法医学杂志, 2024, 40(5): 484-491 DOI: 10.12116/j.issn.1004-5619.2024.541008

综述

STR突变对亲缘关系鉴定的影响

刘京,, 王正, 侯一平, 廖林川,

四川大学华西基础医学与法医学院,四川 成都 610041

The Impact of STR Mutations on Kinship Identification

LIU Jing,, WANG Zheng, HOU Yi-ping, LIAO Lin-chuan,

West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu 610041, China

通讯作者: 廖林川,男,教授,博士后合作导师,主要从事法医学研究;E-mail:linchuanliao@scu.edu.cn

编委: 陶瑞旸

收稿日期: 2024-10-31  

基金资助: 上海市法医学重点实验室暨司法部司法鉴定重点实验室开放课题资助项目.  KF202310
法医遗传学公安部重点实验室开放课题资助项目.  2023FGKFKT03

Received: 2024-10-31  

作者简介 About authors

刘京(1993—),女,博士,助理研究员,主要从事法医遗传学研究;E-mail:liujing2381@scu.edu.cn

摘要

亲缘关系鉴定是法医遗传学研究的重要领域,广泛应用于遗产纠纷、刑事侦查以及重大灾害案件中受害者的识别等。目前,基于毛细管电泳的STR分析仍然是亲缘关系鉴定的主要方法,但STR突变对亲缘关系鉴定的影响还需探索。本文综述了亲缘关系鉴定的理论基础以及国内外研究现状,并针对STR突变对亲缘关系鉴定的影响这一挑战进行展望,探讨可能的解决途径,以期获得STR突变对亲缘关系鉴定影响的规律性认识,提升亲缘关系分析的准确性。

关键词: 法医遗传学 ; 亲缘关系鉴定 ; STR突变 ; 遗传标记 ; 分析方法 ; 综述

Abstract

Kinship identification is an important field of forensic genetics research, which can be widely applied in inheritance disputes, criminal investigations, and the identification of victims in major disaster cases. At present, capillary electrophoresis-based STR analysis is still the main method for kinship identification, but the impact of STR mutations on kinship identification needs further exploration. This paper reviews the theoretical basis and research status at home and abroad of kinship identification. The challenge of STR mutation impact on kinship identification is prospected, and possible solutions are discussed in order to obtain a regular understanding of the impact of STR mutation on kinship identification and improve the accuracy of kinship analysis.

Keywords: forensic genetics ; kinship identification ; STR mutation ; genetic marker ; analysis method ; review

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本文引用格式

刘京, 王正, 侯一平, 廖林川. STR突变对亲缘关系鉴定的影响. 法医学杂志[J], 2024, 40(5): 484-491 DOI:10.12116/j.issn.1004-5619.2024.541008

LIU Jing, WANG Zheng, HOU Yi-ping, LIAO Lin-chuan. The Impact of STR Mutations on Kinship Identification. Journal of Forensic Medicine[J], 2024, 40(5): 484-491 DOI:10.12116/j.issn.1004-5619.2024.541008

法医学亲缘关系鉴定是指通过医学、生物学等方法检测人类遗传标记,判断有争议的个体之间是否存在某种特定亲缘关系的科学技术手段,在法医学鉴定实践中有广泛的应用需求,如遗产纠纷、打拐、器官移植、失踪人员寻找、刑事侦查以及重大灾害或战争中受害者的识别等[1-3]。亲缘关系鉴定既包括父母与子女之间的亲子关系鉴定,也包括同胞(兄弟姐妹)、半同胞(同父异母或同母异父的兄弟姐妹)、叔侄、堂表亲、爷孙甚至隔数代的个体之间的复杂亲缘关系鉴定。目前,基于毛细管电泳的STR分析仍然是亲缘关系鉴定的主要方法[4-5],但STR突变对亲缘关系鉴定的影响尚处于探索阶段,是亲缘关系鉴定亟待解决的科学问题。本文拟阐述亲缘关系鉴定的理论基础以及所运用遗传标记和分析技术等的国内外研究现状,探讨STR突变对亲缘关系鉴定的影响并进行展望。

1 亲缘关系鉴定的理论基础

父母与子女之间亲子关系鉴定所依据的理论基础为子女必然会有一条染色体来自父亲或者母亲,在无突变发生的情况下,子女任何一条常染色体上的基因座都与父亲或者母亲共享一个等位基因。除亲子关系外,无论个体间是否具有亲缘关系,任何一条常染色体上的基因座都有可能存在两个等位基因相同或一个等位基因相同或不享有相同的等位基因,因此,其他亲缘关系鉴定无法用亲子关系鉴定理论和方法来解决。其他亲缘关系鉴定所依据的理论基础为有亲缘关系个体间共享等位基因的概率比随机个体间共享等位基因的概率大,亲缘关系越近则共享等位基因的概率越大,即有亲缘关系个体间共享的等位基因数量比随机个体间共享的等位基因数量多,亲缘关系越近则共享的等位基因数量越多[6-7]。目前关于亲子关系鉴定的研究已经成熟,现行《法庭科学DNA亲子鉴定规范》(GA/T 965—2011)、《亲权鉴定技术规范》(GB/T 37223—2018)等行业标准和国家标准对于某个基因座不符合遗传规律(如在减数分裂过程中发生了突变)也有相应的解决办法,但在其他亲缘关系鉴定中,突变通常不容易被观察到,对鉴定结果的影响仍需探讨。

