메뉴 건너뛰기




Volumn 101, Issue 1, 2017, Pages 75-86

Integrative Genetic and Epigenetic Analysis Uncovers Regulatory Mechanisms of Autoimmune Disease

Author keywords

DNase I hypersensitivity site; fine mapping; genome wide association study; non coding variation

Indexed keywords

ARTICLE; AUTOIMMUNE DISEASE; BASE PAIRING; DNA FOOTPRINTING; DNASE I HYPERSENSITIVE SITE; EPIGENETICS; GENE EXPRESSION; GENE IDENTIFICATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC REGULATION; HUMAN; MATHEMATICAL PARAMETERS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ALLELE; ANTIBODY SPECIFICITY; CHROMOSOMAL MAPPING; CHROMOSOME 6; GENETIC EPIGENESIS; GENETIC PREDISPOSITION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; INFLAMMATION; METABOLISM; REGULATORY SEQUENCE; REPRODUCIBILITY; RISK FACTOR;

EID: 85026696904     PISSN: 00029297     EISSN: 15376605     Source Type: Journal    
DOI: 10.1016/j.ajhg.2017.06.001     Document Type: Article
Times cited : (24)

References (59)
  • 1
    • 57749193136 scopus 로고    scopus 로고
    • Detecting shared pathogenesis from the shared genetics of immune-related diseases
    • Zhernakova, A., van Diemen, C.C., Wijmenga, C., Detecting shared pathogenesis from the shared genetics of immune-related diseases. Nat. Rev. Genet. 10 (2009), 43–55.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 43-55
    • Zhernakova, A.1    van Diemen, C.C.2    Wijmenga, C.3
  • 2
    • 77950355043 scopus 로고    scopus 로고
    • Unraveling the genetics of autoimmunity
    • Zenewicz, L.A., Abraham, C., Flavell, R.A., Cho, J.H., Unraveling the genetics of autoimmunity. Cell 140 (2010), 791–797.
    • (2010) Cell , vol.140 , pp. 791-797
    • Zenewicz, L.A.1    Abraham, C.2    Flavell, R.A.3    Cho, J.H.4
  • 3
    • 84873086126 scopus 로고    scopus 로고
    • Chromatin marks identify critical cell types for fine mapping complex trait variants
    • Trynka, G., Sandor, C., Han, B., Xu, H., Stranger, B.E., Liu, X.S., Raychaudhuri, S., Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. 45 (2013), 124–130.
    • (2013) Nat. Genet. , vol.45 , pp. 124-130
    • Trynka, G.1    Sandor, C.2    Han, B.3    Xu, H.4    Stranger, B.E.5    Liu, X.S.6    Raychaudhuri, S.7
  • 6
    • 84891697734 scopus 로고    scopus 로고
    • Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits
    • Corradin, O., Saiakhova, A., Akhtar-Zaidi, B., Myeroff, L., Willis, J., Cowper-Sal lari, R., Lupien, M., Markowitz, S., Scacheri, P.C., Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res. 24 (2014), 1–13.
    • (2014) Genome Res. , vol.24 , pp. 1-13
    • Corradin, O.1    Saiakhova, A.2    Akhtar-Zaidi, B.3    Myeroff, L.4    Willis, J.5    Cowper-Sal lari, R.6    Lupien, M.7    Markowitz, S.8    Scacheri, P.C.9
  • 8
    • 85000443086 scopus 로고    scopus 로고
    • Partitioning heritability by functional annotation using genome-wide association summary statistics
    • Finucane, H.K., Bulik-Sullivan, B., Gusev, A., Trynka, G., Reshef, Y., Loh, P.R., Anttila, V., Xu, H., Zang, C., Farh, K., et al. ReproGen Consortium Schizophrenia Working Group of the Psychiatric Genomics Consortium, RACI Consortium. Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat. Genet. 47 (2015), 1228–1235.
    • (2015) Nat. Genet. , vol.47 , pp. 1228-1235
    • Finucane, H.K.1    Bulik-Sullivan, B.2    Gusev, A.3    Trynka, G.4    Reshef, Y.5    Loh, P.R.6    Anttila, V.7    Xu, H.8    Zang, C.9    Farh, K.10
  • 9
    • 84922273141 scopus 로고    scopus 로고
    • Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases
    • Gusev, A., Lee, S.H., Trynka, G., Finucane, H., Vilhjálmsson, B.J., Xu, H., Zang, C., Ripke, S., Bulik-Sullivan, B., Stahl, E., et al. Schizophrenia Working Group of the Psychiatric Genomics Consortium SWE-SCZ Consortium Schizophrenia Working Group of the Psychiatric Genomics Consortium, SWE-SCZ Consortium. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am. J. Hum. Genet. 95 (2014), 535–552.
    • (2014) Am. J. Hum. Genet. , vol.95 , pp. 535-552
