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Volumn 6, Issue , 2015, Pages

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(62)  Allum, Fiona a   Shao, Xiaojian a   Guénard, Frédéric b   Simon, Marie Michelle a   Busche, Stephan a   Caron, Maxime a   Lambourne, John a   Lessard, Julie c   Tandre, Karolina d   Hedman, Åsa K d   Kwan, Tony a   Ge, Bing a   Rönnblom, Lars d,e,f,g   McCarthy, Mark I h   Deloukas, Panos i   Richmond, Todd j   Burgess, Daniel j   Spector, Timothy D k   Tchernof, André c   Marceau, Simon c   more..


Author keywords

[No Author keywords available]

Indexed keywords

CD36 ANTIGEN; HIGH DENSITY LIPOPROTEIN CHOLESTEROL; TRIACYLGLYCEROL;

EID: 84931274676     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms8211     Document Type: Article
Times cited : (84)

References (41)
  • 1
    • 84863986133 scopus 로고    scopus 로고
    • Functions of dna methylation: Islands, start sites, gene bodies and beyond
    • Jones, P. A. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat. Rev. Genet. 13, 484-492 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 484-492
    • Jones, P.A.1
  • 2
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of dna elements in the human genome
    • Consortium, E. P. et al. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1
  • 3
    • 84890172667 scopus 로고    scopus 로고
    • Global analysis of dna methylation variation in adipose tissue from twins reveals links to disease-Associated variants in distal regulatory elements
    • Grundberg, E. et al. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-Associated variants in distal regulatory elements. Am. J. Hum. Genet. 93, 876-890 (2013).
    • (2013) Am. J. Hum. Genet. , vol.93 , pp. 876-890
    • Grundberg, E.1
  • 4
    • 79953706343 scopus 로고    scopus 로고
    • Tobaccosmoking-related differential dna methylation: 27k discovery and replication
    • Breitling, L. P., Yang, R., Korn, B., Burwinkel, B., & Brenner, H. Tobaccosmoking-related differential DNA methylation: 27K discovery and replication. Am. J. Hum. Genet. 88, 450-457 (2011).
    • (2011) Am. J. Hum. Genet. , vol.88 , pp. 450-457
    • Breitling, L.P.1    Yang, R.2    Korn, B.3    Burwinkel, B.4    Brenner, H.5
  • 5
    • 84897489039 scopus 로고    scopus 로고
    • The relationship between dna methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
    • Wagner, J. R. et al. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol. 15, R37 (2014).
    • (2014) Genome Biol. , vol.15 , pp. R37
    • Wagner, J.R.1
  • 6
    • 84897452599 scopus 로고    scopus 로고
    • Genome-wide dna methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion
    • Dayeh, T. et al. Genome-wide DNA methylation analysis of human pancreatic islets from type 2 diabetic and non-diabetic donors identifies candidate genes that influence insulin secretion. PLoS Genet. 10, -1004160 (2014).
    • (2014) PLoS Genet. , vol.10 , pp. 1004160
    • Dayeh, T.1
  • 7
    • 84873576566 scopus 로고    scopus 로고
    • Epigenome-wide association data implicate dna methylation as an intermediary of genetic risk in rheumatoid arthritis
    • Liu, Y. et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat. Biotechnol. 31, 142-147 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 142-147
    • Liu, Y.1
  • 8
    • 84921316380 scopus 로고    scopus 로고
    • Dna methylation and body-mass index: A genome-wide analysis
    • Dick, K. J. et al. DNA methylation and body-mass index: a genome-wide analysis. Lancet 383, 1990-1998 (2014).
    • (2014) Lancet , vol.383 , pp. 1990-1998
    • Dick, K.J.1
  • 9
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-Associated variation in regulatory dna
    • Maurano, M. T. et al. Systematic localization of common disease-Associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1
  • 10
    • 79955583542 scopus 로고    scopus 로고
    • Mapping and analysis of chromatin state dynamics in nine human cell types
    • Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
    • (2011) Nature , vol.473 , pp. 43-49
    • Ernst, J.1
  • 11
    • 84882884517 scopus 로고    scopus 로고
    • Charting a dynamic dna methylation landscape of the human genome
    • Ziller, M. J. et al. Charting a dynamic DNA methylation landscape of the human genome. Nature 500, 477-481 (2013).
    • (2013) Nature , vol.500 , pp. 477-481
    • Ziller, M.J.1
  • 12
    • 69749092741 scopus 로고    scopus 로고
    • High definition profiling of mammalian dna methylation by array capture and single molecule bisulfite sequencing
