메뉴 건너뛰기




Volumn 167, Issue 3, 2016, Pages 643-656.e17

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

Author keywords

eQTL mapping; evolution; immune response; monocytes; natural selection; Neandertal admixture; population genetics; transcriptional responses

Indexed keywords

INTERLEUKIN 12P40; TOLL LIKE RECEPTOR 1; TOLL LIKE RECEPTOR 2; TOLL LIKE RECEPTOR 4; TOLL LIKE RECEPTOR 7; TOLL LIKE RECEPTOR 8; RNA; TOLL LIKE RECEPTOR;

EID: 84992187388     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.09.024     Document Type: Article
Times cited : (317)

References (84)
  • 2
    • 69749099417 scopus 로고    scopus 로고
    • Fast model-based estimation of ancestry in unrelated individuals
    • Alexander, D.H., Novembre, J., Lange, K., Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19 (2009), 1655–1664.
    • (2009) Genome Res. , vol.19 , pp. 1655-1664
    • Alexander, D.H.1    Novembre, J.2    Lange, K.3
  • 4
    • 67650102353 scopus 로고    scopus 로고
    • Scavenger receptors: role in innate immunity and microbial pathogenesis
    • Areschoug, T., Gordon, S., Scavenger receptors: role in innate immunity and microbial pathogenesis. Cell. Microbiol. 11 (2009), 1160–1169.
    • (2009) Cell. Microbiol. , vol.11 , pp. 1160-1169
    • Areschoug, T.1    Gordon, S.2
  • 8
    • 84856387609 scopus 로고    scopus 로고
    • Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection
    • Barreiro, L.B., Tailleux, L., Pai, A.A., Gicquel, B., Marioni, J.C., Gilad, Y., Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection. Proc. Natl. Acad. Sci. USA 109 (2012), 1204–1209.
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 1204-1209
    • Barreiro, L.B.1    Tailleux, L.2    Pai, A.A.3    Gicquel, B.4    Marioni, J.C.5    Gilad, Y.6
  • 11
    • 84908378499 scopus 로고    scopus 로고
    • The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease
    • Brinkworth, J.F., Barreiro, L.B., The contribution of natural selection to present-day susceptibility to chronic inflammatory and autoimmune disease. Curr. Opin. Immunol. 31 (2014), 66–78.
    • (2014) Curr. Opin. Immunol. , vol.31 , pp. 66-78
    • Brinkworth, J.F.1    Barreiro, L.B.2
  • 12
    • 84930336482 scopus 로고    scopus 로고
    • Host genetic variation influences gene expression response to rhinovirus infection
    • Çalışkan, M., Baker, S.W., Gilad, Y., Ober, C., Host genetic variation influences gene expression response to rhinovirus infection. PLoS Genet., 11, 2015, e1005111.
    • (2015) PLoS Genet. , vol.11 , pp. e1005111
    • Çalışkan, M.1    Baker, S.W.2    Gilad, Y.3    Ober, C.4
  • 15
    • 77649260327 scopus 로고    scopus 로고
    • Population differentiation as a test for selective sweeps
    • Chen, H., Patterson, N., Reich, D., Population differentiation as a test for selective sweeps. Genome Res. 20 (2010), 393–402.
    • (2010) Genome Res. , vol.20 , pp. 393-402
    • Chen, H.1    Patterson, N.2    Reich, D.3
  • 16
    • 84954244556 scopus 로고    scopus 로고
    • Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human Toll-like receptors
    • Dannemann, M., Andrés, A.M., Kelso, J., Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human Toll-like receptors. Am. J. Hum. Genet. 98 (2016), 22–33.
    • (2016) Am. J. Hum. Genet. , vol.98 , pp. 22-33
    • Dannemann, M.1    Andrés, A.M.2    Kelso, J.3
  • 17
    • 84871952176 scopus 로고    scopus 로고
    • Improved whole-chromosome phasing for disease and population genetic studies
    • Delaneau, O., Zagury, J.F., Marchini, J., Improved whole-chromosome phasing for disease and population genetic studies. Nat. Methods 10 (2013), 5–6.
    • (2013) Nat. Methods , vol.10 , pp. 5-6
    • Delaneau, O.1    Zagury, J.F.2    Marchini, J.3
  • 20
    • 84926632357 scopus 로고    scopus 로고
    • Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues
    • Ernst, J., Kellis, M., Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat. Biotechnol. 33 (2015), 364–376.
    • (2015) Nat. Biotechnol. , vol.33 , pp. 364-376
    • Ernst, J.1    Kellis, M.2
  • 21
    • 84904893878 scopus 로고    scopus 로고
    • Genetics of gene expression in immunity to infection
    • Fairfax, B.P., Knight, J.C., Genetics of gene expression in immunity to infection. Curr. Opin. Immunol. 30 (2014), 63–71.
    • (2014) Curr. Opin. Immunol. , vol.30 , pp. 63-71
    • Fairfax, B.P.1    Knight, J.C.2
