A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa.
A map of copy number variations in the Tunisian population: a valuable tool for medical genomics in North Africa.
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DOI：
10.1038/s41525-020-00166-5
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发表时间：
2021-01-08
影响因子：
5.3
通讯作者：
Abdelhak S
中科院分区：
文献类型：
--
作者：
Romdhane L;Mezzi N;Dallali H;Messaoud O;Shan J;Fakhro KA;Kefi R;Chouchane L;Abdelhak S
拷贝数变异（CNV）被认为是人类基因组中最常见的结构变异类型。一些CNV可以作用于人类表型多样性，包括罕见的孟德尔疾病和基因组疾病。北非人口在公共基因数据库中的单核苷酸变异和较大的基因组突变方面仍然代表性不足。在这项研究中，我们提出了第一个CNV地图的北非人口使用的Affyteles全基因组SNP（单核苷酸多态性）阵列6.0阵列基因分型强度数据调用CNV在102突尼斯健康个体。两个软件，PennCNV和Birdsuite，被用来调用CNVs，以提供可靠的数据。随后进行生物信息学分析，以探索其特征和模式。突尼斯人群的CNV图谱包括1083个CNV，跨越61.443 Mb的基因组。CNV长度范围为1.017 ~ 2.074 Mb，平均56.734 kb。缺失占57.43%的CNVs，而重复和混合基因座较少。据报道，被CNV破坏的103个基因导致155种孟德尔疾病/表型。据报道，药物反应基因也受到CNV的影响。缺失和重复片段重叠的基因数据以及它们内部和周围的序列特性也为CNV的功能和健康影响提供了见解。这些发现为突尼斯人口以及北非种族相似人口的遗传多样性和个性化医疗提供了有价值的线索。
Copy number variation (CNV) is considered as the most frequent type of structural variation in the human genome. Some CNVs can act on human phenotype diversity, encompassing rare Mendelian diseases and genomic disorders. The North African populations remain underrepresented in public genetic databases in terms of single-nucleotide variants as well as for larger genomic mutations. In this study, we present the first CNV map for a North African population using the Affymetrix Genome-Wide SNP (single-nucleotide polymorphism) array 6.0 array genotyping intensity data to call CNVs in 102 Tunisian healthy individuals. Two softwares, PennCNV and Birdsuite, were used to call CNVs in order to provide reliable data. Subsequent bioinformatic analyses were performed to explore their features and patterns. The CNV map of the Tunisian population includes 1083 CNVs spanning 61.443 Mb of the genome. The CNV length ranged from 1.017 kb to 2.074 Mb with an average of 56.734 kb. Deletions represent 57.43% of the identified CNVs, while duplications and the mixed loci are less represented. One hundred and three genes disrupted by CNVs are reported to cause 155 Mendelian diseases/phenotypes. Drug response genes were also reported to be affected by CNVs. Data on genes overlapped by deletions and duplications segments and the sequence properties in and around them also provided insights into the functional and health impacts of CNVs. These findings represent valuable clues to genetic diversity and personalized medicine in the Tunisian population as well as in the ethnically similar populations from North Africa.
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