基于单核苷酸多态性基因型的实现亲缘关系的有效估计
Efficient Estimation of Realized Kinship from Single Nucleotide Polymorphism Genotypes.
作者信息
Wang Bowen, Sverdlov Serge, Thompson Elizabeth
机构信息
Department of Statistics, University of Washington, Seattle, Washington 98195-4322.
Department of Statistics, University of Washington, Seattle, Washington 98195-4322
出版信息
Genetics. 2017 Mar;205(3):1063-1078. doi: 10.1534/genetics.116.197004. Epub 2017 Jan 18.
Abstract
Realized kinship is a key statistic in analyses of genetic data involving relatedness of individuals or structure of populations. There are several estimators of kinship that make use of dense SNP genotypes. We introduce a class of estimators, of which some existing estimators are special cases. Within this class, we derive properties of the estimators and determine an optimal estimator. Additionally, we introduce an alternative marker weighting that takes allelic associations [linkage disequilibrium (LD)] into account, and apply this weighting to several estimators. In a simulation study, we show that improved estimators are obtained (1) by optimal weighting of markers, (2) by taking physical contiguity of genome into account, and (3) by weighting on the basis of LD.
摘要
实现的亲缘关系是涉及个体亲缘关系或群体结构的遗传数据分析中的关键统计量。有几种利用密集单核苷酸多态性（SNP）基因型的亲缘关系估计方法。我们引入了一类估计方法，一些现有的估计方法是其特殊情况。在这类方法中，我们推导了估计方法的性质并确定了最优估计方法。此外，我们引入了一种考虑等位基因关联[连锁不平衡（LD）]的替代标记加权方法，并将此加权方法应用于几种估计方法。在一项模拟研究中，我们表明通过（1）对标记进行最优加权、（2）考虑基因组的物理连续性以及（3）基于连锁不平衡进行加权，可以获得改进的估计方法。
相似文献
1
Efficient Estimation of Realized Kinship from Single Nucleotide Polymorphism Genotypes.基于单核苷酸多态性基因型的实现亲缘关系的有效估计
Genetics. 2017 Mar;205(3):1063-1078. doi: 10.1534/genetics.116.197004. Epub 2017 Jan 18.
2
Linkage disequilibrium across two different single-nucleotide polymorphism genome scans.两个不同单核苷酸多态性全基因组扫描的连锁不平衡。
BMC Genet. 2005 Dec 30;6 Suppl 1(Suppl 1):S86. doi: 10.1186/1471-2156-6-S1-S86.
3
Using selection index theory to estimate consistency of multi-locus linkage disequilibrium across populations.利用选择指数理论估计多基因座连锁不平衡在不同群体间的一致性。
BMC Genet. 2015 Jul 19;16:87. doi: 10.1186/s12863-015-0252-6.
4
Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds.利用系谱、50k SNP芯片基因型和全序列数据对三个牛品种的近亲繁殖进行估计。
BMC Genet. 2015 Jul 22;16:88. doi: 10.1186/s12863-015-0227-7.
5
Comparing heritability estimators under alternative structures of linkage disequilibrium.比较连锁不平衡不同结构下的遗传力估计值。
G3 (Bethesda). 2022 Jul 29;12(8). doi: 10.1093/g3journal/jkac134.
6
Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies.为关联研究新设计的大型葡萄（欧亚种葡萄）多样性群体的遗传多样性、连锁不平衡及效能
BMC Plant Biol. 2016 Mar 22;16:74. doi: 10.1186/s12870-016-0754-z.
7
Identity by descent estimation with dense genome-wide genotype data.基于全基因组高密度基因型数据的亲缘关系估计。
Genet Epidemiol. 2011 Sep;35(6):557-67. doi: 10.1002/gepi.20606. Epub 2011 Jul 18.
8
Simulating autosomal genotypes with realistic linkage disequilibrium and a spiked-in genetic effect.模拟具有真实连锁不平衡和插入遗传效应的常染色体基因型。
BMC Bioinformatics. 2018 Jan 2;19(1):2. doi: 10.1186/s12859-017-2004-2.
9
A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction.一种用于 SNP 遗传力估计和基因组预测的新型连锁不平衡校正基因组关系矩阵。
Heredity (Edinb). 2018 Apr;120(4):356-368. doi: 10.1038/s41437-017-0023-4. Epub 2017 Dec 14.
10
Estimating FST and kinship for arbitrary population structures.估计任意群体结构的 FST 和亲缘关系。
PLoS Genet. 2021 Jan 19;17(1):e1009241. doi: 10.1371/journal.pgen.1009241. eCollection 2021 Jan.
引用本文的文献
1
Kinship estimation bias carries over to heritability estimation bias using variance components.亲属关系估计偏差会延续到使用方差成分的遗传力估计偏差中。
bioRxiv. 2025 May 15:2025.05.13.653659. doi: 10.1101/2025.05.13.653659.
