FP-TDI SNP scoring by manual and statistical procedures: A study of error rates and types
FP-TDI SNP scoring by manual and statistical procedures: A study of error rates and types
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DOI：
10.2144/03343dd04
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发表时间：
2003-03-01
期刊：
影响因子：
2.7
通讯作者：
Chen, X
中科院分区：
文献类型：
--
作者：
van den Oord, EJCG;Jiang, Y;Chen, X
对于在普通实验室中常用的技术，例如荧光偏振检测与模板导向，染料终止剂掺入（FP-TDI），SNP基因型评分通常是手动完成的。在这里，我们研究的错误率和缺失的基因型获得这种程序。我们还介绍了三种统计基因型评分方法，以检查它们是否形成一个可行的替代方案。数据由来自268个家系的约1400个个体中的8个SNPs分型组成。统计程序在几个内部标准上表现得更好，例如孟德尔错误的数量，并且与两名评分员重新评分的不一致基因型表现出更高的一致性。最好的结果与统计程序，纳入信息的误差结构中的FP-TDI数据。我们估计，如果基因型手动评分，错误率约为1.6%。这些错误中约有0.6%可以解释为数据操作错误，剩下的1%是由于可能的不正确评分。由于数据处理错误（1.7%）和保守评分（1.6%），手工评分中缺失的基因型增加了3.3%。
For technologies that are commonly used in ordinary laboratories such as fluorescence-polarization detection with template-directed, dye-terminator incorporation (FP-TDI), SNP genotype scoring is usually done manually. Here we study rates of errors and missing genotypes obtained with this procedure. We also introduce three statistical genotype scoring methods to examine whether they form a viable alternative. Data consisted of eight SNPs typed in about 1400 individuals from 268 pedigrees. The statistical procedures performed better on several internal criteria, such as the number of Mendelian errors, and showed much higher agreement with discrepant genotypes re-scored by two raters. The best results were obtained with the statistical procedure that incorporated information about regularities in the error structure Of the FP-TDI data. We estimated that there were about 1.6% more errors if genotypes were scored manually. About 0.6% of these errors could be explained by data manipulation errors, leaving 1% as the result of possible incorrect scoring. There were 3.3% more missing genotypes in the manual scoring due to errors in data manipulation (1.7%) and conservative scoring (1.6%).