A SNP panel for identification of DNA and RNA specimens.
Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, BIOS consortium, 't Hoen PAC.
BMC Genomics
19 :
2018
90
22
Genome-wide identification of directed gene networks using large-scale population genomics data.
Luijk R, Dekkers KF, van Iterson M, Arindrarto W, Claringbould A, Hop P, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, Franke L, 't Hoen PAC, Jansen R, van Meurs J, Mei H, Slagboom PE, Heijmans BT, van Zwet EW, BIOS (Biobank-based Integrative Omics Study) Consortium.
Nat Commun
9 :
2018
3097
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Autosomal genetic variation is associated with DNA methylation in regions variably escaping X-chromosome inactivation.
Luijk R, Wu H, Ward-Caviness CK, Hannon E, Carnero-Montoro E, Min JL, Mandaviya P, Müller-Nurasyid M, Mei H, van der Maarel SM, BIOS Consortium, Relton C, Mill J, Waldenberger M, Bell JT, Jansen R, Zhernakova A, Franke L, 't Hoen PAC, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, van Meurs J, Daxinger L, Slagboom PE, van Zwet EW, Heijmans BT.
Nat Commun
9 :
2018
3738
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A linear mixed-model approach to study multivariate gene-environment interactions.
Moore R, Casale FP, Jan Bonder M, Horta D, BIOS Consortium, Franke L, Barroso I, Stegle O.
Nat Genet
51 :
2019
180-186
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Skewed X-inactivation is common in the general female population.
Shvetsova E, Sofronova A, Monajemi R, Gagalova K, Draisma HHM, White SJ, Santen GWE, Chuva de Sousa Lopes SM, Heijmans BT, van Meurs J, Jansen R, Franke L, Kiełbasa SM, den Dunnen JT, 't Hoen PAC, BIOS consortium, GoNL consortium.
Eur J Hum Genet
27 :
2019
455-465
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Epigenome-wide association study of serum cotinine in current smokers reveals novel genetically driven loci.
Gupta R, van Dongen J, Fu Y, Abdellaoui A, Tyndale RF, Velagapudi V, Boomsma DI, Korhonen T, Kaprio J, Loukola A, Ollikainen M.
Clin Epigenetics
11 :
2019
1
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DNA methylation signatures of educational attainment.
van Dongen J, Bonder MJ, Dekkers KF, Nivard MG, van Iterson M, Willemsen G, Beekman M, van der Spek A, van Meurs JBJ, Franke L, Heijmans BT, van Duijn CM, Slagboom PE, Boomsma DI, BIOS consortium.
NPJ Sci Learn
3 :
2018
7
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The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus.
Schlicht K, Nyczka P, Caliebe A, Freitag-Wolf S, Claringbould A, Franke L, Võsa U, BIOS Consortium, Kardia SLR, Smith JA, Zhao W, Gieger C, Peters A, Prokisch H, Strauch K, KORA Study Group, Baurecht H, Weidinger S, Rosenstiel P, Hütt MT, Knecht C, Szymczak S, Krawczak M.
Hum Genet
138 :
2019
375-388
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Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults.
van Dongen J, Zilhão NR, Sugden K, BIOS Consortium, Hannon EJ, Mill J, Caspi A, Agnew-Blais J, Arseneault L, Corcoran DL, Moffitt TE, Poulton R, Franke B, Boomsma DI.
Biol Psychiatry
86 :
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599-607
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RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting.
Jadhav B, Monajemi R, Gagalova KK, Ho D, Draisma HHM, van de Wiel MA, Franke L, Heijmans BT, van Meurs J, Jansen R, GoNL Consortium, BIOS Consortium, 't Hoen PAC, Sharp AJ, Kiełbasa SM.
BMC Biol
17 :
2019
50
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Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies.
van Rooij J, Mandaviya PR, Claringbould A, Felix JF, van Dongen J, Jansen R, Franke L, BIOS consortium, 't Hoen PAC, Heijmans B, van Meurs JBJ.
Genome Biol
20 :
2019
235
23
Genome-wide analysis of constitutional DNA methylation in familial melanoma.
Salgado C, Gruis N, BIOS Consortium, Heijmans BT, Oosting J, van Doorn R.
Clin Epigenetics
12 :
2020
43
3
A Survey of Rare Epigenetic Variation in 23,116 Human Genomes Identifies Disease-Relevant Epivariations and CGG Expansions.