  • 23
    • 34248573475 scopus 로고    scopus 로고
    • A multiethnic, multicenter cohort of patients with systemic lupus erythematosus (SLE) as a model for the study of ethnic disparities in SLE
    • Fernández, M., Alarcón, G.S., Calvo-Alén, J., Andrade, R., McGwin, G. Jr., Vilá, L.M., Reveille, J.D., LUMINA Study Group. A multiethnic, multicenter cohort of patients with systemic lupus erythematosus (SLE) as a model for the study of ethnic disparities in SLE. Arthritis Rheum. 57 (2007), 576–584.
    • (2007) Arthritis Rheum. , vol.57 , pp. 576-584
    • Fernández, M.1    Alarcón, G.S.2    Calvo-Alén, J.3    Andrade, R.4    McGwin, G.5    Vilá, L.M.6    Reveille, J.D.7
  • 24
    • 84880076219 scopus 로고    scopus 로고
    • Gene expression drives local adaptation in humans
    • Fraser, H.B., Gene expression drives local adaptation in humans. Genome Res. 23 (2013), 1089–1096.
    • (2013) Genome Res. , vol.23 , pp. 1089-1096
    • Fraser, H.B.1
  • 26
    • 84901440603 scopus 로고    scopus 로고
    • Human genome variability, natural selection and infectious diseases
    • Fumagalli, M., Sironi, M., Human genome variability, natural selection and infectious diseases. Curr. Opin. Immunol. 30 (2014), 9–16.
    • (2014) Curr. Opin. Immunol. , vol.30 , pp. 9-16
    • Fumagalli, M.1    Sironi, M.2
  • 27
    • 33644525606 scopus 로고    scopus 로고
    • The human specific CCR1 antagonist CP-481,715 inhibits cell infiltration and inflammatory responses in human CCR1 transgenic mice
    • Gladue, R.P., Cole, S.H., Roach, M.L., Tylaska, L.A., Nelson, R.T., Shepard, R.M., McNeish, J.D., Ogborne, K.T., Neote, K.S., The human specific CCR1 antagonist CP-481,715 inhibits cell infiltration and inflammatory responses in human CCR1 transgenic mice. J. Immunol. 176 (2006), 3141–3148.
    • (2006) J. Immunol. , vol.176 , pp. 3141-3148
    • Gladue, R.P.1    Cole, S.H.2    Roach, M.L.3    Tylaska, L.A.4    Nelson, R.T.5    Shepard, R.M.6    McNeish, J.D.7    Ogborne, K.T.8    Neote, K.S.9
  • 29
    • 67349176068 scopus 로고    scopus 로고
    • Genetics in geographically structured populations: defining, estimating and interpreting F(ST)
    • Holsinger, K.E., Weir, B.S., Genetics in geographically structured populations: defining, estimating and interpreting F(ST). Nat. Rev. Genet. 10 (2009), 639–650.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 639-650
    • Holsinger, K.E.1    Weir, B.S.2
  • 30
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • Howie, B.N., Donnelly, P., Marchini, J., A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet., 5, 2009, e1000529.
    • (2009) PLoS Genet. , vol.5 , pp. e1000529
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 33
    • 40449127195 scopus 로고    scopus 로고
    • Chemokine receptor CX3CR1 mediates skin wound healing by promoting macrophage and fibroblast accumulation and function
    • Ishida, Y., Gao, J.L., Murphy, P.M., Chemokine receptor CX3CR1 mediates skin wound healing by promoting macrophage and fibroblast accumulation and function. J. Immunol. 180 (2008), 569–579.
    • (2008) J. Immunol. , vol.180 , pp. 569-579
    • Ishida, Y.1    Gao, J.L.2    Murphy, P.M.3
  • 35
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W.E., Li, C., Rabinovic, A., Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8 (2007), 118–127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 36
    • 84901014110 scopus 로고    scopus 로고
    • Natural selection and infectious disease in human populations
    • Karlsson, E.K., Kwiatkowski, D.P., Sabeti, P.C., Natural selection and infectious disease in human populations. Nat. Rev. Genet. 15 (2014), 379–393.
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 379-393
    • Karlsson, E.K.1    Kwiatkowski, D.P.2    Sabeti, P.C.3
  • 37
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S.L., TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, 2013, R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 38
    • 84920895781 scopus 로고    scopus 로고
    • Negative regulation of melanoma differentiation-associated gene 5 (MDA5)-dependent antiviral innate immune responses by Arf-like protein 5B
    • Kitai, Y., Takeuchi, O., Kawasaki, T., Ori, D., Sueyoshi, T., Murase, M., Akira, S., Kawai, T., Negative regulation of melanoma differentiation-associated gene 5 (MDA5)-dependent antiviral innate immune responses by Arf-like protein 5B. J. Biol. Chem. 290 (2015), 1269–1280.
