Romdhane Lilia, Mezzi Nessrine, Dallali Hamza, Messaoud Olfa, Shan Jingxuan, Fakhro Khalid A, Kefi Rym, Chouchane Lotfi, Abdelhak Sonia
Biomedical Genomics and Oncogenetics Laboratory (LR16IPT05), Institut Pasteur de Tunis, Tunis, Tunisia.
Department of Biology, Faculty of Science of Bizerte, Jarzouna, Tunisia.
NPJ Genom Med. 2021 Jan 8;6(1):3. doi: 10.1038/s41525-020-00166-5.
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.
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。在单核苷酸变异以及较大的基因组突变方面，北非人群在公共遗传数据库中的代表性仍然不足。在本研究中，我们利用Affymetrix全基因组SNP（单核苷酸多态性）6.0阵列基因分型强度数据，为一个北非人群绘制了首张CNV图谱，以在102名突尼斯健康个体中检测CNV。使用了PennCNV和Birdsuite这两种软件来检测CNV，以提供可靠的数据。随后进行了生物信息学分析，以探索它们的特征和模式。突尼斯人群的CNV图谱包含1083个CNV，覆盖基因组的61.443 Mb。CNV长度范围为1.017 kb至2.074 Mb，平均为56.734 kb。缺失占已鉴定CNV的57.43%，而重复和混合位点的占比则较小。据报道，103个被CNV破坏的基因可导致155种孟德尔疾病/表型。也有报道称药物反应基因受CNV影响。关于被缺失和重复片段重叠的基因的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群以及来自北非的种族相似人群的遗传多样性和个性化医疗提供了有价值的线索。
