Genome-wide copy number variations in a large cohort of bantu African children

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 a...

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Bibliographic Details
Published in:	BMC medical genomics 2021-05, Vol.14 (1), p.129-129, Article 129
Main Authors:	Yilmaz, Feyza, Null, Megan, Astling, David, Yu, Hung-Chun, Cole, Joanne, Santorico, Stephanie A, Hallgrimsson, Benedikt, Manyama, Mange, Spritz, Richard A, Hendricks, Audrey E, Shaikh, Tamim H
Format:	Article
Language:	eng
Subjects:	African Algorithms Analysis Bantu Bantu-speaking peoples Causes of CNV Congenital diseases Copy number Copy number variation Copy number variations Demographic aspects Disease DNA Copy Number Variations DNA probes Genes Genetic aspects Genetic disorders Genome-wide Genomes Genomics Genotyping Health aspects Medical research Medicine, Experimental Pediatric research Population Population studies Prader-Willi syndrome Structure Variation
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Summary:	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.
ISSN:	1755-8794 1755-8794