@article{fdi:010078999,
  title = {{C}opy number variation in human genomes from three major ethno-linguistic groups in {A}frica},
  author = {{N}yangiri, {O}. {A}. and {N}oyes, {H}. and {M}ulindwa, {J}. and {I}lboudo, {H}. and {K}abore, {J}. {W}. and {A}houty, {B}. and {K}offi, {M}. and {A}sina, {O}. {F}. and {M}umba, {D}. and {O}fon, {E}. and {S}imo, {G}. and {K}imuda, {M}. {P}. and {E}nyaru, {J}. and {A}libu, {V}. {P}. and {K}amoto, {K}. and {C}hisi, {J}. and {S}imuunza, {M}. and {C}amara, {M}. and {S}idibe, {I}. and {M}ac{L}eod, {A}. and {B}ucheton, {B}runo and {H}all, {N}. and {H}ertz-{F}owler, {C}. and {M}atovu, {E}. and {T}rypano{GEN} {R}esearch {G}roup and {H}3{A}frica {C}onsortium},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground {C}opy number variation is an important class of genomic variation that has been reported in 75% of the human genome. {H}owever, it is underreported in {A}frican populations. {C}opy number variants ({CNV}s) could have important impacts on disease susceptibility and environmental adaptation. {T}o describe {CNV}s and their possible impacts in {A}fricans, we sequenced genomes of 232 individuals from three major {A}frican ethno-linguistic groups: (1) {N}iger {C}ongo {A} from {G}uinea and {C}ote d'{I}voire, (2) {N}iger {C}ongo {B} from {U}ganda and the {D}emocratic {R}epublic of {C}ongo and (3) {N}ilo-{S}aharans from {U}ganda. {W}e used {G}enome{STR}i{P} and cn.{MOPS} to identify copy number variant regions ({CNVR}s). {R}esults {W}e detected 7608 {CNVR}s, of which 2172 were only deletions, 2384 were only insertions and 3052 had both. {W}e detected 224 previously un-described {CNVR}s. {T}he majority of novel {CNVR}s were present at low frequency and were not shared between populations. {W}e tested for evidence of selection associated with {CNV}s and also for population structure. {S}ignatures of selection identified previously, using {SNP}s from the same populations, were overrepresented in {CNVR}s. {W}hen {CNV}s were tagged with {SNP} haplotypes to identify {SNP}s that could predict the presence of {CNV}s, we identified haplotypes tagging 3096 {CNVR}s, 372 {CNVR}s had {SNP}s with evidence of selection (i{HS}>3) and 222 {CNVR}s had both. {T}his was more than expected (p<0.0001) and included loci where {CNV}s have previously been associated with {HIV}, {R}hesus {D} and preeclampsia. {W}hen integrated with 1000 {G}enomes {CNV} data, we replicated their observation of population stratification by continent but no clustering by populations within {A}frica, despite inclusion of {N}ilo-{S}aharans and {N}iger-{C}ongo populations within our dataset. {C}onclusions {N}ovel {CNVR}s in the current study increase representation of {A}frican diversity in the database of genomic variants. {O}ver-representation of {CNVR}s in {SNP} signatures of selection and an excess of {SNP}s that both tag {CNV}s and are subject to selection show that {CNV}s may be the actual targets of selection at some loci. {H}owever, unlike {SNP}s, {CNV}s alone do not resolve {A}frican ethno-linguistic groups. {T}ag haplotypes for {CNV}s identified may be useful in predicting {A}frican {CNV}s in future studies where only {SNP} data is available.},
  keywords = {{CNV} ; {S}tructural variation ; {N}iger {C}ongo {A} ; {N}iger {C}ongo {B} ; {N}ilo-{S}aharan ; {S}ignatures of selection ; {A}daptation ; {T}ag haplotypes ; {AFRIQUE}},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {21},
  numero = {1},
  pages = {art. 289 [15]},
  ISSN = {1471-2164},
  year = {2020},
  DOI = {10.1186/s12864-020-6669-y},
  URL = {https://www.documentation.ird.fr/hor/fdi:010078999},
}