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Runs of homozygosity in sub-Saharan African populations provide insights into complex demographic histories - Human Genetics

  • ️Ramsay, Michèle
  • ️Tue Jul 16 2019

  • Alvarez G et al (2009) The role of inbreeding in the extinction of a European royal dynasty. PLoS One 4:e5174. https://doi.org/10.1371/journal.pone.0005174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bekpen C et al (2017) Segmental duplications and evolutionary acquisition of UV damage response in the SPATA31 gene family of primates and humans. BMC Genom 18:222. https://doi.org/10.1186/s12864-017-3595-8

    Article  CAS  Google Scholar 

  • Bittles AH (2012) Consanguinity in context. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Bledsoe C (2002) Contingent lives: fertility, time, and aging in West Africa. The University of Chicago Press, Chicago

    Book  Google Scholar 

  • Brandes U (2007) Optimal leaf ordering of complete binary trees. J Discret Algorithms 5:546–552. https://doi.org/10.1016/j.jda.2006.09.003

    Article  Google Scholar 

  • Broman KW, Weber JL (1999) Long homozygous chromosomal segments in reference families from the centre d’Etude du polymorphisme humain. Am J Hum Genet 65:1493–1500. https://doi.org/10.1086/302661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Busby GB et al (2016) Admixture into and within sub-Saharan Africa. Elife. https://doi.org/10.7554/elife.15266

    Article  PubMed  PubMed Central  Google Scholar 

  • Caldwell JC et al (1992) The family and sexual networking in sub-Saharan Africa: historical regional differences and present-day implications. Popul Stud 46:385–410

    Article  Google Scholar 

  • Campbell MC, Tishkoff SA (2008) African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genom Hum Genet 9:403–433. https://doi.org/10.1146/annurev.genom.9.081307.164258

    Article  CAS  Google Scholar 

  • Ceballos FC et al (2018a) Assessing runs of homozygosity: a comparison of SNP Array and whole genome sequence low coverage data. BMC Genom 19:106. https://doi.org/10.1186/s12864-018-4489-0

    Article  Google Scholar 

  • Ceballos FC et al (2018b) Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 19:220–234. https://doi.org/10.1038/nrg.2017.109

    Article  CAS  PubMed  Google Scholar 

  • Chen H et al (2010) Population differentiation as a test for selective sweeps. Genome Res 20:393–402. https://doi.org/10.1101/gr.100545.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chimusa ER et al (2015) A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations. PLoS Genet 11:e1005052. https://doi.org/10.1371/journal.pgen.1005052

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Choudhury A et al (2017) Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nat Commun 8:2062. https://doi.org/10.1038/s41467-017-00663-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. https://doi.org/10.1038/nature11247

    Article  CAS  Google Scholar 

  • Curtis D (2007) Extended homozygosity is not usually due to cytogenetic abnormality. BMC Genet 8:67. https://doi.org/10.1186/1471-2156-8-67

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Curtis D et al (2008) Study of regions of extended homozygosity provides a powerful method to explore haplotype structure of human populations. Ann Hum Genet 72:261–278. https://doi.org/10.1086/503875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daya M et al (2013) A panel of ancestry informative markers for the complex five-way admixed South African coloured population. PLoS One 8:e82224. https://doi.org/10.1371/journal.pone.0082224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fu X et al (2006) cAMP-response element-binding protein mediates acid-induced NADPH oxidase NOX5-S expression in Barrett esophageal adenocarcinoma cells. J Biol Chem 281:20368–20382. https://doi.org/10.1074/jbc.m603353200

    Article  CAS  PubMed  Google Scholar 

  • Gandini F et al (2016) Mapping human dispersals into the Horn of Africa from Arabian Ice Age refugia using mitogenomes. Sci Rep 6:25472. https://doi.org/10.1038/srep25472

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gibson J et al (2006) Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 15:789–795. https://doi.org/10.1093/hmg/ddi493

    Article  CAS  PubMed  Google Scholar 

  • Grossman SR et al (2013) Identifying recent adaptations in large-scale genomic data. Cell 152:703–713. https://doi.org/10.1016/j.cell.2013.01.035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gunderson RC (1980) Connecting your pedigree into royal, noble and medieval families. Genealogical Society of Utah, Salt Lake City

    Google Scholar 

  • Gurdasani D et al (2015) The African genome variation project shapes medical genetics in Africa. Nature 517:327–332. https://doi.org/10.1038/nature13997

    Article  CAS  PubMed  Google Scholar 

  • H3 Africa Consortium et al (2014) Research capacity. Enabling the genomic revolution in Africa. Science 344:1346–1348. https://doi.org/10.1126/science.1251546

    Article  Google Scholar 

  • Hampshire KR, Smith MT (2001) Consanguineous marriage among the fulani. Hum Biol 73:597–603