    • (2015) J. Biol. Chem. , vol.290 , pp. 1269-1280
    • Kitai, Y.1    Takeuchi, O.2    Kawasaki, T.3    Ori, D.4    Sueyoshi, T.5    Murase, M.6    Akira, S.7    Kawai, T.8
  • 41
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: an R package for weighted correlation network analysis
    • Langfelder, P., Horvath, S., WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 9, 2008, 559.
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 44
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H., A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27 (2011), 2987–2993.
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 45
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 51
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
    • McLaren, W., Pritchard, B., Rios, D., Chen, Y., Flicek, P., Cunningham, F., Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26 (2010), 2069–2070.
    • (2010) Bioinformatics , vol.26 , pp. 2069-2070
    • McLaren, W.1    Pritchard, B.2    Rios, D.3    Chen, Y.4    Flicek, P.5    Cunningham, F.6
  • 52
    • 84875617235 scopus 로고    scopus 로고
    • Neandertal origin of genetic variation at the cluster of OAS immunity genes
    • Mendez, F.L., Watkins, J.C., Hammer, M.F., Neandertal origin of genetic variation at the cluster of OAS immunity genes. Mol. Biol. Evol. 30 (2013), 798–801.
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 798-801
    • Mendez, F.L.1    Watkins, J.C.2    Hammer, M.F.3
  • 53
    • 79952902493 scopus 로고    scopus 로고
    • From expression QTLs to personalized transcriptomics
    • Montgomery, S.B., Dermitzakis, E.T., From expression QTLs to personalized transcriptomics. Nat. Rev. Genet. 12 (2011), 277–282.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 277-282
    • Montgomery, S.B.1    Dermitzakis, E.T.2
  • 56
    • 84882449068 scopus 로고    scopus 로고
    • Genetic insights into common pathways and complex relationships among immune-mediated diseases
    • Parkes, M., Cortes, A., van Heel, D.A., Brown, M.A., Genetic insights into common pathways and complex relationships among immune-mediated diseases. Nat. Rev. Genet. 14 (2013), 661–673.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 661-673
    • Parkes, M.1    Cortes, A.2    van Heel, D.A.3    Brown, M.A.4
  • 58
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • Patterson, N., Price, A.L., Reich, D., Population structure and eigenanalysis. PLoS Genet., 2, 2006, e190.
    • (2006) PLoS Genet. , vol.2 , pp. e190
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 59
    • 84898723939 scopus 로고    scopus 로고
    • Joint analysis of functional genomic data and genome-wide association studies of 18 human traits
    • Pickrell, J.K., Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am. J. Hum. Genet. 94 (2014), 559–573.
    • (2014) Am. J. Hum. Genet. , vol.94 , pp. 559-573
    • Pickrell, J.K.1
  • 62
    • 84876833883 scopus 로고    scopus 로고
    • Type I IFN triggers RIG-I/TLR3/NLRP3-dependent inflammasome activation in influenza A virus infected cells
    • Pothlichet, J., Meunier, I., Davis, B.K., Ting, J.P., Skamene, E., von Messling, V., Vidal, S.M., Type I IFN triggers RIG-I/TLR3/NLRP3-dependent inflammasome activation in influenza A virus infected cells. PLoS Pathog., 9, 2013, e1003256.
    • (2013) PLoS Pathog. , vol.9 , pp. e1003256
    • Pothlichet, J.1    Meunier, I.2    Davis, B.K.3    Ting, J.P.4    Skamene, E.5    von Messling, V.6    Vidal, S.M.7
  • 64
    • 84875415375 scopus 로고    scopus 로고
    • Population genetic tools for dissecting innate immunity in humans
    • Quintana-Murci, L., Clark, A.G., Population genetic tools for dissecting innate immunity in humans. Nat. Rev. Immunol. 13 (2013), 280–293.
    • (2013) Nat. Rev. Immunol. , vol.13 , pp. 280-293
    • Quintana-Murci, L.1    Clark, A.G.2
  • 65
    • 35548956882 scopus 로고    scopus 로고
    • Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases
    • Quintana-Murci, L., Alcaïs, A., Abel, L., Casanova, J.L., Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases. Nat. Immunol. 8 (2007), 1165–1171.
    • (2007) Nat. Immunol. , vol.8 , pp. 1165-1171
    • Quintana-Murci, L.1    Alcaïs, A.2    Abel, L.3    Casanova, J.L.4
  • 67
    • 60149084519 scopus 로고    scopus 로고