    • Gusev, A.1    Lee, S.H.2    Trynka, G.3    Finucane, H.4    Vilhjálmsson, B.J.5    Xu, H.6    Zang, C.7    Ripke, S.8    Bulik-Sullivan, B.9    Stahl, E.10
  • 11
    • 84938982145 scopus 로고    scopus 로고
    • Leveraging functional-annotation data in trans-ethnic fine-mapping studies
    • Kichaev, G., Pasaniuc, B., Leveraging functional-annotation data in trans-ethnic fine-mapping studies. Am. J. Hum. Genet. 97 (2015), 260–271.
    • (2015) Am. J. Hum. Genet. , vol.97 , pp. 260-271
    • Kichaev, G.1    Pasaniuc, B.2
  • 12
    • 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
  • 14
    • 84887058596 scopus 로고    scopus 로고
    • Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
    • Beecham, A.H., Patsopoulos, N.A., Xifara, D.K., Davis, M.F., Kemppinen, A., Cotsapas, C., Shah, T.S., Spencer, C., Booth, D., Goris, A., et al. International Multiple Sclerosis Genetics Consortium (IMSGC) Wellcome Trust Case Control Consortium 2 (WTCCC2), International IBD Genetics Consortium (IIBDGC). Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45 (2013), 1353–1360.
    • (2013) Nat. Genet. , vol.45 , pp. 1353-1360
    • Beecham, A.H.1    Patsopoulos, N.A.2    Xifara, D.K.3    Davis, M.F.4    Kemppinen, A.5    Cotsapas, C.6    Shah, T.S.7    Spencer, C.8    Booth, D.9    Goris, A.10
  • 16
    • 84877123760 scopus 로고    scopus 로고
    • Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
    • Sheffield, N.C., Thurman, R.E., Song, L., Safi, A., Stamatoyannopoulos, J.A., Lenhard, B., Crawford, G.E., Furey, T.S., Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 23 (2013), 777–788.
    • (2013) Genome Res. , vol.23 , pp. 777-788
    • Sheffield, N.C.1    Thurman, R.E.2    Song, L.3    Safi, A.4    Stamatoyannopoulos, J.A.5    Lenhard, B.6    Crawford, G.E.7    Furey, T.S.8
  • 21
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright, A.J., Van Dongen, S., Ouzounis, C.A., An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30 (2002), 1575–1584.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 22
    • 84255194782 scopus 로고    scopus 로고
    • Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci
    • Patsopoulos, N.A., Esposito, F., Reischl, J., Lehr, S., Bauer, D., Heubach, J., Sandbrink, R., Pohl, C., Edan, G., Kappos, L., et al. Bayer Pharma MS Genetics Working Group Steering Committees of Studies Evaluating IFNβ-1b and a CCR1-Antagonist ANZgene Consortium GeneMSA, International Multiple Sclerosis Genetics Consortium. Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. Ann. Neurol. 70 (2011), 897–912.
    • (2011) Ann. Neurol. , vol.70 , pp. 897-912
    • Patsopoulos, N.A.1    Esposito, F.2    Reischl, J.3    Lehr, S.4    Bauer, D.5    Heubach, J.6    Sandbrink, R.7    Pohl, C.8    Edan, G.9    Kappos, L.10
  • 23
    • 84940771118 scopus 로고    scopus 로고
    • Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations
    • Liu, J.Z., van Sommeren, S., Huang, H., Ng, S.C., Alberts, R., Takahashi, A., Ripke, S., Lee, J.C., Jostins, L., Shah, T., et al. International Multiple Sclerosis Genetics Consortium, International IBD Genetics Consortium. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47 (2015), 979–986.
    • (2015) Nat. Genet. , vol.47 , pp. 979-986
    • Liu, J.Z.1    van Sommeren, S.2    Huang, H.3    Ng, S.C.4    Alberts, R.5    Takahashi, A.6    Ripke, S.7    Lee, J.C.8    Jostins, L.9    Shah, T.10
  • 25
    • 82255192188 scopus 로고    scopus 로고
    • Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease
    • Trynka, G., Hunt, K.A., Bockett, N.A., Romanos, J., Mistry, V., Szperl, A., Bakker, S.F., Bardella, M.T., Bhaw-Rosun, L., Castillejo, G., et al. Spanish Consortium on the Genetics of Coeliac Disease (CEGEC) PreventCD Study Group, Wellcome Trust Case Control Consortium (WTCCC). Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 43 (2011), 1193–1201.
    • (2011) Nat. Genet. , vol.43 , pp. 1193-1201
    • Trynka, G.1    Hunt, K.A.2    Bockett, N.A.3    Romanos, J.4    Mistry, V.5    Szperl, A.6    Bakker, S.F.7    Bardella, M.T.8    Bhaw-Rosun, L.9    Castillejo, G.10