Garg P, Jadhav B, Rodriguez OL, Patel N, Martin-Trujillo A, Jain M, Metsu S, Olsen H, Paten B, Ritz B, Kooy RF, Gecz J, Sharp AJ.
Am J Hum Genet
107 :
2020
654-669
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Correction for both common and rare cell types in blood is important to identify genes that correlate with age.
Pellegrino-Coppola D, Claringbould A, Stutvoet M, BIOS Consortium, Boomsma DI, Ikram MA, Slagboom PE, Westra HJ, Franke L.
BMC Genomics
22 :
2021
184
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Predicting Complex Traits and Exposures From Polygenic Scores and Blood and Buccal DNA Methylation Profiles.
Odintsova VV, Rebattu V, Hagenbeek FA, Pool R, Beck JJ, Ehli EA, van Beijsterveldt CEM, Ligthart L, Willemsen G, de Geus EJC, Hottenga JJ, Boomsma DI, van Dongen J.
Front Psychiatry
12 :
2021
688464
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Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation.
Min JL, Hemani G, Hannon E, Dekkers KF, Castillo-Fernandez J, Luijk R, Carnero-Montoro E, Lawson DJ, Burrows K, Suderman M, Bretherick AD, Richardson TG, Klughammer J, Iotchkova V, Sharp G, Al Khleifat A, Shatunov A, Iacoangeli A, McArdle WL, Ho KM, Kumar A, Söderhäll C, Soriano-Tárraga C, Giralt-Steinhauer E, Kazmi N, Mason D, McRae AF, Corcoran DL, Sugden K, Kasela S, Cardona A, Day FR, Cugliari G, Viberti C, Guarrera S, Lerro M, Gupta R, Bollepalli S, Mandaviya P, Zeng Y, Clarke TK, Walker RM, Schmoll V, Czamara D, Ruiz-Arenas C, Rezwan FI, Marioni RE, Lin T, Awaloff Y, Germain M, Aïssi D, Zwamborn R, van Eijk K, Dekker A, van Dongen J, Hottenga JJ, Willemsen G, Xu CJ, Barturen G, Català-Moll F, Kerick M, Wang C, Melton P, Elliott HR, Shin J, Bernard M, Yet I, Smart M, Gorrie-Stone T, BIOS Consortium, Shaw C, Al Chalabi A, Ring SM, Pershagen G, Melén E, Jiménez-Conde J, Roquer J, Lawlor DA, Wright J, Martin NG, Montgomery GW, Moffitt TE, Poulton R, Esko T, Milani L, Metspalu A, Perry JRB, Ong KK, Wareham NJ, Matullo G, Sacerdote C, Panico S, Caspi A, Arseneault L, Gagnon F, Ollikainen M, Kaprio J, Felix JF, Rivadeneira F, Tiemeier H, van IJzendoorn MH, Uitterlinden AG, Jaddoe VWV, Haley C, McIntosh AM, Evans KL, Murray A, Räikkönen K, Lahti J, Nohr EA, Sørensen TIA, Hansen T, Morgen CS, Binder EB, Lucae S, Gonzalez JR, Bustamante M, Sunyer J, Holloway JW, Karmaus W, Zhang H, Deary IJ, Wray NR, Starr JM, Beekman M, van Heemst D, Slagboom PE, Morange PE, Trégouët DA, Veldink JH, Davies GE, de Geus EJC, Boomsma DI, Vonk JM, Brunekreef B, Koppelman GH, Alarcón-Riquelme ME, Huang RC, Pennell CE, van Meurs J, Ikram MA, Hughes AD, Tillin T, Chaturvedi N, Pausova Z, Paus T, Spector TD, Kumari M, Schalkwyk LC, Visscher PM, Davey Smith G, Bock C, Gaunt TR, Bell JT, Heijmans BT, Mill J, Relton CL.