    • Hodges, E. et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 19, 1593-1605 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1593-1605
    • Hodges, E.1
  • 13
    • 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, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 14
    • 58249088335 scopus 로고    scopus 로고
    • Duodenal switch improved standard biliopancreatic diversion: A retrospective study
    • Marceau, P. et al. Duodenal switch improved standard biliopancreatic diversion: a retrospective study. Surg. Obes. Relat. Dis. 5, 43-47 (2009).
    • (2009) Surg. Obes. Relat. Dis. , vol.5 , pp. 43-47
    • Marceau, P.1
  • 15
    • 0035897696 scopus 로고    scopus 로고
    • Expert panel on detection, e. Executive summary of the third report of the national cholesterol education program (ncep) expert panel on detection, evaluation, and treatment of high blood cholesterol in adults adult treatment panel iii)
    • Expert Panel on Detection, E. Executive summary of the third report of the National Cholesterol Education Program (NCEP) expert panel on Detection, Evaluation, and Treatment of high blood cholesterol in adults (Adult Treatment Panel III). JAMA 285, 2486 (2001).
    • (2001) JAMA , vol.285 , pp. 2486
  • 16
    • 84886834154 scopus 로고    scopus 로고
    • Identification of active regulatory regions from dna methylation data
    • Burger, L., Gaidatzis, D., Schübeler, D., & Stadler, M. B. Identification of active regulatory regions from DNA methylation data. Nucleic Acids Res. 41, -155-155 (2013).
    • (2013) Nucleic Acids Res. , vol.41 , pp. 155-155
    • Burger, L.1    Gaidatzis, D.2    Schübeler, D.3    Stadler, M.B.4
  • 17
    • 84990924267 scopus 로고    scopus 로고
    • Functional normalization of 450k methylation array data improves replication in large cancer studies
    • Fortin, J.-P. et al. Functional normalization of 450k methylation array data improves replication in large cancer studies. bioRxiv 15, 503 (2014).
    • (2014) BioRxiv , vol.15 , pp. 503
    • Fortin, J.-P.1
  • 19
    • 0035670640 scopus 로고    scopus 로고
    • Are twins and singletons comparable? A study of disease-related and lifestyle characteristics in adult women
    • Andrew, T. et al. Are twins and singletons comparable? A study of disease-related and lifestyle characteristics in adult women. Twin Res. 4, 464-477 (2001).
    • (2001) Twin Res. , vol.4 , pp. 464-477
    • Andrew, T.1
  • 20
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin dna-binding proteins and nucleosome position
    • Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 21
    • 67649216515 scopus 로고    scopus 로고
    • Cd36, a scavenger receptor involved in immunity, metabolism, angiogenesis, and behavior
    • Silverstein, R. L., & Febbraio, M. CD36, a scavenger receptor involved in immunity, metabolism, angiogenesis, and behavior. Sci. Signal. 2, r-3 (2009).
    • (2009) Sci. Signal. , vol.2 , pp. r-3
    • Silverstein, R.L.1    Febbraio, M.2
  • 23
    • 34547451564 scopus 로고    scopus 로고
    • Molecular basis of human cd36 gene mutations
    • Rać, M. E., Safranow, K., & Poncyljusz, W. Molecular basis of human CD36 gene mutations. Mol. Med. 13, 288 (2007).
    • (2007) Mol. Med. , vol.13 , pp. 288
    • Rać, M.E.1    Safranow, K.2    Poncyljusz, W.3
  • 24
    • 84902257688 scopus 로고    scopus 로고
    • Circulating scd36 is associated with unhealthy fat distribution and elevated circulating triglycerides in morbidly obese individuals
    • Knøsgaard, L., Thomsen, S., Støckel, M., Vestergaard, H., & Handberg, A. Circulating sCD36 is associated with unhealthy fat distribution and elevated circulating triglycerides in morbidly obese individuals. Nutr. Diabetes 4, -114 (2014).
    • (2014) Nutr. Diabetes , vol.4 , pp. 114
    • Knøsgaard, L.1    Thomsen, S.2    Støckel, M.3    Vestergaard, H.4    Handberg, A.5
  • 25
    • 84878828157 scopus 로고    scopus 로고
    • Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations
    • Coram, M. A. et al. Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. Am. J. Hum. Genet. 92, 904-916 (2013).
    • (2013) Am. J. Hum. Genet. , vol.92 , pp. 904-916
    • Coram, M.A.1
  • 26
    • 79960556965 scopus 로고    scopus 로고
    • Epigenome-wide association studies for common human diseases
    • Rakyan, V. K., Down, T. A., Balding, D. J., & Beck, S. Epigenome-wide association studies for common human diseases. Nat. Rev. Genet. 12, 529-541 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 529-541
    • Rakyan, V.K.1    Down, T.A.2    Balding, D.J.3    Beck, S.4
  • 28
