Genetic Parameters of SNP Loci in Next Generation Sequencing Kits and Their Comparison
ZHOU Mi1, ZHANG Ke2, WANG Jun3
1. Wuhu Public Security Bureau, Wuhu 241000, China; 2. Management Office of Physical Evidence, Department of Public Security of Anhui Province, Hefei 230061, China; 3. School of Computer & Information Science, Anhui Polytechnic University, Wuhu 241000, China
摘要 目的 计算二代测序试剂盒SNP位点的遗传学参数，与STR基因座进行对比，以建立SNP和STR的系统效能换算比例。 方法 对二代测序试剂盒（ForenSeqTM DNA Signature Prep试剂盒和Precision ID Identity Panel试剂盒）共101个SNP位点进行Hardy-Weinberg平衡检验，计算SNP位点在个体识别、标准三联体鉴定、二联体鉴定及双亲皆疑鉴定中的各项系统效能参数，并与STR基因座进行对比。 结果 除无基因型频率数据的2个位点外，99个SNP位点符合Hardy-Weinberg平衡检验（P>0.05）。ForenSeqTM DNA Signature Prep试剂盒94个SNP位点的累积个体识别率（cumulative discrimination power，CDP）为1-1.152 1×10-34，累积三联体非父排除率（cumulative probability of exclusion in trios，CPEtrio）为1-4.416 9×10-8，累积二联体非父排除率（cumulative probability of exclusion in duos，CPEduo）为1-8.483 7×10-5，双亲皆疑累积排除率（cumulative probability of exclusion in alleged parents cases，CPEAP）为1-1.222 7×10-12。Precision ID Identity Panel试剂盒90个SNP位点的CDP为1-2.052 4×10-33，CPEtrio为1-8.709 3×10-8，CPEduo为1-1.163 8×10-4，CPEAP为1-3.725 7×10-12。在个体识别、标准三联体鉴定、二联体鉴定、双亲皆疑鉴定中，分别平均有2.85、4.51、4.88、4.55个SNP位点等于1个STR基因座的系统效能。 结论 二代测序试剂盒SNP位点的系统效能较高，多个SNP位点联合可应用于法庭科学中的个体识别和亲子鉴定。
Objective To calculate genetic parameters of SNP loci in next generation sequencing kits, and to compare them with STR loci for establishing the conversion ratio between SNP and STR system effectiveness. Methods Hardy-Weinberg equilibrium tests were performed in 101 SNP loci of next generation sequencing kits （ForenSeqTM DNA Signature Prep kit and Precision ID Identity Panel kit）. The parameters of system effectiveness of SNP loci in the cases of personal identification, trios, duos, and alleged parents were calculated, which were compared with the genetic parameters of STR loci. Results Except 2 loci without the data of genotype frequency, other 99 SNP loci conformed to Hardy-Weinberg equilibrium tests （P>0.05）. In ForenSeqTM DNA Signature Prep kit, the CDP of 94 SNP loci was 1-1.152 1×10-34, CPEtrio was 1-4.416 9×10-8, CPEduo was 1-8.483 7×10-5, and CPEAP was 1-1.222 7×10-12. In Precision ID Identity kit, the CDP was 1-2.052 4×10-33, CPEtrio was 1-8.709 3×10-8, CPEduo was 1-1.163 8×10-4, and CPEAP was 1-3.725 7×10-12. In the cases of personal identification, trios, duos and alleged parents, the system effectiveness of 2.85, 4.51, 4.88 and 4.55 SNP loci was equal to that of 1 STR locus, respectively. Conclusion With high system effectiveness of SNP loci, the next generation sequencing kits is suitable for personal identification and paternity testing in forensic science.