Nat Genet
53 :
2021
1311-1321
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Identical twins carry a persistent epigenetic signature of early genome programming.
van Dongen J, Gordon SD, McRae AF, Odintsova VV, Mbarek H, Breeze CE, Sugden K, Lundgren S, Castillo-Fernandez JE, Hannon E, Moffitt TE, Hagenbeek FA, van Beijsterveldt CEM, Jan Hottenga J, Tsai PC, BIOS Consortium, Genetics of DNA Methylation Consortium, Min JL, Hemani G, Ehli EA, Paul F, Stern CD, Heijmans BT, Slagboom PE, Daxinger L, van der Maarel SM, de Geus EJC, Willemsen G, Montgomery GW, Reversade B, Ollikainen M, Kaprio J, Spector TD, Bell JT, Mill J, Caspi A, Martin NG, Boomsma DI.
Nat Commun
12 :
2021
5618
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DNA methylation in peripheral tissues and left-handedness.
Odintsova VV, Suderman M, Hagenbeek FA, Caramaschi D, Hottenga JJ, Pool R, BIOS Consortium, Dolan CV, Ligthart L, van Beijsterveldt CEM, Willemsen G, de Geus EJC, Beck JJ, Ehli EA, Cuellar-Partida G, Evans DM, Medland SE, Relton CL, Boomsma DI, van Dongen J.
Sci Rep
12 :
2022
5606
5
Limited evidence for blood eQTLs in human sexual dimorphism.
Porcu E, Claringbould A, Weihs A, Lepik K, BIOS Consortium, Richardson TG, Völker U, Santoni FA, Teumer A, Franke L, Reymond A, Kutalik Z.
Genome Med
14 :
2022
89
4
Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations.
Lepamets M, Auwerx C, Nõukas M, Claringbould A, Porcu E, Kals M, Jürgenson T, Estonian Biobank Research Team, Morris AP, Võsa U, Bochud M, Stringhini S, Wijmenga C, Franke L, Peterson H, Vilo J, Lepik K, Mägi R, Kutalik Z.
HGG Adv
3 :
2022
100133
2
Lipid-induced transcriptomic changes in blood link to lipid metabolism and allergic response.
Dekkers KF, Slieker RC, Ioan-Facsinay A, van Iterson M, BIOS consortium, Ikram MA, van Greevenbroek MMJ, Veldink JH, Franke L, Boomsma DI, Slagboom PE, Jukema JW, Heijmans BT.
Nat Commun
14 :
2023
544
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Effects of smoking on genome-wide DNA methylation profiles: A study of discordant and concordant monozygotic twin pairs.
van Dongen J, Willemsen G, BIOS Consortium, de Geus EJC, Boomsma DI, Neale MC.
Elife
12 :
2023
e83286
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Genome-Wide DNA Methylation Profiles in Whole-Blood and Buccal Samples-Cross-Sectional, Longitudinal, and across Platforms.
Van Asselt AJ, Beck JJ, Finnicum CT, Johnson BN, Kallsen N, Hottenga JJ, de Geus EJC, Bios Consortium, Boomsma DI, Ehli EA, van Dongen J.
Int J Mol Sci
24 :
2023
14640
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Comprehensive evaluation of smoking exposures and their interactions on DNA methylation.
Hoang TT, Lee Y, McCartney DL, Kersten ETG, Page CM, Hulls PM, Lee M, Walker RM, Breeze CE, Bennett BD, Burkholder AB, Ward J, Brantsæter AL, Caspersen IH, Motsinger-Reif AA, Richards M, White JD, Zhao S, Richmond RC, Magnus MC, BIOS Consortium, Koppelman GH, Evans KL, Marioni RE, Håberg SE, London SJ.
EBioMedicine
100 :
2024
104956
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PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs.
Vochteloo M, Deelen P, Vink B, BIOS Consortium, Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L.
Genome Biol
25 :
2024
29
1
Phenotype prediction using biologically interpretable neural networks on multi-cohort multi-omics data.
van Hilten A, van Rooij J, BIOS consortium, Ikram MA, Niessen WJ, van Meurs JBJ, Roshchupkin GV.
NPJ Syst Biol Appl
10 :
2024
81
0
Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation.
Wu J, Palasantzas V, Andreu-Sánchez S, Plösch T, Leonard S, Li S, Bonder MJ, Westra HJ, van Meurs J, Ghanbari M, Franke L, Zhernakova A, Fu J, Hoogerland JA, Zhernakova DV.
Clin Epigenetics
16 :
2024
104
0
A comprehensive map of the aging blood methylome in humans.
Seale K, Teschendorff A, Reiner AP, Voisin S, Eynon N.
Genome Biol
25 :
2024
240
0
