Genotyping of three candidate genes after whole-genome preamplification of DNA collected from buccal cells
Genotyping of three candidate genes after whole-genome preamplification of DNA collected from buccal cells
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DOI：
10.1023/a:1021007701808
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发表时间：
2003-01-01
影响因子：
2.6
通讯作者：
Smolen, A
中科院分区：
文献类型：
--
作者：
Anchordoquy, HC;McGeary, C;Smolen, A
从口腔细胞方法中获得的基因组DNA的量对于大规模遗传学项目来说可能是次优的，因为DNA的量可能不足以进行所提出的分析的数量。引物延伸预扩增（PEP）方法，可以扩增整个基因组100倍或更多，提供了一个潜在的解决方案，这个问题。我们比较了PEP口腔DNA与来自科罗拉多纵向双胞胎研究的97个家庭的315个个体的基因组口腔DNA的三个位点：多巴胺转运蛋白，多巴胺D4受体和5-羟色胺转运蛋白。共评估了1890个基因组和1890个PEP等位基因，在单次测定后，1670个比较（88%）一致。53个个体有一个或多个失败的初始聚合酶链反应（PCR），共有81个失败的PCR，占162个缺失的等位基因调用。将失败的PCR重复一次，并恢复了146个缺失的等位基因调用。基因组和PEP DNA等位基因调用之间的比较显示，37个个体有一个或多个差异，总共有52个不一致。其中，18例发现初始PEP结果正确，25例发现初始基因组结果正确，9例无法解析。总体而言，基因组和PEP DNA样品的真实调用，缺失数据和基因分型错误的比率几乎相同：在评估的1890种基因型中，在1845种基因组和1840种PEP样品中发现了真实调用，在18种基因组和16种PEP样品中发现了缺失基因型，在18种基因组和25种PEP样品中发现了错误分配。这些结果表明，常规的全基因组预扩增的基因组DNA是一个合适的方法提供DNA基因型这些位点。
The amount of genomic DNA obtained from buccal cell methods may be suboptimal for large-scale genetics projects, because the quantity of DNA may be insufficient for the number of analyses proposed. Primer extension preamplification (PEP) methods that can amplify the entire genome 100-fold or more, offer a potential solution to this problem. We compared PEP buccal DNA with genomic buccal DNA from 315 individuals from 97 families of the Colorado Longitudinal Twin Study for three loci: the dopamine transporter, dopamine D4 receptor, and serotonin transporter. A total of 1890 genomic and 1890 PEP alleles were assessed, and 1670 comparisons (88%) agreed after a single determination. Fifty-three individuals had one or more failed initial polymerase chain reactions (PCR), with 81 failed PCRs in total, accounting for 162 missing allele calls. The failed PCRs were repeated once, and 146 of the missing allele calls were recovered. Comparisons between genomic and PEP DNA allele calls showed 37 individuals had one or more discrepancies, for a total of 52 inconsistencies. Of these, the initial PEP result was found to be correct in 18 cases, the initial genomic result was found to be correct in 25 cases, and 9 could not be resolved. Overall, rates of true calls, missing data, and genotyping errors for genomic and PEP DNA samples were nearly identical: of the 1890 genotypes assessed, true calls were found in 1845 genomic and 1840 PEP samples, missing genotypes in 18 genomic and 16 PEP samples, and incorrect assignments in 18 genomic and 25 PEP samples. These results suggest that routine whole-genome preamplification of genomic DNA is an appropriate method for providing DNA to genotype these loci.