2 亲缘关系鉴定中运用的DNA遗传标记

目前,用于亲缘关系鉴定的DNA遗传标记有常染色体DNA遗传标记和非常染色体DNA遗传标记两大类。前者主要包括常染色体上的STR[4-5]、SNP[68-11]、微单倍型(microhaplotype,MH)[12-15]以及组合遗传标记[16-18];后者主要是指mtDNA(母系遗传特征)、X染色体DNA遗传标记和Y染色体DNA遗传标记(父系遗传特征)[19-20]

2.1 常染色体DNA遗传标记

STR的多态性高,在基因组中分布广泛,具有鉴别能力强、结果准确性高及便于检测等优点,是亲缘关系鉴定中运用最普遍的遗传标记[34-521-28]。O’CONNOR等[24]的研究表明,基于高加索人群的13个DNA联合索引系统(Combined DNA Index System,CODIS)基因座数据分析全同胞对的假阳性率为2.7%,假阴性率为3.3%。TAMURA等[25]评估了PowerPlex Fusion系统、GlobalFiler试剂盒和PowerPlex 21系统(分别包含20~22个常染色体STR)在不同亲缘关系鉴定中的效能,结果表明,以上系统可有效运用于全同胞及二级亲缘关系鉴定,但在一代堂(表)亲关系鉴定中效能较差。2017年,GROVER等[26]构建了一个包含23个常染色体STR基因座的FlexPlex27试剂盒,通过与CODIS 13和CODIS 20进行比较,发现其亲缘关系鉴定效能明显改善。此外,LIU等[27]基于二代测序平台构建了一个包含42个常染色体STR基因座的检测体系,其用于二级亲缘关系鉴定的效能与ForenSeq DNA Signature Prep试剂盒[29]相似。以上研究表明,随着STR数量的增加,亲缘关系鉴定效能得到显著提高。然而,STR突变率较高(~10-3每世代)[30],对亲缘关系鉴定的结果可能产生影响。

SNP突变率极低(~10-8每世代)[31],稳定性高,检测片段短,适用于涉及微量、降解生物检材的亲缘关系鉴定,但SNP多为二等位基因遗传标记,因此通常需要几百甚至上千个遗传标记才能达到与几十个STR相似的效能[32-33]。有研究[34]构建了一个包含50个SNP的检测体系(SNPforID),可作为STR分析的补充方法,成为解决存在特殊情况(如突变、微量降解DNA)的亲缘关系鉴定的有力手段。MO等[32]构建的二代测序SNP检测体系(SNP2kin)包含472个SNP,可以将二级及以下亲属与无关个体区分开来。

微单倍型的突变率和SNP相似,有研究[12]构建了一个包含87个微单倍型遗传标记的检测体系,其平均有效等位基因数(effective number of allele,Ae)为7.02,足以鉴定二级及以下亲缘关系,但对于三级及以上亲缘关系的鉴定错误率较高。此外,DU等[15]构建了一个包含188个微单倍型(平均Ae为2.926 7)的检测体系,当累积似然比(cumulative likelihood ratio,CLR)的确认阈值和排除阈值分别设为104和10-4时,83.36%的二级亲缘关系鉴定能给出明确意见,且错误率小于10-5

组合遗传标记为法医学实践中复杂亲缘关系的鉴定提供了新策略[16-18]。2019年,LI等[29]运用商品化的组合遗传标记试剂盒ForenSeq DNA Signature Prep进行亲缘关系分析,结果显示,该试剂盒能解决亲子鉴定和全同胞关系鉴定案件,且能识别出大部分的二级亲缘关系。2022年,XU等[17]应用55个STR和94个SNP的组合进行亲缘关系分析,结果显示,对于二级和三级亲缘关系鉴定,其系统效能分别为94.43%和64.34%,错误率分别小于0.001和0.05。同年,ZHANG等[16]应用56个STR、52个SNP和72个插入/缺失(insertion/deletion,InDel)遗传标记组合进行亲缘关系分析,结果显示,该组合可将一级亲属与二级或三级亲属区分开来。

