Genome-wide copy number variations in a large cohort of bantu African children.
Genome-wide copy number variations in a large cohort of bantu African children.
复制标题
DOI：
10.1186/s12920-021-00978-z
复制
发表时间：
2021-05-17
影响因子：
2.7
通讯作者：
Shaikh TH
中科院分区：
文献类型：
--
作者：
Yilmaz F;Null M;Astling D;Yu HC;Cole J;Santorico SA;Hallgrimsson B;Manyama M;Spritz RA;Hendricks AE;Shaikh TH
拷贝数变异(CNV)占个体间基因组变异的很大比例。然而，大多数基因组变异研究都集中在单核苷酸变异(SNV)上，对大队列中CNV的全基因组分析有限，特别是在包括非洲裔人在内的遗传学研究中代表性不足的人群中。我们对来自坦桑尼亚的 >； 3400名健康的班图非洲人进行了全基因组拷贝数分析。来自高密度(>； 250万个探针)基因分型阵列的信号强度数据用于CNV呼叫，包括PennCNV、DNAcopy和VanillaIce三种算法。严格的质量标准和筛选标准被用来获得高置信度的CNV。我们发现了超过400,000个大于1kb的CNV，平均每个人有120个CNV(SE = 2.57)。我们检测到866个大的CNV(≥ 300kb)，其中一些基因组区域重叠，以前与多种先天性畸形综合征有关，包括普拉德-威利/安杰曼综合征(1型)和22q11.2缺失综合征。此外，在我们的队列中看到的几个常见的CNV(≥ 5%)与以前与发育障碍相关的基因重叠。这些发现可能有助于改进表型结果和影响以前与疾病有关的基因和基因组区域的变异的外显性。我们的研究提供了非洲血统个体CNV的最大数据集之一，使在非洲人群的研究和临床研究中观察到的CNV的临床评估和疾病关联得到改善。网上版载有补充材料，可在10.1186/s12920-021-00978-z查阅。
Copy number variations (CNVs) account for a substantial proportion of inter-individual genomic variation. However, a majority of genomic variation studies have focused on single-nucleotide variations (SNVs), with limited genome-wide analysis of CNVs in large cohorts, especially in populations that are under-represented in genetic studies including people of African descent. We carried out a genome-wide copy number analysis in > 3400 healthy Bantu Africans from Tanzania. Signal intensity data from high density (> 2.5 million probes) genotyping arrays were used for CNV calling with three algorithms including PennCNV, DNAcopy and VanillaICE. Stringent quality metrics and filtering criteria were applied to obtain high confidence CNVs. We identified over 400,000 CNVs larger than 1 kilobase (kb), for an average of 120 CNVs (SE = 2.57) per individual. We detected 866 large CNVs (≥ 300 kb), some of which overlapped genomic regions previously associated with multiple congenital anomaly syndromes, including Prader-Willi/Angelman syndrome (Type1) and 22q11.2 deletion syndrome. Furthermore, several of the common CNVs seen in our cohort (≥ 5%) overlap genes previously associated with developmental disorders. These findings may help refine the phenotypic outcomes and penetrance of variations affecting genes and genomic regions previously implicated in diseases. Our study provides one of the largest datasets of CNVs from individuals of African ancestry, enabling improved clinical evaluation and disease association of CNVs observed in research and clinical studies in African populations. The online version contains supplementary material available at 10.1186/s12920-021-00978-z.
登录
查看更多内容
影响因子：
64.8
作者：
Gurdasani, Deepti;Carstensen, Tommy;Tekola-Ayele, Fasil;Pagani, Luca;Tachmazidou, Ioanna;Hatzikotoulas, Konstantinos;Karthikeyan, Savita;Iles, Louise;Pollard, Martin O.;Choudhury, Ananyo;Ritchie, GrahamR. S.;Xue, Yali;Asimit, Jennifer;Nsubuga, Rebecca N.;Young, Elizabeth H.;Pomilla, Cristina;Kivinen, Katja;Rockett, Kirk;Kamali, Anatoli;Doumatey, Ayo P.;Asiki, Gershim;Seeley, Janet;Sisay-Joof, Fatoumatta;Jallow, Muminatou;Tollman, Stephen;Mekonnen, Ephrem;Ekong, Rosemary;Oljira, Tamiru;Bradman, Neil;Bojang, Kalifa;Ramsay, Michele;Adeyemo, Adebowale;Bekele, Endashaw;Motala, Ayesha;Norris, Shane A.;Pirie, Fraser;Kaleebu, Pontiano;Kwiatkowski, Dominic;Tyler-Smith, Chris;Rotimi, Charles;Zeggini, Eleftheria;Sandhu, Manjinder S.
通讯作者：
Sandhu, Manjinder S.
来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
48
作者：
Kidd, Jeffrey M.;Sampas, Nick;Antonacci, Francesca;Graves, Tina;Fulton, Robert;Hayden, Hillary S.;Alkan, Can;Malig, Maika;Ventura, Mario;Giannuzzi, Giuliana;Kallicki, Joelle;Anderson, Paige;Tsalenko, Anya;Yamada, N. Alice;Tsang, Peter;Kaul, Rajinder;Wilson, Richard K.;Bruhn, Laurakay;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
4.5
作者：
Cole JB;Manyama M;Kimwaga E;Mathayo J;Larson JR;Liberton DK;Lukowiak K;Ferrara TM;Riccardi SL;Li M;Mio W;Prochazkova M;Williams T;Li H;Jones KL;Klein OD;Santorico SA;Hallgrimsson B;Spritz RA
通讯作者：
Spritz RA
影响因子：
64.5
作者：
Gurdasani, Deepti;Carstensen, Tommy;Sandhu, Manj S.
通讯作者：
Sandhu, Manj S.