Faculty of Health Sciences, Oslo and Akershus University College, Oslo, Norway.
Forensic Sci Int Genet. 2012 Dec;6(6):798-809. doi: 10.1016/j.fsigen.2012.03.002. Epub 2012 Apr 6.
A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy-Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (F(ST)) was 0.09. The average estimate of inbreeding (F(IS)) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10(-9) and the total average probability of sibling identity was lower than 1.3×10(-4). The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.
一组 13 个二核苷酸 STR 基因座（G1A、G10B、G1D、G10L、MU05、MU09、MU10、MU15、MU23、MU26、MU50、MU51、MU59）被选为北欧棕熊（Ursus arctos）法医 DNA 分析系统的候选标记。我们报告了这些标记在灵敏度、物种特异性和性能（精密度、杂合子平衡和等位基因峰突率）方面的验证结果。所有 STR 均使用 0.6ng 模板输入进行扩增，在交叉物种扩增测试中没有出现错误的熊基因型。验证实验表明，等位基因峰突率和杂合子平衡比人类法医分析中使用的四核苷酸基因座更为显著。在验证的基因座中，等位基因峰突率和杂合子平衡的比值升高，表明这些二核苷酸 STR 不适合在混合物中解释个体基因型。根据实验验证的结果，我们讨论了在单源样本中分析二核苷酸 STR 时所面临的挑战。常见等位基因的序列研究表明，一般来说，等位基因的大小变化与重复次数的变化相对应。通过序列分析进行特征描述的样本可以作为实验室间校准的标准 DNA 样本。在 13 个候选 STR 中，对来自北欧 8 个棕熊种群的 479 个个体进行了分析。在 MU26 基因座，由于该基因座可能存在无效等位基因，导致预期杂合度与实际观察值存在较大偏差，因此该基因座被排除为潜在的法医标记。除了 G10B 和 MU10 基因座分别在一个种群中存在显著偏离哈迪-温伯格平衡的预期外，其余基因座均未显示出显著偏离哈迪-温伯格平衡的预期。有 9 个基因座的比较显示，在 8 个种群中的一个或两个种群中存在显著的连锁不平衡。在一些种群比较中检测到明显的遗传分化，种群间平均结构分化（F(ST)）估计值为 0.09。平均近交系数（F(IS)）估计值为 0.005。考虑到种群结构和近交，在 8 个种群中的每个种群的总平均个体识别概率均低于 1.1×10(-9)，总平均兄弟姐妹识别概率均低于 1.3×10(-4)。这些测量结果表明，如果在 DNA 分析系统中应用这 12 个 STR，那么将提供个体特异性证据。
