Detection rates for genotyping errors in SNPs using the trio design
Detection rates for genotyping errors in SNPs using the trio design
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DOI：
10.1159/000068836
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发表时间：
2002-01-01
期刊：
影响因子：
1.8
通讯作者：
Ziegler, A
中科院分区：
文献类型：
--
作者：
Geller, F;Ziegler, A
分析传递不平衡的一种众所周知的方法是研究由受影响的孩子及其父母组成的三人组中的单核苷酸多态性 (SNP)。结果可能因错误给出的基因型而产生偏差。各种原因，其中样本交换或错误的谱系结构，代表了有偏见的结果的可能来源。由于良好的研究条件以及通过一系列独立标记检查正确的谱系结构可以部分排除这些错误，因此造成错误的其余主要原因是基因分型错误。一些错误可以通过孟德尔检查来检测，而另一些则与谱系结构兼容。基因分型错误的程度可以通过调查孟德尔检查检测到的基因分型错误的比率来估计。在许多研究中，TDT 仅研究特定基因组区域的一个 SNP，这使得孟德尔检查成为控制基因分型错误的唯一工具。根据检测到的错误率，可以估计真实的错误率。戈登等人。 [Hum Hered 1999;49:65-70] 考虑了基因分型错误的情况，该错误是随机且独立地发生的，以一定的固定概率错误地确定了等位基因。实际上，确定的是 SNP 基因型，而不是单个等位基因。因此，我们根据基因型研究检测到的错误的比例（检测率）。 Gordon 等人报告的检测率在 25% 到 30% 之间，与此相反，考虑到数据中可能存在的错误结构，我们获得了 39% 到 61% 之间的更高检测率。我们的结论是，检测率可能远高于戈登等人报告的检测率。版权所有 (C) 2002 S. Karger AG，巴塞尔。
One well-known approach for the analysis of transmission-disequilibrium is the investigation of single nucleotide polymorphisms (SNPs) in trios consisting of an affected child and its parents. Results may be biased by erroneously given genotypes. Various reasons, among them sample swap or wrong pedigree structure, represent a possible source for biased results. As these can be partly ruled out by good study conditions together with checks for correct pedigree structure by a series of independent markers, the remaining main cause for errors is genotyping errors. Some of the errors can be detected by Mendelian checks whilst others are compatible with the pedigree structure. The extent of genotyping errors can be estimated by investigating the rate of detected genotyping errors by Mendelian checks. In many studies only one SNP of a specific genomic region is investigated by TDT which leaves Mendelian checks as the only tool to control genotyping errors. From the rate of detected errors the true error rate can be estimated. Gordon et al. [Hum Hered 1999;49:65-70] considered the case of genotyping errors that occur randomly and independently with some fixed probability for the wrong ascertainment of an allele. In practice, instead of single alleles, SNP genotypes are determined. Therefore, we study the proportion of detected errors (detection rate) based on genotypes. In contrast to Gordon et al., who reported detection rates between 25 and 30%, we obtain higher detection rates ranging from 39 up to 61% considering likely error structures in the data. We conclude that detection rates are probably substantially higher than those reported by Gordon et al. Copyright (C) 2002 S. Karger AG, Basel.