  • 27
    • 84878739093 scopus 로고    scopus 로고
    • Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis
    • Hinks, A., Cobb, J., Marion, M.C., Prahalad, S., Sudman, M., Bowes, J., Martin, P., Comeau, M.E., Sajuthi, S., Andrews, R., et al. Boston Children's JIA Registry British Society of Paediatric and Adolescent Rheumatology (BSPAR) Study Group Childhood Arthritis Prospective Study (CAPS) Childhood Arthritis Response to Medication Study (CHARMS) German Society for Pediatric Rheumatology (GKJR) JIA Gene Expression Study NIAMS JIA Genetic Registry TREAT Study, United Kingdom Juvenile Idiopathic Arthritis Genetics Consortium (UKJIAGC). Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. Nat. Genet. 45 (2013), 664–669.
    • (2013) Nat. Genet. , vol.45 , pp. 664-669
    • Hinks, A.1    Cobb, J.2    Marion, M.C.3    Prahalad, S.4    Sudman, M.5    Bowes, J.6    Martin, P.7    Comeau, M.E.8    Sajuthi, S.9    Andrews, R.10
  • 28
    • 84870512735 scopus 로고    scopus 로고
    • Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity
    • Tsoi, L.C., Spain, S.L., Knight, J., Ellinghaus, E., Stuart, P.E., Capon, F., Ding, J., Li, Y., Tejasvi, T., Gudjonsson, J.E., et al. Collaborative Association Study of Psoriasis (CASP) Genetic Analysis of Psoriasis Consortium Psoriasis Association Genetics Extension, Wellcome Trust Case Control Consortium 2. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat. Genet. 44 (2012), 1341–1348.
    • (2012) Nat. Genet. , vol.44 , pp. 1341-1348
    • Tsoi, L.C.1    Spain, S.L.2    Knight, J.3    Ellinghaus, E.4    Stuart, P.E.5    Capon, F.6    Ding, J.7    Li, Y.8    Tejasvi, T.9    Gudjonsson, J.E.10
  • 29
    • 84894288992 scopus 로고    scopus 로고
    • Genetics of rheumatoid arthritis contributes to biology and drug discovery
    • Okada, Y., Wu, D., Trynka, G., Raj, T., Terao, C., Ikari, K., Kochi, Y., Ohmura, K., Suzuki, A., Yoshida, S., et al. RACI consortium, GARNET consortium. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506 (2014), 376–381.
    • (2014) Nature , vol.506 , pp. 376-381
    • Okada, Y.1    Wu, D.2    Trynka, G.3    Raj, T.4    Terao, C.5    Ikari, K.6    Kochi, Y.7    Ohmura, K.8    Suzuki, A.9    Yoshida, S.10
  • 31
    • 84942244702 scopus 로고    scopus 로고
    • International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways
    • Cordell, H.J., Han, Y., Mells, G.F., Li, Y., Hirschfield, G.M., Greene, C.S., Xie, G., Juran, B.D., Zhu, D., Qian, D.C., et al. Canadian-US PBC Consortium Italian PBC Genetics Study Group, UK-PBC Consortium. International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways. Nat. Commun., 6, 2015, 8019.
    • (2015) Nat. Commun. , vol.6 , pp. 8019
    • Cordell, H.J.1    Han, Y.2    Mells, G.F.3    Li, Y.4    Hirschfield, G.M.5    Greene, C.S.6    Xie, G.7    Juran, B.D.8    Zhu, D.9    Qian, D.C.10
  • 33
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Royal Stat. Soc. B 57 (1995), 289–300.
    • (1995) J. Royal Stat. Soc. B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 34
    • 85013155806 scopus 로고    scopus 로고
    • Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types
    • Chun, S., Casparino, A., Patsopoulos, N.A., Croteau-Chonka, D.C., Raby, B.A., De Jager, P.L., Sunyaev, S.R., Cotsapas, C., Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat. Genet. 49 (2017), 600–605.
    • (2017) Nat. Genet. , vol.49 , pp. 600-605
    • Chun, S.1    Casparino, A.2    Patsopoulos, N.A.3    Croteau-Chonka, D.C.4    Raby, B.A.5    De Jager, P.L.6    Sunyaev, S.R.7    Cotsapas, C.8
  • 36
  • 37
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: automating chromatin-state discovery and characterization
    • Ernst, J., Kellis, M., ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9 (2012), 215–216.
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 38
    • 79960279940 scopus 로고    scopus 로고
    • Promise and pitfalls of the Immunochip
    • Cortes, A., Brown, M.A., Promise and pitfalls of the Immunochip. Arthritis Res. Ther., 13, 2011, 101.
