The mission of the BIOS Consortium is to create a large-scale data infrastructure and to bring together BBMRI researchers focusing on integrative omics studies in Dutch Biobanks.

The advent of the genome-wide association study (GWAS) led to the successful identification of thousands of variants that are robustly associated with complex disease phenotypes. Dutch biobanks played a substantial role in these discoveries. For most of these variants, however, the mechanisms through which they contribute to these phenotypes remain unknown. The BIOS Consortium applies a functional genomics approach that integrates genome-wide genetic data with data on the epigenome and transcriptome to elucidate these mechanisms. Over 4000 samples from BBMRI-NL biobanks with in-depth information on disease phenotypes and GWAS data are being enriched with RNA-sequencing and genome-wide DNA methylation data. The same is true for samples with whole-genome sequencing data from GoNL. This unique data infrastructure provides a powerful platform to evaluate key questions in integrative omics from establishing comprehensive eQTL and meQTL catalogues to linking molecular pathways across omics levels to phenotypic outcomes.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

12 Datasets 29 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001001622	BBMRI - BIOS project - Freeze 1 - Fastq files	Illumina HiSeq 2000	2199
EGAD00001001623	BBMRI - BIOS project - Freeze 1 - Bam files		2117
EGAD00001003757	BBMRI - BIOS project - Freeze 2 - Fastq files	Illumina HiSeq 2000	3686
EGAD00001003758	BBMRI - BIOS project - Freeze 2 - Bam files	Illumina HiSeq 2000	3686
EGAD00001003784	BBMRI - BIOS project - Freeze 2 - Bam files - unrelated samples	Illumina HiSeq 2000	3559
EGAD00001003785	BBMRI - BIOS project - Freeze 2 - Fastq files - unrelated samples	Illumina HiSeq 2000	3559
EGAD00001003786	BBMRI - BIOS project - Freeze 2 - Bam files - GoNL samples	Illumina HiSeq 2000	420
EGAD00001003787	BBMRI - BIOS project - Freeze 2 - Fastq files - GoNL samples	Illumina HiSeq 2000	420
EGAD00001003937	BBMRI - BIOS project - Freeze 2 - Bam files - Imprinting analysis	Illumina HiSeq 2000	131
EGAD00010000887	Freeze 1 of the RP3 project	Illumina Human Methylation 450k BeadChip	3898
EGAD00010001416	BBMRI - BIOS project - Freeze 2 - methylation	Illumina Human Methylation 450k BeadChip	4386
EGAD00010001420	Read counts determined using HTSeq-count for the BBMRI BIOS Freeze 2 RNAseq data	RNAseq	3560

Publications	Citations
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	23
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	14
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	14
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	78
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	82
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	20
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	31
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	3
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: 2019 599-607	25
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	16
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	4
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	32
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	5
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	12
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	200
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	23
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	6
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	5
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	4
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	4
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	5
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	2
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	3
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	3
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	2
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
Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study. Demirkan A, van Dongen J, Finnicum CT, Westra HJ, Jankipersadsing S, Willemsen G, Ijzerman RG, Boomsma DI, Ehli EA, Bonder MJ, Fu J, Franke L, Wijmenga C, de Geus EJC, Kurilshikov A, Zhernakova A. BMC Genomics 25: 2024 1224	0