基于二代测序平台的90个常染色体SNP分型研究

目的基于二代测序平台进行90个常染色体SNP位点分型,调查其在中国广东汉族人群中的多态性,评估其法医学应用价值。方法采集100例中国广东汉族无关个体外周血样,采用Auto Mate Express TM提取样本DNA,使用HID-Ion Ampli Seq?Identity Panel分型体系复合扩增90个SNP位点制备文库,Ion One Touch?2进行乳化PCR,Ion PGM?平台进行测序,Torrent_Suite_v4.4.2软件及HID_SNP_Genotyper_v4.3.1插件进行数据分析,计算常用法医学参数并与该群体Goldeneye TM 20A体系的检测效能进行比较。结果经Bonferroni法校正后,90个常染色体SNP位点分布均符合Hardy-Weinberg平衡,不存在连锁不平衡现象。各位点平均杂合度(Ho)为0.423,平均个体识别力(DP)为0.560,平均多态信息含量(PIC)为0.329。90个SNP体系的累积个体识别率(CDP)为(1-1.20×10~(-33)),大于20A体系;三联体累积非父排除率(CPE_(tri))为0.999 999 911,二联体累积非父排除率(CPE_(duo))为0.999 882,均小于20A。结论 90个常染色体SNP检测体系可独立应用于法医个体识别和三联体亲子鉴定,并辅助进行二联体亲子鉴定。

Genotyping of 90 autosomal SNPs based on next generation sequencing

Objective To investigate the genetic polymorphism of 90 autosomal SNPs in Guangdong Han population and assess their value in forensic medicine based on next generation sequencing. Methods Blood samples were collected from 100 unrelated individuals. Through using AutoMate ExpressTM Nucleic Acid Extraction System, DNA was extracted. HID-Ion AmpliSeq? Identity Panel was applied for library preparation while Ion OneTouch? 2 system (OT2) was employed for emulsion PCR (emPCR). NGS was performed on the Ion PGM? system. Sequencing results were analysed using the Torrent Suite v4.4.2 with the HID_SNP_Genotyper v4.3.1 plugin. The forensic parameters were calculated and compared with GoldeneyeTM 20A systems. Results According to the Bonferroni correction, the genotypes of 90 autosomal SNPs were in accordance with Hardy-Weinberg equilibrium and no linkage disequilibrium was observed. The average Ho of 90 autosomal SNPs was 0.423, the average DP was 0.560 and the average PIC was 0.329. The CDP (cumulative power of discrimination) of 90 autosomal SNPs system was 1-1.20×10-33, which was greater than that of 20A System. The CPEtri (cumulative excluding probability of trio paternity) was 0.999 999 911 and the CPEduo (cumulative excluding probability of duo paternity) was 0.999 882. Both of these two parameters were below that of 20A System. Conclusion It suggested that the 90 autosomal SNPs System can be applied to forensic individual discrimination and trio paternity testing independently. Besides, it is supposed to be used in the duo paternity testing as an assistant measure.