检查,不确定基因型的百分比仍未解决: 取决于SNP基因座和扩增的成功程度,从0% 到11% 不等。这与以前的发现是一致的。最大似然分类分析允许分配一些不确定的基因型,并识别一些可能错误分类的样本。尽管重新键入,但它们的百分比仍然相对较高,因此需要针对这些不合规情况的替代技术。

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