基于二代测序的24个STR基因座序列多态性
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摘要
目的对95名中国汉族无关个体的24个STR基因座序列多态性进行调查。方法采用Thermo Fisher公司25重早期测试试剂盒进行STR基因座复合扩增,应用HID-Ion AmpliSeq~(TM)文库试剂盒进行文库构建,使用Ion PGM~(TM)基因测序仪进行测序反应,对Ion Torrent Suite~(TM) v4.6软件显示的STR基因分型结果分析评估,使用PowerStats分析软件计算法庭科学参数,并与STR长度多态性的参数进行比较。结果 24个STR基因座共观察到252个不同重复序列的等位基因。其中,12个STR基因座具有相同长度的不同等位基因核心序列,其累计随机匹配概率为3.5×10~(-15),其累计非父排除率达0.999 998 2。序列多态与长度多态STR的累计随机匹配概率相差两个数量级。结论针对调查的中国汉族人群,本文24个序列多态STR基因座具有较好的个体识别能力,该数据为法医STR基因座序列多态性研究提供很好的参考。
Objective To investigate the sequence polymorphism of 24 STRs in unrelated Chinese Han individuals. Methods Multiplexed amplification was performed using a 25-plex early access STR panel from Thermo Fisher Scientific. Libraries were constructed using the HID-Ion AmpliSeqTM library kit, and sequenced on the Ion PGM~(TM) platform. STR alleles were called using the Ion Torrent SuiteTM v4.6 software, and forensic parameters were calculated using the PowerStats software and then compared with the parameters of genetic polymorphism. Results A total of 252 sequence-based alleles were observed in 24 STR loci. 12 of the 24 loci have different allelic core sequences of the same length. The cumulative matching probability of these 12 loci was 3.5×10~(-15), and the cumulative probability of exclusion was 0.9999982. The sequence-based and length-based cumulative matching probability differs by two orders of magnitude. Conclusion In the Chinese Han population surveyed, the 24 sequence-based autosomal STRs exhibited good capacity for individual identification. The data provide a good reference for the study of sequence-based genetic polymorphism of forensic STRs.
Objective To investigate the sequence polymorphism of 24 STRs in unrelated Chinese Han individuals. Methods Multiplexed amplification was performed using a 25-plex early access STR panel from Thermo Fisher Scientific. Libraries were constructed using the HID-Ion AmpliSeqTM library kit, and sequenced on the Ion PGM~(TM) platform. STR alleles were called using the Ion Torrent SuiteTM v4.6 software, and forensic parameters were calculated using the PowerStats software and then compared with the parameters of genetic polymorphism. Results A total of 252 sequence-based alleles were observed in 24 STR loci. 12 of the 24 loci have different allelic core sequences of the same length. The cumulative matching probability of these 12 loci was 3.5×10~(-15), and the cumulative probability of exclusion was 0.9999982. The sequence-based and length-based cumulative matching probability differs by two orders of magnitude. Conclusion In the Chinese Han population surveyed, the 24 sequence-based autosomal STRs exhibited good capacity for individual identification. The data provide a good reference for the study of sequence-based genetic polymorphism of forensic STRs.
引文
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[12]王乐,叶健,白雪,等.二代测序技术及其在法医遗传学中的应用[J].刑事技术,2015,40(5):353-358.
[13]饶旼,赵鹏,张驰,等.基于二代测序的混合检材精细化分型研究[J].中国法医学杂志,2018,33(1):22-25,30.
[2]Bornman DM,Hester ME,Schuetter JM,et al.Shortread,high-throughput sequencing technology for STRgenotyping[J].Biotech Rapid Dispatches,2012,1-6.
[3]Scheible M,Loreille O,Just R,et al.Short tandem repeat sequencing on the 454 platform[J].Forensic Sci Int Genet,2011,3(1):e357-e358.
[4]Van Neste C,Van Nieuwerburgh F,Van Hoofstat D,et al.Forensic STR analysis using massive parallel sequencing[J].Forensic Sci Int Genet,2012,6(6):810-818.
[5]Scheible M,Loreille O,Just R,et al.Short tandem repeat typing on the 454 platform:strategies and considerations for targeted sequencing of common forensic markers[J].Forensic Sci Int Genet,2014,12:107-119.
[6]Gelardi C,Rockenbauer E,Dalsgaard S,et al.Second generation sequencing of three STRs D3S1358,D12S391and D21S11 in Danes and a new nomenclature for sequenced STR alleles[J].Forensic Sci Int Genet,2014,12:38-41.
[7]Peck MA,Brandhagen MD,Marshall C,et al.Concordance and reproducibility of a next generation mtGenome sequencing method for high-quality samples using the Illumina MiSeq[J].Forensic Sci Int Genet,2016,24:103-111.
[8]Gettings KB,Kiesler KM,Faith SA,et al.Sequence variation of 22 autosomal STR loci detected by next generation sequencing[J].Forensic Sci Int Genet,2016,21:15-21.
[9]赵鹏,张广峰,刘京,等.长度多态与序列多态STR模型法庭科学参数比较[J].中国法医学杂志,2017,32(6):642-644,648.
[10]PowerStats.http://www.promega.com/geneticstools/[CP].1999.
[11]Zhao X,Li H,Wang Z,et al.Massively parallel sequencing of 10 autosomal STRs in Chinese using the ion torrent personal genome machine(PGM)[J].Forensic Sci Int Genet,2016,25:34-38.
[12]王乐,叶健,白雪,等.二代测序技术及其在法医遗传学中的应用[J].刑事技术,2015,40(5):353-358.
[13]饶旼,赵鹏,张驰,等.基于二代测序的混合检材精细化分型研究[J].中国法医学杂志,2018,33(1):22-25,30.