2.2 非常染色体DNA遗传标记

mtDNA具有母系遗传特征。在大型灾难或战争的受害者遗骸鉴定和考古等案件中,可能会遇到微量或高度降解的生物检材,mtDNA对于涉及此类检材的亲缘关系鉴定起到了突出作用[1-235-36]。例如,俄国沙皇Romanov家族遗骸的鉴定正是通过检测mtDNA最终得以确定[37]。此外,涉及同卵双生子的亲缘关系鉴定可以利用mtDNA异质性进行甄别[38]

用于亲缘关系分析的X染色体DNA遗传标记主要是X-STR[39-42],其具有伴性遗传的特征,表现为特有的性连锁特点,在某些特殊的亲缘关系鉴定案件中具有重要意义,如缺乏双亲的全同胞姐妹或半同胞姐妹(同父异母)亲缘关系鉴定、祖母-孙女亲缘关系鉴定以及外祖父母-外孙亲缘关系鉴定等。ZIDKOVA等[40]的研究结果证明Investigator Argus X-12系统在姐妹亲缘关系鉴定中非常有用,其似然比(likelihood ratio,LR)值与基于常染色体STR试剂盒计算所得的LR值相似。2021年,PERERA等[42]运用16个X-STR解决了全同胞姐妹以及亲代缺失的亲缘关系鉴定案例。需要注意的是,在计算相应亲缘关系鉴定参数的过程中需要考虑X-STR基因座之间的连锁情况。

Y染色体DNA遗传标记主要包括Y-STR和Y-SNP,具有父系遗传特征[43]。在刑事侦查领域,应用Y-STR可以开展家系排查并辅助父系亲缘关系鉴定,通过“以Y找群”,侦查人员可迅速锁定犯罪嫌疑人所在家系群体,为案件提供侦查线索,从而提高破案效率,节省破案的人力、物力、财力和时间[44]。例如,2016年甘肃白银连环杀人案正是通过Y-STR家系排查缩小调查范围才得以侦破[45]

然而,mtDNA和Y染色体DNA遗传标记用于亲缘关系鉴定时,针对的是一组个体,通常需要其他证据佐证从而判断被检个体间具体的亲缘关系层级,且受限于生物检材来源个体的性别。

3 亲缘关系鉴定的分析方法

现阶段,亲缘关系鉴定的分析方法主要包括状态一致性(identity by state,IBS)、血缘一致性(identity by descent,IBD)、LR以及矩量法(method of moment,MoM)等[46]。其中IBS法主要基于STR遗传标记,LR法可基于STR和SNP等遗传标记,而IBD法和MoM法主要基于SNP遗传标记[847-49]

IBS法[50]是指通过计算两个体之间相同等位基因的个数(即IBS评分),并设定一定阈值判定亲缘关系层级。IBS评分的计算公式为IBS=2×A2+1×A1+0×A0N=A2+A1+A0,其中N为总的遗传标记数量,A0A1A2分别表示两个体间共享0、1和2个等位基因的遗传标记数量[51]。该方法在国内运用普遍,如国家标准《生物学全同胞关系鉴定技术规范》(GB/T 43641—2024)就包含IBS法,其计算简单、直接、快速,无需遗传标记的频率信息,适用于大型数据库中的家系搜索,但未考虑STR突变的影响,普适性差,不适用于近亲婚配的案例,无法将大部分二级亲属与无关个体区分开来[51-52]

IBD法[853-54]是指基于两个体之间的IBD片段长度[通常用重组频率的测量单位厘摩(centimorgan,cM)衡量]进行亲缘关系层级推断的方法,因此又称为IBD片段法。IBD表现为个体间共有的DNA片段来源于一个共同的祖先,两者之间共享的IBD片段越长(短),则亲缘关系越近(远)[11]。根据是否将等位基因分配给父系或母系染色体,IBD法可分为定相和非定相两种[49]。基于定相法的软件包括GERMLINE[55]、iLASH[56]、RaPID[57]和hap-IBD[58],基于非定相法的软件包括TRUFFLE[59]和IBIS[60]。IBD法推断亲缘关系层级的准确性较高,但计算量大,且易受到分型错误的影响,因此不适用于微量、降解检材[1061]

LR法[62]是目前亲缘关系鉴定中最常用且最经典的方法,通过计算被鉴定个体间为特定亲缘关系的概率与被鉴定个体间为无关个体的概率的比值进行判断,其算法包括家系重建法[63]、ITO法[64]、Lander-Green算法[65]以及Elston-Stewart算法[66]等。其中,Lander-Green的计算时间随基因座数量增加呈线性增加,随个体数量增加呈指数增加,而Elston-Stewart则不同,计算时间随个体数量增加呈线性增加,随基因座数量增加呈指数增加。LR法的计算复杂(除ITO法),通常需要运用各种软件,如EasyDNA、Familias以及Fore-Statistics等[67-69]。不同软件预设的突变模型不同,在同一亲缘关系鉴定案件中,计算所得LR值可能存在一定差异。

