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基于有限突变模型和大规模数据的19个常染色体STR的实际突变率研究【专刊】

刘志勇1,任贺2,陈冲3,张京晶4,张晓梦5,石妍3,石林玉5,陈滢3,程凤5,贾莉3,陈曼6,范庆炜7,张家榕5,李万婷5,王萌春5,任子林8,刘雅诚9,倪铭8,孙宏钰10,严江伟5   

  1. 1. 中山大学中山医学院
    2. 北京警察学院
    3. 北京通达首诚司法鉴定所
    4. 北京华彦科技有限公司司法鉴定所
    5. 山西医科大学法医学院
    6. 南方医科大学法医学院
    7. 川北医学院法医学系
    8. 北京辐射医学研究所
    9. 北京市刑事技术科学研究所
    10. 中山大学
  • 收稿日期:2021-06-02 修回日期:2021-08-30 出版日期:2021-08-31 发布日期:2021-08-31
  • 通讯作者: 严江伟
  • 基金资助:
    国家自然基金重点项目

Actual mutational research of 19 autosomal STRs based on restricted model from big data

  • Received:2021-06-02 Revised:2021-08-30 Online:2021-08-31 Published:2021-08-31
  • Contact: Jiangwei -Yan

摘要: 短串联重复序列(short tandem repeat,STR)已广泛用于法医学亲子鉴定和个体识别中,但STR的突变可能会影响其结果的解释。在大多数类似研究中,由于忽略“隐性”突变现象,STR的突变率被低估。鉴于此,为获得更加准确的STR实际突变率,本研究使用Slooten与Ricciardi提出的有限突变模型和大规模数据,对28,313例(78,739个体)中国北京汉族已确认亲生关系的亲子鉴定案的20个常染色体STR基因座(D3S1358、D1S1656、D13S317、Penta E、D16S539、D18S51、D2S1338、CSF1PO、Penta D、TH01、vWA、D21S11、D6S1043、D7S820、D5S818、TPOX、D8S1179、D12S391、D19S433和FGA;由于有限突变模型中未包含D6S1043的矫正参数,因此本文实际计算其余19个STR基因座的突变率)进行了调查。结果发现,所有基因座均存在突变现象,总计发生1665个突变事件,包括1614个一步突变,34个两步突变,8个三步突变和9个非整步突变。基因座特异性的平均实际突变率在三联体中为0.00007700(TPOX)~0.00459050(FGA),在二联体中为0.00000000(TPOX)~0.00344850(FGA)。此外,本研究还分析了表面和实际突变率、三联体和二联体突变率、父源和母源的突变率之间的关系。研究表明,实际突变率多大于表面突变率,而且μ1*/μ2*(表面突变率)的比值通常也大于μ1/μ2(实际突变率)(μ1*,μ1; μ2*, μ2分别是一步和两步的突变率),即更多的“隐性”突变被释放出来。而且父源和母源的三联体和二联体的突变率也有存在差异。随后,将这些突变率数据与已发表的中国其他汉族人口的相关研究进行比较,展现出了STR突变率的时间与区域差异。由于样本量大,本研究中还报告了一些少见的突变事件,例如同卵双胞胎突变和“假四步突变”等。综上所述,本研究通过大量数据获得了接近真实的STR突变率的估计值,不仅可为中国法医DNA数据库和群体遗传学数据库提供重要的基础数据,也对开展法医学个体识别、亲权鉴定和遗传学研究具有重要的意义。

关键词: 常染色体STR, 有限突变模型, 亲子鉴定, 中国汉族人群, 突变分析

Abstract: Short tandem repeat (STR) markers have been widely used in forensic paternity testing and individual identification, but the STR mutation might impact on the forensic result interpretation. Importantly, the STR mutation rate was un-derestimated due to ignoring the "hidden" mutation phenomenon in most similar studies. Considering this, we use Slooten and Ricciardi’s restricted mutation model based on big data to obtain more accurate mutation rates for each marker. In this paper, the mutations of 20 autosomal STRs loci (D3S1358, D1S1656, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D6S1043, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, and FGA; The restricted model does not include the correction factor of D6S1043, this paper calculates remaining 19 STR loci mutation rates) were investigated in 28,313 (Total: 78,739 individuals) confirmed parent-age-testing cases in Chinese Han population. As a result, total 1665 mutations were found in all loci, including 1614 one-steps, 34 two-steps, 8 three-steps, and 9 nonintegral mutations. The loci-specific average mutation rates ranged from 0.00007700 (TPOX) to 0.00459050 (FGA) in trio’s and 0.00000000 (TPOX) to 0.00344850 (FGA) in duo’s. We analyzed the relationship between mutation rates of the apparent and actual, the trio’s and duo’s, the paternal and maternal, respectively. The results demonstrated that the actual mutation rates are more than the apparent mostly, and the values of μ1*/μ2*(apparent) are also greater than μ1/μ2 (actual) commonly (μ1*, μ1; μ2*, μ2 are the mutation rates of one-step and two-step). Therefore, the “hidden” mutations are identified. In addition, the mutations rates of trio’s and duo’s, the paternal and maternal, exhibit significant difference. Next, those mutation data are used to do a comparison with the studies of other Han populations in China, which present the temporal and regional disparities. Due to the large sample size, some rare mutation events, such as monozygotic (MZ) mutation and “fake four-step mu-tation”, are also reported in this study. In conclusion, the estimation values of actual mutations are obtained based on big data, they can not only provide basic data for the Chinese forensic DNA and population genetics databases, but also have important significance for the development of forensic individual identification, paternity testing and genetics research.

Key words: Autosomal STR, restricted mutation model, parentage testing, Chinese Han population, mutational analysis