The application of short and highly polymorphic microhaplotype loci in paternity testing and sibling testing of temperature-dependent degraded samples.
The application of short and highly polymorphic microhaplotype loci in paternity testing and sibling testing of temperature-dependent degraded samples.
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短高多态性微单倍型基因座在温度依赖性降解样品亲子鉴定和同胞鉴定中的应用
DOI：
10.3389/fgene.2022.983811
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发表时间：
2022
影响因子：
3.7
通讯作者：
Zha, Lagabaiyila
中科院分区：
文献类型：
--
作者：
Wen, Dan;Xing, Hao;Liu, Ying;Li, Jienan;Qu, Weifeng;He, Wei;Wang, Chudong;Xu, Ruyi;Liu, Yi;Jia, Hongtao;Zha, Lagabaiyila
当样本降解时，亲子鉴定和兄弟姐妹鉴定变得更加复杂和困难。但目前常用的遗传标记（STR和SNP）由于其自身的缺点并不能完全解决这一问题。Kidd课题组提出的新型遗传标记微单倍型结合了STR和SNP的优点，有望成为降解样本亲缘关系检验的一种有前途的遗传标记。因此，本研究拟选取适当数量的高度多态性的SNP微单倍型位点，利用新一代测序技术进行检测，分析其检测降解样本的能力，并基于收集的96个无关个体计算其法医学参数，模拟亲属关系对，评价其在亲子鉴定和同胞鉴定中的有效性，并与15个STR基因座进行比较。最后，建立了一个短而高度多态的微单倍型面板，包含36个高度多态的基于SNP的微单倍型位点，长度小于100 bp，Ae大于3.00，其中29个微单倍型位点不能拒绝Hardy-Weinberg平衡和Bonferroni校正后的连锁平衡。这29个微单倍型位点的CPD和CPE分别为1 - 2.96E-26和1 - 5.45E-09。在用100 ° C热水孵育40分钟和60分钟的降解样品中没有观察到等位基因丢失。根据模拟亲属关系分析，亲子关系对无关个体在4/− 4阈值的有效性达到98.39%，同胞关系对无关个体在2/− 2阈值的有效性为93.01%，15个STR基因座的等位基因频率（86.75%）高于无血缘关系个体（81.73%）。在将我们的29个微单倍型位点与其他50个短且高度多态的微单倍型位点组合后，在2/-2的阈值下，对于关系半同胞与无关个体以及全同胞与半同胞的有效性值分别为82.42%和90.89%。我们开发的短而高度多态的微单倍型面板可能非常有用的亲子鉴定和全同胞测试在降解样品中，并结合其他研究人员报道的短而高度多态的微单倍型位点，可能有助于分析更远的亲属关系。
Paternity testing and sibling testing become more complex and difficult when samples degrade. But the commonly used genetic markers (STR and SNP) cannot completely solve this problem due to some disadvantages. The novel genetic marker microhaplotype proposed by Kidd’s research group combines the advantages of STR and SNP and is expected to become a promising genetic marker for kinship testing in degraded samples. Therefore, in this study, we intended to select an appropriate number of highly polymorphic SNP-based microhaplotype loci, detect them by the next-generation sequencing technology, analyze their ability to detect degraded samples, calculate their forensic parameters based on the collected 96 unrelated individuals, and evaluate their effectiveness in paternity testing and sibling testing by simulating kinship relationship pairs, which were also compared to 15 STR loci. Finally, a short and highly polymorphic microhaplotype panel was developed, containing 36 highly polymorphic SNP-based microhaplotype loci with lengths smaller than 100 bp and A e greater than 3.00, of which 29 microhaplotype loci could not reject the Hardy-Weinberg equilibrium and linkage equilibrium after the Bonferroni correction. The CPD and CPE of these 29 microhaplotype loci were 1-2.96E-26 and 1-5.45E-09, respectively. No allele dropout was observed in degraded samples incubated with 100°C hot water for 40min and 60min. According to the simulated kinship analysis, the effectiveness at the threshold of 4/−4 reached 98.39% for relationship parent-child vs. unrelated individuals, and the effectiveness at the threshold of 2/−2 for relationship full-sibling vs. unrelated individuals was 93.01%, which was greater than that of 15 STR loci (86.75% for relationship parent-child vs. unrelated individuals and 81.73% for relationship full-sibling vs. unrelated individuals). After combining our 29 microhaplotype loci with other 50 short and highly polymorphic microhaplotype loci, the effectiveness values at the threshold of 2/−2 were 82.42% and 90.89% for relationship half-sibling vs. unrelated individuals and full-sibling vs. half-sibling. The short and highly polymorphic microhaplotype panel we developed may be very useful for paternity testing and full sibling testing in degraded samples, and in combination with short and highly polymorphic microhaplotype loci reported by other researchers, may be helpful to analyze more distant kinship relationships.
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影响因子：
2.1
作者：
Staadig A;Tillmar A
通讯作者：
Tillmar A
20个高度多态性微单倍型的构建和法医应用
影响因子：
3.5
作者：
Kureshi, Aliye;Li, Jienan;Zha, Lagabaiyila
通讯作者：
Zha, Lagabaiyila
影响因子：
64.8
作者：
Sudmant PH;Rausch T;Gardner EJ;Handsaker RE;Abyzov A;Huddleston J;Zhang Y;Ye K;Jun G;Fritz MH;Konkel MK;Malhotra A;Stütz AM;Shi X;Casale FP;Chen J;Hormozdiari F;Dayama G;Chen K;Malig M;Chaisson MJP;Walter K;Meiers S;Kashin S;Garrison E;Auton A;Lam HYK;Mu XJ;Alkan C;Antaki D;Bae T;Cerveira E;Chines P;Chong Z;Clarke L;Dal E;Ding L;Emery S;Fan X;Gujral M;Kahveci F;Kidd JM;Kong Y;Lameijer EW;McCarthy S;Flicek P;Gibbs RA;Marth G;Mason CE;Menelaou A;Muzny DM;Nelson BJ;Noor A;Parrish NF;Pendleton M;Quitadamo A;Raeder B;Schadt EE;Romanovitch M;Schlattl A;Sebra R;Shabalin AA;Untergasser A;Walker JA;Wang M;Yu F;Zhang C;Zhang J;Zheng-Bradley X;Zhou W;Zichner T;Sebat J;Batzer MA;McCarroll SA;1000 Genomes Project Consortium;Mills RE;Gerstein MB;Bashir A;Stegle O;Devine SE;Lee C;Eichler EE;Korbel JO
通讯作者：
Korbel JO
影响因子：
3.1
作者：
de la Puente, M.;Phillips, C.;Lareu, M., V
通讯作者：
Lareu, M., V
影响因子：
9.5
作者：
Thorvaldsdóttir H;Robinson JT;Mesirov JP
通讯作者：
Mesirov JP