    Article  CAS  PubMed  Google Scholar 

  • Hartl DL, Clark AG (2007) Principles of population genetics. Sinauer Associates, Sunderland

    Google Scholar 

  • Henn BM et al (2011) Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proc Natl Acad Sci USA 108:5154–5162. https://doi.org/10.1073/pnas.1017511108

    Article  PubMed  PubMed Central  Google Scholar 

  • Henn BM et al (2016) Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci USA 113:E440–E449. https://doi.org/10.1073/pnas.1510805112

    Article  CAS  PubMed  Google Scholar 

  • Higasa K et al (2009) Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions. PLoS Genet 5:e1000468. https://doi.org/10.1371/journal.pgen.1000468

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hollfelder N et al (2017) Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations. PLoS Genet 13:e1006976. https://doi.org/10.1371/journal.pgen.1006976

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howrigan DP et al (2011) Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genom 12:460. https://doi.org/10.1371/journal.pone.0028787

    Article  CAS  Google Scholar 

  • International HapMap C et al (2007) A second generation human haplotype map of over 31 million SNPs. Nature 449:851–861. https://doi.org/10.1038/nature06258

    Article  CAS  Google Scholar 

  • Jacobs T et al (2002) Murine malaria is exacerbated by CTLA-4 blockade. J Immunol 169:2323–2329. https://doi.org/10.4049/jimmunol.169.5.2323

    Article  CAS  PubMed  Google Scholar 

  • Jacquard A (1975) Inbreeding—one word, several meanings. Theor Popul Biol 7:338–363. https://doi.org/10.1016/0040-5809(75)90024-6

    Article  CAS  PubMed  Google Scholar 

  • Joshi PK et al (2015) Directional dominance on stature and cognition in diverse human populations. Nature 523:459–462. https://doi.org/10.1016/j.ajhg.2015.06.001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HL et al (2014) Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. Nat Commun 5:5692. https://doi.org/10.1038/ncomms6692

    Article  CAS  PubMed  Google Scholar 

  • Kirin M et al (2010) Genomic runs of homozygosity record population history and consanguinity. PLoS One 5:e13996. https://doi.org/10.1534/genetics.111.130922

    Article  PubMed  PubMed Central  Google Scholar 

  • Lauriat TL et al (2006) Characterization of KIAA0513, a novel signaling molecule that interacts with modulators of neuroplasticity, apoptosis, and the cytoskeleton. Brain Res 1121:1–11. https://doi.org/10.1016/j.brainres.2006.08.099

    Article  CAS  PubMed  Google Scholar 

  • Lencz T et al (2007) Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 104:19942–19947. https://doi.org/10.1073/pnas.0710021104

    Article  PubMed  PubMed Central  Google Scholar 

  • Lesthaeghe R et al (1989) The nuptiality regimens in Sub-Saharan Africa. In: Lesthaeghe R (ed) REproduction and social organization in sub-Saharan Africa. University of California Press, Berkeley

    Google Scholar 

  • Liu X et al (2013) Detecting and characterizing genomic signatures of positive selection in global populations. Am J Hum Genet 92:866–881. https://doi.org/10.1016/j.ajhg.2013.04.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lopez Herraez D et al (2009) Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 4:e7888. https://doi.org/10.1371/journal.pone.0007888

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lopman B, Gregson S (2008) When did HIV incidence peak in Harare, Zimbabwe?. Back-calculation from mortality statistics. PLoS One 3:e1711. https://doi.org/10.1371/journal.pone.0001711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Machado P et al (2010) Malaria: looking for selection signatures in the human PKLR gene region. Br J Haematol 149:775–784. https://doi.org/10.1111/j.1365-2141.2010.08165.x

    Article  CAS  PubMed  Google Scholar 

  • Martin AR et al (2017) Human demographic history impacts genetic risk prediction across diverse populations. Am J Hum Genet 100:635–649. https://doi.org/10.1016/j.ajhg.2017.03.004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martin AR et al (2019) Clinical use of current polygenic risk scores may exacerbate health disparities. Nat Genet 51:584–591. https://doi.org/10.1038/s41588-019-0379-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martins GA et al (2001) Fas–FasL interaction modulates nitric oxide production in Trypanosoma cruzi-infected mice. Immunology 103:122–129. https://doi.org/10.1046/j.1365-2567.2001.01216.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McQuillan R et al (2008) Runs of homozygosity in European populations. Am J Hum Genet 83:359–372. https://doi.org/10.1007/s10048-009-0182-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McQuillan R et al (2012) Evidence of inbreeding depression on human height. PLoS Genet 8:e1002655. https://doi.org/10.1371/journal.pgen.1002655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mendizabal I et al (2012) Adaptive evolution of loci covarying with the human African pygmy phenotype. Hum Genet 131:1305–1317. https://doi.org/10.1007/s00439-012-1157-3

