Copy number variation in human genomes from three major ethno-linguistic groups in Africa
Copy number variation in human genomes from three major ethno-linguistic groups in Africa
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DOI：
10.1186/s12864-020-6669-y
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发表时间：
2020-04-10
期刊：
影响因子：
4.4
通讯作者：
Matovu, Enock
中科院分区：
文献类型：
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作者：
Nyangiri, Oscar A.;Noyes, Harry;Matovu, Enock
背景拷贝数变异是一类重要的基因组变异，已报道在75%的人类基因组中存在。然而，在非洲人口中报告不足。拷贝数变异（CNVs）可能对疾病易感性和环境适应性产生重要影响。为了描述CNVs及其在非洲人中可能的影响，我们对来自三个主要非洲民族语言群体的232名个体的基因组进行了测序：（1）来自几内亚和科特迪瓦的尼日尔刚果A，（2）来自乌干达和刚果民主共和国的尼日尔刚果B，以及（3）来自乌干达的尼罗-撒哈拉人。结果共检测到7608个拷贝数变异区（CNVRs），其中缺失型2172个，插入型2384个，两者兼有型3052个。我们检测到224个以前未描述的CNVRs。大多数新的CNVRs出现频率较低，并且在人群之间不共享。我们测试了与CNVs相关的选择证据以及群体结构。先前使用来自相同人群的SNP识别的选择的签名在CNVRs中被过度代表。当用SNP单倍型标记CNV以鉴定可以预测CNV存在的SNP时，我们鉴定了标记3096个CNVRs的单倍型，372个CNVRs具有选择证据（iHS>3）的SNP，222个CNVRs两者都具有。这比预期的要好（p
BackgroundCopy number variation is an important class of genomic variation that has been reported in 75% of the human genome. However, it is underreported in African populations. Copy number variants (CNVs) could have important impacts on disease susceptibility and environmental adaptation. To describe CNVs and their possible impacts in Africans, we sequenced genomes of 232 individuals from three major African ethno-linguistic groups: (1) Niger Congo A from Guinea and Cote d'Ivoire, (2) Niger Congo B from Uganda and the Democratic Republic of Congo and (3) Nilo-Saharans from Uganda. We used GenomeSTRiP and cn.MOPS to identify copy number variant regions (CNVRs).ResultsWe detected 7608 CNVRs, of which 2172 were only deletions, 2384 were only insertions and 3052 had both. We detected 224 previously un-described CNVRs. The majority of novel CNVRs were present at low frequency and were not shared between populations. We tested for evidence of selection associated with CNVs and also for population structure. Signatures of selection identified previously, using SNPs from the same populations, were overrepresented in CNVRs. When CNVs were tagged with SNP haplotypes to identify SNPs that could predict the presence of CNVs, we identified haplotypes tagging 3096 CNVRs, 372 CNVRs had SNPs with evidence of selection (iHS>3) and 222 CNVRs had both. This was more than expected (p