    • (2011) Arthritis Res. Ther. , vol.13 , pp. 101
    • Cortes, A.1    Brown, M.A.2
  • 39
    • 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
  • 41
    • 84937424402 scopus 로고    scopus 로고
    • Disentangling the effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex-trait loci
    • Trynka, G., Westra, H.J., Slowikowski, K., Hu, X., Xu, H., Stranger, B.E., Klein, R.J., Han, B., Raychaudhuri, S., Disentangling the effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex-trait loci. Am. J. Hum. Genet. 97 (2015), 139–152.
    • (2015) Am. J. Hum. Genet. , vol.97 , pp. 139-152
    • Trynka, G.1    Westra, H.J.2    Slowikowski, K.3    Hu, X.4    Xu, H.5    Stranger, B.E.6    Klein, R.J.7    Han, B.8    Raychaudhuri, S.9
  • 43
    • 84964772502 scopus 로고    scopus 로고
    • Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci
    • Ellinghaus, D., Jostins, L., Spain, S.L., Cortes, A., Bethune, J., Han, B., Park, Y.R., Raychaudhuri, S., Pouget, J.G., Hübenthal, M., et al. International IBD Genetics Consortium (IIBDGC) International Genetics of Ankylosing Spondylitis Consortium (IGAS) International PSC Study Group (IPSCSG) Genetic Analysis of Psoriasis Consortium (GAPC), Psoriasis Association Genetics Extension (PAGE). Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat. Genet. 48 (2016), 510–518.
    • (2016) Nat. Genet. , vol.48 , pp. 510-518
    • Ellinghaus, D.1    Jostins, L.2    Spain, S.L.3    Cortes, A.4    Bethune, J.5    Han, B.6    Park, Y.R.7    Raychaudhuri, S.8    Pouget, J.G.9    Hübenthal, M.10
  • 45
    • 84923946495 scopus 로고    scopus 로고
    • LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
    • Bulik-Sullivan, B.K., Loh, P.R., Finucane, H.K., Ripke, S., Yang, J., Patterson, N., Daly, M.J., Price, A.L., Neale, B.M., Schizophrenia Working Group of the Psychiatric Genomics Consortium. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47 (2015), 291–295.
    • (2015) Nat. Genet. , vol.47 , pp. 291-295
    • Bulik-Sullivan, B.K.1    Loh, P.R.2    Finucane, H.K.3    Ripke, S.4    Yang, J.5    Patterson, N.6    Daly, M.J.7    Price, A.L.8    Neale, B.M.9
  • 49
    • 50549096379 scopus 로고    scopus 로고
    • Genetic influence on immune phenotype revealed strain-specific variations in peripheral blood lineages
    • Petkova, S.B., Yuan, R., Tsaih, S.W., Schott, W., Roopenian, D.C., Paigen, B., Genetic influence on immune phenotype revealed strain-specific variations in peripheral blood lineages. Physiol. Genomics 34 (2008), 304–314.
    • (2008) Physiol. Genomics , vol.34 , pp. 304-314
    • Petkova, S.B.1    Yuan, R.2    Tsaih, S.W.3    Schott, W.4    Roopenian, D.C.5    Paigen, B.6
  • 51
    • 84884592445 scopus 로고    scopus 로고
    • Genic intolerance to functional variation and the interpretation of personal genomes
    • Petrovski, S., Wang, Q., Heinzen, E.L., Allen, A.S., Goldstein, D.B., Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet., 9, 2013, e1003709.
    • (2013) PLoS Genet. , vol.9 , pp. e1003709
    • Petrovski, S.1    Wang, Q.2    Heinzen, E.L.3    Allen, A.S.4    Goldstein, D.B.5
  • 55
  • 56
    • 83455238470 scopus 로고    scopus 로고
    • IL-19 as a potential therapeutic in autoimmune and inflammatory diseases
    • Azuma, Y.T., Nakajima, H., Takeuchi, T., IL-19 as a potential therapeutic in autoimmune and inflammatory diseases. Curr. Pharm. Des. 17 (2011), 3776–3780.
    • (2011) Curr. Pharm. Des. , vol.17 , pp. 3776-3780
    • Azuma, Y.T.1    Nakajima, H.2    Takeuchi, T.3
  • 58
    • 84895858942 scopus 로고    scopus 로고
    • A general framework for estimating the relative pathogenicity of human genetic variants
    • Kircher, M., Witten, D.M., Jain, P., O'Roak, B.J., Cooper, G.M., Shendure, J., A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46 (2014), 310–315.
    • (2014) Nat. Genet. , vol.46 , pp. 310-315
    • Kircher, M.1    Witten, D.M.2    Jain, P.3    O'Roak, B.J.4    Cooper, G.M.5    Shendure, J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.