Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa

Mulindwa, Julius; Noyes, Harry; Ilboudo, Hamidou; Nyangiri, Oscar A.; Koffi, Mathurin; Mumba, Dieudonné; Simo, Gustave; Enyaru, John; Chisi, John; Simuunza, Martin; Alibu, Vincent P.; Lejon, Veerle; Jammoneau, Vincent; MacLeod, Annette; Bucheton, Bruno; Hertz‐Fowler, Christiane; Sidibé, Issa; Matovu, Enock

doi:10.1101/186700

Cited by 2 publications

(2 citation statements)

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“…To confirm that the inability to resolve populations within Africa was not an artefact of the dataset, we combined our data with 1000 Genomes Project data and found that samples clustered by continent of origin but not at any finer scale. In contrast to these observations Nilo-Saharans, Niger Congo A and Niger Congo B have been shown to cluster separately in SNP based PCA [21]. CNV data therefore have low resolution in distinguishing intra-continental populations despite genomic CNV accounting for at least seven times more genomic base variation than SNP [36].…”

Section: Population Structure Wgs Cnvs Resolve Continental Populationmentioning

confidence: 69%

“…In order to identify CNVs with potentially functional effects we tested for association between CNVRs and loci that have been identified as under selection, with integrated haplotype score (iHS > 3.0) in the UNL population in a separate study of the same data [21]. There were 12,278 SNPs with evidence of selection (−log10 iHS p > 3.0), of these 1805 were within CNVRs, more than twice as many as would be expected by chance (χ = 1822, p < 10 − 10 ) ( Table 3), indicating a positive bias of selection on human CNVRs as shown in a previous study [22].…”

Section: Cnvrs Are Overrepresented At Loci Under Selectionmentioning

confidence: 99%

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Copy number variation in human genomes from three major ethno-linguistic groups in Africa

et al. 2020

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Background: Copy 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 Côte 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). Results: We 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 < 0.0001) and included loci where CNVs have previously been associated with HIV, Rhesus D and preeclampsia. When integrated with 1000 Genomes CNV data, we replicated their observation of population stratification by continent but no clustering by populations within Africa, despite inclusion of Nilo-Saharans and Niger-Congo populations within our dataset. Conclusions: Novel CNVRs in the current study increase representation of African diversity in the database of genomic variants. Over-representation of CNVRs in SNP signatures of selection and an excess of SNPs that both tag CNVs and are subject to selection show that CNVs may be the actual targets of selection at some loci. However, unlike SNPs, CNVs alone do not resolve African ethno-linguistic groups. Tag haplotypes for CNVs identified may be useful in predicting African CNVs in future studies where only SNP data is available.

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Section: Population Structure Wgs Cnvs Resolve Continental Populationmentioning

confidence: 69%

Section: Cnvrs Are Overrepresented At Loci Under Selectionmentioning

confidence: 99%

Copy number variation in human genomes from three major ethno-linguistic groups in Africa

et al. 2020

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Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt"

et al. 2019

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Populations in sub-Saharan Africa have historically been exposed to intense selection from chronic infection with falciparum malaria. Interestingly, populations with the highest malaria intensity can be identified by the increased occurrence of endemic Burkitt Lymphoma (eBL), a pediatric cancer that affects populations with intense malaria exposure, in the so called “eBL belt” in sub-Saharan Africa. However, the effects of intense malaria exposure and sub-Saharan populations’ genetic histories remain poorly explored. To determine if historical migrations and intense malaria exposure have shaped the genetic composition of the eBL belt populations, we genotyped ~4.3 million SNPs in 1,708 individuals from Ghana and Northern Uganda, located on opposite sides of eBL belt and with ≥ 7 months/year of intense malaria exposure and published evidence of high incidence of BL. Among 35 Ghanaian tribes, we showed a predominantly West-Central African ancestry and genomic footprints of gene flow from Gambian and East African populations. In Uganda, the North West population showed a predominantly Nilotic ancestry, and the North Central population was a mixture of Nilotic and Southern Bantu ancestry, while the Southwest Ugandan population showed a predominant Southern Bantu ancestry. Our results support the hypothesis of diverse ancestral origins of the Ugandan, Kenyan and Tanzanian Great Lakes African populations, reflecting a confluence of Nilotic, Cushitic and Bantu migrations in the last 3000 years. Natural selection analyses suggest, for the first time, a strong positive selection signal in the ATP2B4 gene (rs10900588) in Northern Ugandan populations. These findings provide important baseline genomic data to facilitate disease association studies, including of eBL, in eBL belt populations.

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Evidence of population specific selection inferred from 289 genome sequences of Nilo-Saharan and Niger-Congo linguistic groups in Africa

Abstract: 10! Background 11!

Cited by 2 publications

References 82 publications

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

Genetic signatures of gene flow and malaria-driven natural selection in sub-Saharan populations of the "endemic Burkitt Lymphoma belt"

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