Application of mixsep software package: Performance verification of male-mixed DNA analysis.
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 (R(2)=-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.
Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China.
Na
N
Hu
Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China.
Bin
B
Cong
Department of Statistics, Institute of Statistics, Renmin University of China, Beijing 100872, P.R. China.
Tao
T
Gao
Department of Statistics, Institute of Statistics, Renmin University of China, Beijing 100872, P.R. China.
Yu
Y
Chen
Laboratory of Forensic DNA Testing, Institute of Forensic Science, Public Security Department of Shanxi, Taiyuan, Shanxi 030001, P.R. China.
Junyi
J
Shen
Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China.
Shujin
S
Li
Department of Forensic Medicine, Hebei Key Laboratory of Forensic Medicine, Hebei Medical University, Shijiazhuang, Hebei 050017, P.R. China.
Chunling
C
Ma
D000483:Alleles; D057205:Automation, Laboratory; D001773:Blood Cells / Q000737:chemistry; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D016172:DNA Fingerprinting / Q000706:statistics & numerical data*; D005453:Fluorescence; D053803:Forensic Genetics / Q000295:instrumentation / Q000379:methods*; D005787:Gene Frequency; D056426:Genetic Loci; D006801:Humans; D008297:Male; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
D004247:DNA