基于高密度单核苷酸多态性的共祖远亲缘关系预测算法准确性研究
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作者单位:

1)中国政法大学,证据科学教育部重点实验室,北京 100088;2)公安部鉴定中心,法医遗传学公安部重点实验室,现场物证溯源技术国家工程实验室,北京 100038;3)江苏师范大学生命科学学院,江苏省系统发育与比较基因组学重点实验室,徐州 221116

作者简介:

李彩霞 Tel: 010-83752706, E-mail: licaixia@tsinghua.org.cn赵东 Tel: 15010055761, E-mail: dzfslm@163.comLI Cai-Xia. Tel: 86-10-83752706, E-mail: licaixia@tsinghua.org.cnZHAO Dong. Tel: 86-15010055761, E-mail: dzfslm@163.com

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基金项目:

国家自然科学基金(82171870),公安部技术研究计划(2021JSZ15)和中央级公益性科研院所基本科研业务费(2021JB004)资助项目。


Accuracy Research on The Distant Kinship Relationship Prediction by IBD Algorithm
Author:
Affiliation:

1)Key Laboratory of Evidence Science, Ministry of Education, China University of Political Science and Law, Beijing 100088, China;2)Key Laboratory of Forensic Genetics, Ministry of Public Security, National Engineering Laboratory for Forensic Science, Institute of Forensic Science, Beijing 100038, China;3)Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou 221116, China

Fund Project:

This work was supported by grants from The National Natural Science Foundation of China (82171870), the Ministry of Public Security Technology Research Program (2021JSZ15), and the Fundamental Research Funds for Institute of Forensic Science (2021JB004).

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    摘要:

    目的 研究构建基于共祖(identity-by-descent,IBD)片段算法预测远亲缘关系分析流程并评估预测准确性。方法 采用高密度单核苷酸多态性(single nucleotide polymorphism,SNP)芯片对253份家系样本进行检测,研究基于IBD片段算法的分析流程进行两两个体间亲缘关系预测,评估预测准确性。随机减少SNP位点,评估位点数对算法预测准确性的影响。结果 IBD片段算法预测1~7级亲缘关系平均置信区间准确率为94.72%,预测可信度为99.77%,6级及以上亲缘关系预测时出现假阴性。随着SNP数量减少,预测准确性会出现一定程度的下降。结论 IBD片段算法可用于7级以内亲缘关系的预测,该算法在群体遗传学、法医遗传学等领域有重要应用价值。

    Abstract:

    Objective To construct an analysis process for identity-by-descent (IBD) algorithm to predict distant relatives and evaluate the prediction accuracy.Methods 253 family samples were detected by using high-density whole genome single nucleotide polymorphism (SNP) chip. IBD algorithm was used to predict the genetic relationship between pairs of individuals, and the prediction accuracy was evaluated. The number of SNPs was randomly reduced to evaluate the effect of SNP numbers on the accuracy of the algorithm prediction.Results Among 1-7th kinship degree, the average confidence interval accuracy of IBD algorithm was 94.72%, and the prediction credibility was 99.77%. The false negative of IBD algorithm was found when kinship degree is 6 or higher. When the number of SNPs decreases, the prediction accuracy will decline to a certain extent.Conclusion The IBD algorithm can accurately predict the genetic relationship within the seventh kinship degree, and it has important application value in population genetics, forensic genealogy inference and other fields.

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刘京,李晶,杨澜,管珊珊,魏以梁,赵雯婷,江丽,赵东,李彩霞.基于高密度单核苷酸多态性的共祖远亲缘关系预测算法准确性研究[J].生物化学与生物物理进展,2023,50(12):2980-2990

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  • 收稿日期:2022-11-21
  • 最后修改日期:2023-11-17
  • 接受日期:2023-04-11
  • 在线发布日期: 2023-12-22
  • 出版日期: 2023-12-20