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen, Y. et al. A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116-120 (2012).
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1
  • 29
    • 84868134071 scopus 로고    scopus 로고
    • Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing
    • 21.23. 21-21.23.
    • Johnson, M. D., Mueller, M., Game, L., & Aitman, T. J. Single nucleotide analysis of cytosine methylation by whole-genome shotgun bisulfite sequencing. Curr. Protoc. Mol. Biol. 21.23. 21-21.23. 28 (2012).
    • (2012) Curr. Protoc. Mol. Biol. , pp. 28
    • Johnson, M.D.1    Mueller, M.2    Game, L.3    Aitman, T.J.4
  • 30
    • 0031826757 scopus 로고    scopus 로고
    • Biliopancreatic diversion with duodenal switch
    • Marceau, P. et al. Biliopancreatic diversion with duodenal switch. World. J. Surg. 22, 947-954 (1998).
    • (1998) World. J. Surg. , vol.22 , pp. 947-954
    • Marceau, P.1
  • 31
    • 6344260341 scopus 로고    scopus 로고
    • A survey of genes differentially expressed in subcutaneous and visceral adipose tissue in men
    • Vohl, M. C. et al. A survey of genes differentially expressed in subcutaneous and visceral adipose tissue in men. Obes. Res. 12, 1217-1222 (2004).
    • (2004) Obes. Res. , vol.12 , pp. 1217-1222
    • Vohl, M.C.1
  • 32
    • 0015058419 scopus 로고
    • Determination of plasma glucose by hexokinase-glucose-6-phosphate dehydrogenase method
    • Richterich, R., & Dauwalder, H. [Determination of plasma glucose by hexokinase-glucose-6-phosphate dehydrogenase method]. Schweiz. Med. Wochenschr. 101, 615-618 (1971).
    • (1971) Schweiz. Med. Wochenschr. , vol.101 , pp. 615-618
    • Richterich, R.1    Dauwalder, H.2
  • 33
    • 84863565553 scopus 로고    scopus 로고
    • Bis-snp: Combined dna methylation and snp calling for bisulfite-seq data
    • Liu, Y., Siegmund, K. D., Laird, P. W., & Berman, B. P. Bis-SNP: combined DNA METHYLATION and SNP calling for bisulfite-seq data. Genome Biol. 13, R61 (2012).
    • (2012) Genome Biol. , vol.13 , pp. R61
    • Liu, Y.1    Siegmund, K.D.2    Laird, P.W.3    Berman, B.P.4
  • 34
    • 33745297228 scopus 로고    scopus 로고
    • Regional differences in adipose tissue metabolism in women minor effect of obesity and body fat distribution
    • Tchernof, A. et al. Regional differences in adipose tissue metabolism in women minor effect of obesity and body fat distribution. Diabetes 55, 1353-1360 (2006).
    • (2006) Diabetes , vol.55 , pp. 1353-1360
    • Tchernof, A.1
  • 35
    • 84864483625 scopus 로고    scopus 로고
    • Robina: A user-friendly, integrated software solution for rna-seq-based transcriptomics
    • Lohse, M. et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. W622-W627
    • Lohse, M.1
  • 36
    • 84866127830 scopus 로고    scopus 로고
    • Identifying chip-seq enrichment using macs
    • Feng, J., Liu, T., Qin, B., Zhang, Y., & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728-1740 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 1728-1740
    • Feng, J.1    Liu, T.2    Qin, B.3    Zhang, Y.4    Liu, X.S.5
  • 37
    • 84866742598 scopus 로고    scopus 로고
    • Association of lipa gene polymorphisms with obesityrelated metabolic complications among severely obese patients
    • Guenard, F. et al. Association of LIPA gene polymorphisms with obesityrelated metabolic complications among severely obese patients. Obesity 20, 2075-2082 (2012).
    • (2012) Obesity , vol.20 , pp. 2075-2082
    • Guenard, F.1
  • 38
    • 84887129039 scopus 로고    scopus 로고
    • Line-1 methylation in visceral adipose tissue of severely obese individuals is associated with metabolic syndrome status and related phenotypes
    • Turcot, V. et al. LINE-1 methylation in visceral adipose tissue of severely obese individuals is associated with metabolic syndrome status and related phenotypes. Clin. Epigenet. 4, 10 (2012).
    • (2012) Clin. Epigenet. , vol.4 , pp. 10
    • Turcot, V.1
  • 39
    • 65449136284 scopus 로고    scopus 로고
    • Tophat: Discovering splice junctions with rna-seq
    • Trapnell, C., Pachter, L., & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 40
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short dna sequences to the human genome
    • Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 41
    • 77958471357 scopus 로고    scopus 로고
    • Differential expression analysis for sequence count data
    • Anders, S., & Huber, W. Differential expression analysis for sequence count data. Genome Biol. 11, R106 (2010).
    • (2010) Genome Biol. , vol.11 , pp. R106
    • Anders, S.1    Huber, W.2


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