Table1_Forensic efficiencies of individual identification, kinship testing and ancestral inference in three Yunnan groups based on a self-developed multiple DIP panel.XLSX

Deletion/insertion polymorphism (DIP), as a short insertion/deletion sequence polymorphic genetic marker, has attracted the attention of forensic genetic scientist due to its lack of stutter, short amplicon and abundant ancestral information. In this study, based on a self-developed 43 autosomal deletion/insertion polymorphism (A-DIP) loci panel which could meet the forensic application purposes of individual identification, kinship testing and ancestral inference to some extent, we evaluated the forensic efficiencies of the above three forensic objectives in Chinese Yi, Hani and Miao groups of Yunnan province. The cumulative match probability (CPM) and combined probability of exclusion (CPE) of these three groups were 1.11433E-18, 8.24299E-19, 4.21721E-18; 0.999610217, 0.999629285 and 0.999582084, respectively. Average 96.65% full sibling pairs could be identified from unrelated individual pairs (as likelihood ratios > 1) using this DIP panel, whereas the average false positive rate was 3.69% in three target Yunnan groups. With the biogeographical ancestor prediction models constructed by extreme gradient boosting (XGBoost) and support vector machine (SVM) algorithms, 0.8239 (95% CI 0.7984, 0.8474) of the unrelated individuals could be correctly divided according to the continental origins based on the 43 A-DIPs which were large frequency distribution differentiations among different continental populations. The present results of principal component analysis (PCA), multidimensional scaling (MDS), neighbor joining (NJ) and maximum likelihood (ML) phylogenetic trees and STRUCTURE analyses indicated that these three Yunnan groups had relatively close genetic distances with East Asian populations.

缺失/插入多态性（Deletion/insertion polymorphism, DIP）作为一类短插入缺失序列多态遗传标记，因无滑动峰现象、扩增片段短且蕴含丰富祖先信息，受到法医遗传学家的广泛关注。本研究基于一套自主研发的43个常染色体缺失/插入多态性（autosomal deletion/insertion polymorphism, A-DIP）基因座分型体系，该体系可在一定程度上满足个体识别、亲缘关系鉴定及祖先推断的法医应用需求，我们对该体系在云南彝族、哈尼族和苗族群体中上述三项法医应用目标的效能进行了评估。三个群体的累计匹配概率（cumulative match probability, CPM）与累计排除概率（combined probability of exclusion, CPE）分别为1.11433×10^-18、8.24299×10^-19、4.21721×10^-18，以及0.999610217、0.999629285和0.999582084。使用该DIP分型体系，可从无关个体对中识别出96.65%的全同胞对（似然比>1），而在三个目标云南群体中平均假阳性率为3.69%。基于极端梯度提升（extreme gradient boosting, XGBoost）与支持向量机（support vector machine, SVM）算法构建的生物地理祖先预测模型，借助这43个在不同大陆人群中频率分布差异显著的A-DIP基因座，可将82.39%的无关个体按大陆起源进行正确分类（95%置信区间：0.7984~0.8474）。主成分分析（principal component analysis, PCA）、多维尺度分析（multidimensional scaling, MDS）、邻接接合（neighbor joining, NJ）与最大似然（maximum likelihood, ML）系统发育树分析及STRUCTURE群体结构分析的结果显示，这三个云南群体与东亚人群的遗传距离相对较近。