Application of mixsep software package: Performance verification of male-mixed DNA analysis.
Application of mixsep software package: Performance verification of male-mixed DNA analysis.
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mixsep软件包的应用：男性混合DNA分析的性能验证
DOI：
10.3892/mmr.2015.3710
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发表时间：
2015-08
影响因子：
3.4
通讯作者：
Ma C
中科院分区：
文献类型：
--
作者：
Hu N;Cong B;Gao T;Chen Y;Shen J;Li S;Ma C
根据混合DNA构建原理，构建了雄性混合DNA实验模型（n=297）。这包括使用Applied Biosystems（ABI）7500定量聚合酶链反应系统，并对混合比例进行科学验证（Mx;均方根误差≤0.02）。使用混合DNA分离R软件包mixsep对基因座分离精度进行统计分析，并通过检查不同混合梯度、短串联重复序列（STR）基因座和混合DNA类型的数据分布模式来评估mixsep的分析性能。结果表明，位点分离精度与混合梯度呈负线性相关（R2=-0.7121）。随着混合梯度不平衡度的增加，基因座分离准确度先增加后降低，在1：3（≥90%）的梯度下检测到最高值。混合梯度，即理论Mx，是影响混合DNA分析成功的主要因素之一。在Identifiler®检测的16个STR基因座中，D5 S818、D8 S1179和FGA基因座的分离准确度相对较高（>88%），而D 7S 820基因座的分离准确度中值最低。等位基因丢失（ADO; >15）较多的STR位点均位于黄色和红色通道，包括D18 S51、D19 S433、FGA、TPOX和vWA。这五个基因座的特征是等位基因峰高低，这与ABI 3130 xl遗传分析仪对黄色和红色荧光的低灵敏度一致。的mixsep包的轨迹分离精度有很大的不同，不包括ADO轨迹;包括ADO显着降低了mixsep包的分析性能，这是一致的，在这个软件中缺乏一个ADO功能模块。本研究表明，mixsep软件具有许多优点，并推荐用于混合DNA的分析。该软件易于操作，产生的结果易于理解，具有一定程度的可控性。
An experimental model of male-mixed DNA (n=297) was constructed according to the mixed DNA construction principle. This comprised the use of the Applied Biosystems (ABI) 7500 quantitative polymerase chain reaction system, with scientific validation of mixture proportion (Mx; root-mean-square error ≤0.02). Statistical analysis was performed on locus separation accuracy using mixsep, a DNA mixture separation R-package, and the analytical performance of mixsep was assessed by examining the data distribution pattern of different mixed gradients, short tandem repeat (STR) loci and mixed DNA types. The results showed that locus separation accuracy had a negative linear correlation with the mixed gradient (R2=−0.7121). With increasing mixed gradient imbalance, locus separation accuracy first increased and then decreased, with the highest value detected at a gradient of 1:3 (≥90%). The mixed gradient, which is the theoretical Mx, was one of the primary factors that influenced the success of mixed DNA analysis. Among the 16 STR loci detected by Identifiler®, the separation accuracy was relatively high (>88%) for loci D5S818, D8S1179 and FGA, whereas the median separation accuracy value was lowest for the D7S820 locus. STR loci with relatively large numbers of allelic drop-out (ADO; >15) were all located in the yellow and red channels, including loci D18S51, D19S433, FGA, TPOX and vWA. These five loci featured low allele peak heights, which was consistent with the low sensitivity of the ABI 3130xl Genetic Analyzer to yellow and red fluorescence. The locus separation accuracy of the mixsep package was substantially different with and without the inclusion of ADO loci; inclusion of ADO significantly reduced the analytical performance of the mixsep package, which was consistent with the lack of an ADO functional module in this software. The present study demonstrated that the mixsep software had a number of advantages and was recommended for analysis of mixed DNA. This software was easy to operate and produced understandable results with a degree of controllability.
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影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
1.7
作者：
Tvedebrink, Torben;Eriksen, Poul Svante;Morling, Niels
通讯作者：
Morling, Niels
DOI：
10.1111/j.1467-9876.2010.00722.x
发表时间：
2010-01-01
影响因子：
1.6
作者：
Tvedebrink, Torben;Eriksen, Poul Svante;Morling, Niels
通讯作者：
Morling, Niels
DOI：
10.1016/j.fsigss.2011.09.104
发表时间：
2011-12-01
期刊：
FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES
影响因子：
--
作者：
Tvedebrink, Torben
通讯作者：
Tvedebrink, Torben
DOI：
10.1007/0-387-29362-0_23
发表时间：
2005-01-01
期刊：
BIOINFORMATICS AND COMPUTATIONAL BIOLOGY SOLUTION USING R AND BIOCONDUCTOR
影响因子：
--
作者：
Smyth, GK
通讯作者：
Smyth, GK