    • PASTAA: identifying transcription factors associated with sets of co-regulated genes
    • Roider, H.G., Manke, T., O'Keeffe, S., Vingron, M., Haas, S.A., PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics 25 (2009), 435–442.
    • (2009) Bioinformatics , vol.25 , pp. 435-442
    • Roider, H.G.1    Manke, T.2    O'Keeffe, S.3    Vingron, M.4    Haas, S.A.5
  • 69
    • 84865777825 scopus 로고    scopus 로고
    • Linking disease associations with regulatory information in the human genome
    • Schaub, M.A., Boyle, A.P., Kundaje, A., Batzoglou, S., Snyder, M., Linking disease associations with regulatory information in the human genome. Genome Res. 22 (2012), 1748–1759.
    • (2012) Genome Res. , vol.22 , pp. 1748-1759
    • Schaub, M.A.1    Boyle, A.P.2    Kundaje, A.3    Batzoglou, S.4    Snyder, M.5
  • 70
    • 84861153094 scopus 로고    scopus 로고
    • Matrix eQTL: ultra fast eQTL analysis via large matrix operations
    • Shabalin, A.A., Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics 28 (2012), 1353–1358.
    • (2012) Bioinformatics , vol.28 , pp. 1353-1358
    • Shabalin, A.A.1
  • 72
    • 33846631884 scopus 로고    scopus 로고
    • Common genetic variants account for differences in gene expression among ethnic groups
    • Spielman, R.S., Bastone, L.A., Burdick, J.T., Morley, M., Ewens, W.J., Cheung, V.G., Common genetic variants account for differences in gene expression among ethnic groups. Nat. Genet. 39 (2007), 226–231.
    • (2007) Nat. Genet. , vol.39 , pp. 226-231
    • Spielman, R.S.1    Bastone, L.A.2    Burdick, J.T.3    Morley, M.4    Ewens, W.J.5    Cheung, V.G.6
  • 74
    • 45449097447 scopus 로고    scopus 로고
    • fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
    • Strimmer, K., fdrtool: a versatile R package for estimating local and tail area-based false discovery rates. Bioinformatics 24 (2008), 1461–1462.
    • (2008) Bioinformatics , vol.24 , pp. 1461-1462
    • Strimmer, K.1
  • 75
    • 84863556835 scopus 로고    scopus 로고
    • Evolution and functional impact of rare coding variation from deep sequencing of human exomes
    • Tennessen, J.A., Bigham, A.W., O'Connor, T.D., Fu, W., Kenny, E.E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., et al. Broad GO Seattle GO, NHLBI Exome Sequencing Project. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337 (2012), 64–69.
    • (2012) Science , vol.337 , pp. 64-69
    • Tennessen, J.A.1    Bigham, A.W.2    O'Connor, T.D.3    Fu, W.4    Kenny, E.E.5    Gravel, S.6    McGee, S.7    Do, R.8    Liu, X.9    Jun, G.10
  • 78
    • 84946481204 scopus 로고    scopus 로고
    • WASP: allele-specific software for robust molecular quantitative trait locus discovery
    • van de Geijn, B., McVicker, G., Gilad, Y., Pritchard, J.K., WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat. Methods 12 (2015), 1061–1063.
    • (2015) Nat. Methods , vol.12 , pp. 1061-1063
    • van de Geijn, B.1    McVicker, G.2    Gilad, Y.3    Pritchard, J.K.4
  • 79
    • 84943808524 scopus 로고    scopus 로고
    • Small Amounts of Archaic Admixture Provide Big Insights into Human History
    • Vattathil, S., Akey, J.M., Small Amounts of Archaic Admixture Provide Big Insights into Human History. Cell 163 (2015), 281–284.
    • (2015) Cell , vol.163 , pp. 281-284
    • Vattathil, S.1    Akey, J.M.2
  • 80
    • 84897583960 scopus 로고    scopus 로고
    • Resurrecting surviving Neandertal lineages from modern human genomes
    • Vernot, B., Akey, J.M., Resurrecting surviving Neandertal lineages from modern human genomes. Science 343 (2014), 1017–1021.
    • (2014) Science , vol.343 , pp. 1017-1021
    • Vernot, B.1    Akey, J.M.2
  • 81
    • 84924280285 scopus 로고    scopus 로고
    • Complex history of admixture between modern humans and Neandertals
    • Vernot, B., Akey, J.M., Complex history of admixture between modern humans and Neandertals. Am. J. Hum. Genet. 96 (2015), 448–453.
    • (2015) Am. J. Hum. Genet. , vol.96 , pp. 448-453
    • Vernot, B.1    Akey, J.M.2
  • 83
    • 84865074382 scopus 로고    scopus 로고
    • RSeQC: quality control of RNA-seq experiments
    • Wang, L., Wang, S., Li, W., RSeQC: quality control of RNA-seq experiments. Bioinformatics 28 (2012), 2184–2185.
    • (2012) Bioinformatics , vol.28 , pp. 2184-2185
    • Wang, L.1    Wang, S.2    Li, W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.