    Article  PubMed  PubMed Central  Google Scholar 

  • Montinaro F et al (2015) Unravelling the hidden ancestry of American admixed populations. Nature Commun 6:6596. https://doi.org/10.1038/ncomms7596

    Article  CAS  Google Scholar 

  • Nothnagel M et al (2010) Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum Mol Genet 19:2927–2935. https://doi.org/10.1093/hmg/ddq198

    Article  CAS  PubMed  Google Scholar 

  • Oleksyk TK et al (2008) Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS One 3:e1712. https://doi.org/10.1371/journal.pone.0001712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Opal P et al (2003) Mapmodulin/leucine-rich acidic nuclear protein binds the light chain of microtubule-associated protein 1B and modulates neuritogenesis. J Biol Chem 278:34691–34699. https://doi.org/10.1074/jbc.m302785200

    Article  CAS  PubMed  Google Scholar 

  • Pagani L et al (2012) Ethiopian genetic diversity reveals linguistic stratification and complex influences on the ethiopian gene pool. Am J Hum Genet 91:83–96. https://doi.org/10.1016/j.ajhg.2012.05.015

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patin E et al (2014) The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. Nat Commun 5:3163. https://doi.org/10.1038/ncomms4163

    Article  CAS  PubMed  Google Scholar 

  • Pemberton TJ et al (2012) Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet 91:275–292. https://doi.org/10.1016/j.ajhg.2012.08.030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pickrell JK et al (2014) Ancient west Eurasian ancestry in southern and eastern Africa. Proc Natl Acad Sci USA 111:2632–2637. https://doi.org/10.1073/pnas.1313787111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Popejoy AB, Fullerton SM (2016) Genomics is failing on diversity. Nature 538:161–164. https://doi.org/10.1038/538161a

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Purcell S et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81:559–575. https://doi.org/10.1086/519795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramsay M et al (2016) H3Africa AWI-Gen Collaborative Centre: a resource to study the interplay between genomic and environmental risk factors for cardiometabolic diseases in four sub-Saharan African countries. Global Health Epidemiol Genom 1:e20. https://doi.org/10.1017/gheg.2016.17

    Article  CAS  Google Scholar 

  • Saha N, El Sheikh FS (1988) Inbreeding levels in Khartoum. J Biosoc Sci 20:333–336

    Article  CAS  PubMed  Google Scholar 

  • Schafer ZT et al (2006) Enhanced sensitivity to cytochrome c-induced apoptosis mediated by PHAPI in breast cancer cells. Cancer Res 66:2210–2218. https://doi.org/10.1158/0008-5472.can-05-3923

    Article  CAS  PubMed  Google Scholar 

  • Schapera I (1957) Marriage of near Kin among the Tswana. J Int Afr Stud 27:139–159. https://doi.org/10.2307/1156807

    Article  Google Scholar 

  • Schlebusch CM, Jakobsson M (2018) Tales of human migration, admixture, and selection in Africa. Annu Rev Genom Hum Genet 19:405–428. https://doi.org/10.1146/annurev-genom-083117-021759

    Article  CAS  Google Scholar 

  • Schlebusch CM et al (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338:374–379. https://doi.org/10.1126/science.1227721

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schuster SC et al (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463:943–947. https://doi.org/10.1038/nature08795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scott-Emuakpor AB (1974) The mutation load in an African population. I. an analysis of consanguineous marriages in Nigeria. Am J Hum Genet 26:674–682

    CAS  PubMed  PubMed Central  Google Scholar 

  • Silano M et al (2007) A decapeptide from durum wheat prevents celiac peripheral blood lymphocytes from activation by gliadin peptides. Pediatr Res 61:67–71. https://doi.org/10.1203/01.pdr.0000250173.88049.79

    Article  CAS  PubMed  Google Scholar 

  • Slatkin M (2008) Linkage disequilibrium–understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9:477–485. https://doi.org/10.1038/nrg2361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sudmant PH et al (2015) An integrated map of structural variation in 2504 human genomes. Nature 526:75–81. https://doi.org/10.1038/nature15394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanner RE (1958) Fertility and child mortality in cousin marriages. A study in a moslem community in east Africa. Eugen Rev 49:197–199

    CAS  PubMed  PubMed Central  Google Scholar 

  • Templeton AR, Read B (1996) Inbreeding, one word, several meanings, much confusion. Biol Conserv 75:91–105

    Google Scholar 

  • Wagh K et al (2012) Lactase persistence and lipid pathway selection in the Maasai. PLoS One 7:e44751. https://doi.org/10.1371/journal.pone.0044751

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang ET et al (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA 103:135–140. https://doi.org/10.1073/pnas.0509691102

    Article  CAS  PubMed  Google Scholar 

  • Weir BS (2012) Estimating F-statistics: a historical view. Br J Philos Sci 79:637–643. https://doi.org/10.1086/667904

    Article  Google Scholar