2
Forest tree breeding using genomic Markov causal models: a new approach to genomic tree breeding improvement.利用基因组马尔可夫因果模型进行林木育种：提高基因组树木育种的新方法。
Heredity (Edinb). 2025 May;134(5):280-292. doi: 10.1038/s41437-025-00755-z. Epub 2025 Mar 17.
3
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states.基于潜在的亲缘关系状态估计近亲系数和亲缘系数。
Bioinformatics. 2024 Feb 1;40(2). doi: 10.1093/bioinformatics/btae082.
4
FiMAP: A fast identity-by-descent mapping test for biobank-scale cohorts.FiMAP：一种用于生物库规模队列的快速基于关系的映射测试。
PLoS Genet. 2023 Dec 1;19(12):e1011057. doi: 10.1371/journal.pgen.1011057. eCollection 2023 Dec.
5
Genomic selection for agronomic traits in a winter wheat breeding program.冬小麦育种计划中农艺性状的基因组选择
Theor Appl Genet. 2023 Mar 10;136(3):38. doi: 10.1007/s00122-023-04294-1.
6
Genetic association models are robust to common population kinship estimation biases.遗传关联模型对常见的群体亲缘关系估计偏差具有稳健性。
Genetics. 2023 May 4;224(1). doi: 10.1093/genetics/iyad030.
7
A fast linkage method for population GWAS cohorts with related individuals.一种用于相关个体的群体 GWAS 队列的快速连锁分析方法。
Genet Epidemiol. 2023 Apr;47(3):231-248. doi: 10.1002/gepi.22516. Epub 2023 Feb 5.
8
An unbiased kinship estimation method for genetic data analysis.一种用于遗传数据分析的无偏亲缘关系估计方法。
BMC Bioinformatics. 2022 Dec 6;23(1):525. doi: 10.1186/s12859-022-05082-2.
9
Privacy-aware estimation of relatedness in admixed populations.混合人群中具有隐私意识的亲缘关系估计。
Brief Bioinform. 2022 Nov 19;23(6). doi: 10.1093/bib/bbac473.
10
Robust fingerprinting of genomic databases.基因组数据库的稳健指纹识别。
Bioinformatics. 2022 Jun 24;38(Suppl 1):i143-i152. doi: 10.1093/bioinformatics/btac243.
本文引用的文献
1
Model-free Estimation of Recent Genetic Relatedness.近期遗传相关性的无模型估计
Am J Hum Genet. 2016 Jan 7;98(1):127-48. doi: 10.1016/j.ajhg.2015.11.022.
2
A global reference for human genetic variation.人类遗传变异的全球参考。
Nature. 2015 Oct 1;526(7571):68-74. doi: 10.1038/nature15393.
3
Pedigree-Free Descent-Based Gene Mapping from Population Samples.基于群体样本中无系谱的家系推断的基因定位
Hum Hered. 2015;80(1):21-35. doi: 10.1159/000430841. Epub 2015 Jul 24.
4
Improved heritability estimation from genome-wide SNPs.提高全基因组 SNP 遗传力估计值。
Am J Hum Genet. 2012 Dec 7;91(6):1011-21. doi: 10.1016/j.ajhg.2012.10.010.
5
Estimating kinship in admixed populations.估算混合人群中的亲属关系。
Am J Hum Genet. 2012 Jul 13;91(1):122-38. doi: 10.1016/j.ajhg.2012.05.024. Epub 2012 Jun 28.
6
Inferring coancestry in population samples in the presence of linkage disequilibrium.在连锁不平衡存在的情况下推断群体样本中的共同血统。
Genetics. 2012 Apr;190(4):1447-60. doi: 10.1534/genetics.111.137570. Epub 2012 Jan 31.
7
A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics.一种同时检测多个个体中 IBD 区域的方法 - 应用于疾病遗传学。
Genome Res. 2011 Jul;21(7):1168-80. doi: 10.1101/gr.115360.110. Epub 2011 Apr 14.
8
Linkage analysis without defined pedigrees.无明确家系的连锁分析。
Genet Epidemiol. 2011 Jul;35(5):360-70. doi: 10.1002/gepi.20584. Epub 2011 Apr 4.
9
Variation in actual relationship as a consequence of Mendelian sampling and linkage.孟德尔抽样和连锁导致的实际关系变异。
Genet Res (Camb). 2011 Feb;93(1):47-64. doi: 10.1017/S0016672310000480.
10
Predicting genetic predisposition in humans: the promise of whole-genome markers.预测人类的遗传易感性：全基因组标记的前景。
Nat Rev Genet. 2010 Dec;11(12):880-6. doi: 10.1038/nrg2898. Epub 2010 Nov 3.
Zotero 插件