Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences.
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DOI：
10.1093/nar/gkab224
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发表时间：
2021-05-07
影响因子：
14.9
通讯作者：
Benson G
中科院分区：
文献类型：
--
作者：
Eslami Rasekh M;Hernández Y;Drinan SD;Fuxman Bass JI;Benson G
可变数目串联重复序列（VNTR）是在群体中拷贝数不同的串联重复序列（TR）基因座。使用我们的程序VNTRseek，我们分析了来自2770个个体的人类全基因组测序数据集，以检测小卫星VNTR，即，模式大小≥7 bp的那些。我们检测了35638个VNTR位点，并将5676个归类为常见多态性（即非参考等位基因发生在>5%的群体中）。常见的多态性VNTR基因座被发现富集在具有调控功能的基因组区域，即转录起始位点和增强子。在群体祖先的背景下，常见的多态性VNTR的调查显示，1096个位点包含群体特异性等位基因，这些可以用来分类到超级群体的个人接近完美的准确性。在与基因邻近的VNTR中寻找数量性状位点（eQTL），发现187个基因的表达差异与VNTR基因型相关。我们以几种方式验证了我们的预测，包括实验，通过鉴定长读段中的预测等位基因，以及通过比较显示测序平台之间的一致性。这项研究是迄今为止对人口中小卫星VNTR的最全面分析。
Variable Number Tandem Repeats (VNTRs) are tandem repeat (TR) loci that vary in copy number across a population. Using our program, VNTRseek, we analyzed human whole genome sequencing datasets from 2770 individuals in order to detect minisatellite VNTRs, i.e., those with pattern sizes ≥7 bp. We detected 35 638 VNTR loci and classified 5676 as commonly polymorphic (i.e. with non-reference alleles occurring in >5% of the population). Commonly polymorphic VNTR loci were found to be enriched in genomic regions with regulatory function, i.e. transcription start sites and enhancers. Investigation of the commonly polymorphic VNTRs in the context of population ancestry revealed that 1096 loci contained population-specific alleles and that those could be used to classify individuals into super-populations with near-perfect accuracy. Search for quantitative trait loci (eQTLs), among the VNTRs proximal to genes, indicated that in 187 genes expression differences correlated with VNTR genotype. We validated our predictions in several ways, including experimentally, through the identification of predicted alleles in long reads, and by comparisons showing consistency between sequencing platforms. This study is the most comprehensive analysis of minisatellite VNTRs in the human population to date.
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