MoM法[70]是指通过估算两个体间实际的亲缘系数(kinship coefficient,θ)、科特曼系数(Cotterman coefficient)和关系系数(relatedness coefficient,r)等参数进行亲缘关系层级分析,常用的软件主要是PLINK[71]和KING[72],适用于基于大型数据库的亲缘关系分析,但对于三级及以上亲缘关系的鉴定,其效能较低,且易受到群体遗传结构的影响。

以上分析方法中,部分方法缺乏对STR突变的考虑(如IBS法),部分方法包含的突变模型不同(在同一鉴定情形下获得的亲缘关系鉴定参数可能存在一定偏差),无法确定计算出的亲缘关系鉴定参数(如IBS评分、亲缘关系指数等)对鉴定结果是否有影响。

4 STR突变对亲缘关系鉴定的影响与展望

STR突变的机制主要为复制滑动(replication slippage)或滑动链错配(slipped-strand mispairing,SSM),发生在DNA复制过程中[73-74]。生殖细胞进行减数分裂时会发生一次DNA复制,此时基因组中的STR遗传标记可能会发生复制滑脱造成STR突变,发生STR突变的配子被遗传给后代则会形成不符合遗传规律的现象,从而影响亲缘关系鉴定。在亲缘关系鉴定中,被检个体间亲缘关系层级越大,遭遇STR突变的可能性就越大,对亲缘关系鉴定的影响可能就越大。此外,亲缘关系鉴定运用的STR数量越多,累积的STR突变的可能性则越大,对亲缘关系鉴定的影响也可能越大[75]。目前,一些关于亲缘关系鉴定的行业技术规范或国家标准为减少STR突变对结果产生影响引入了突变率计算相应亲缘关系鉴定参数,常用的亲缘关系分析软件也引入了突变模型以改善STR突变对结果的影响。如2014年KLING等[68]在Familias软件上进行更新迭代,基于逐步突变模型提出了新的突变模型用于处理微变异STR等位基因;2016年,SIMONSSON等[76]提出了平稳突变模型(stationary mutation models),并引入至Familias软件进行了测试。KinBN亲缘关系分析软件[75]也引入了突变模型以优化亲缘关系鉴定参数,其结果显示,忽略STR突变可能会导致假阴性,而考虑突变可能会导致假阳性。不同STR的突变率由于受到基因座重复基序长度、数量和结构的影响可能不同,且同一STR在不同群体中的突变率也可能不同[3077-79],因此,引入突变率时需尤为慎重。目前关于STR突变对亲缘关系鉴定的影响已经引起了学者们的广泛关注[187580-86],然而STR突变对亲缘关系鉴定的影响仍然是法医工作者需要解决的问题。针对以上问题,在未来的研究工作中,法医遗传学科研工作者应该探索可能的解决途径,以期获得STR突变对亲缘关系鉴定影响的规律性认识。

如在大家系样本中同时检测突变率极低的遗传标记和STR遗传标记(两者的系统效能相近),可以获得两组不同层级亲缘关系鉴定参数的分布特点,通过观察两组鉴定参数差值的规律,可以校正用STR进行亲缘关系鉴定的计算误差,以期克服STR突变对亲缘关系鉴定的影响。突变率极低的遗传标记包括SNP和微单倍型等,其中单个SNP效能较低,大约6个SNP的效能相当于1个STR遗传标记[2732],因此,运用SNP进行对比时需要几百个位点。微单倍型结合了多种遗传标记的优点,但通常比大多数STR具有的等位基因更少,因此,要达到与STR相当的效能,需要更多的微单倍型[15]。此外,有研究[87]提出MiniHap这一新型遗传标记突变率极低,通过对196名无关个体进行检测,发现56个MiniHap的平均Ae值为12.16,平均遗传多样性(genetic diversity,GD)即杂合度为0.846 2,平均个体识别率(discrimination power,DP)、平均非父排除率(probability of exclusion,PE)和平均典型父权指数(typical paternity index,TPI)分别为0.912 6、0.585 4和5.268 6。由此可见,MiniHap的法医遗传学效能与STR遗传标记相当,甚至高于STR遗传标记[88],表明MiniHap是潜在的理想亲缘关系鉴定分子,也可以作为以上设想中用于对比STR的一种遗传标记。但MiniHap的片段较长,在涉及降解生物检材的亲缘关系鉴定中运用可能受限,适用于常规的亲缘关系鉴定案件。在未来工作中探索MiniHap等新型遗传标记用于亲缘关系鉴定,有望为亲缘关系鉴定提供全新的技术手段,提升亲缘关系分析的准确性。

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