Changes between Initial Version and Version 1 of BIOS_bios

Timestamp:

Sep 19, 2016 2:12:50 PM (8 years ago)

Author:

rick

Comment:

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BIOS_bios

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+== BIOS ==
+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. [[BR]]
+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 have been enriched with RNA-sequencing (>15 M paired end reads) and genome-wide DNA methylation data (Illumina 450k arrays). 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.
+
+== Access to BIOS data ==
+There are two ways to access BIOS data:
+
+=== 1.  Download of selected data through EGA ===
+RNA-seq, DNA methylation, sex, age and cell count data that has been analyzed in publications can be requested and downloaded from The European Genome-phenome Archive (EGA). The advantage is that data can be downloaded to own computational facilities, but not all data can be accessed (e.g. SNPs). [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOS_DATA_ACCESS_POLICY_CONDITIONS_v4.docx Click here] to download the document for BIOS data requests through EGA. The document includes the data sharing policies.
+
+=== 2.  Analyze all data on a centralized computational facility ===
+For BBMRI-NL researchers, all data shared by participating biobanks including genome-wide SNP data, limited phenotypes, RNA-seq and DNA methylation on all individuals can be analyzed on centralized computational facilities, namely the !LifeScience Grid and the SurfSARA High Performance Computing cloud (https://userinfo.surfsara.nl/systems/grid/new-users). The advantage of this approach is that all available data can be analyzed (including those with a privacy aspect), but the data cannot be downloaded and a relatively strict security protocol has to be adopted. Please, fill out this [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSdataaccessrequest.doc form] if you wish to request access to BIOS data at the SurfSARA servers. To complete this request, you will also need to sign the [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSCodeOfConduct.pdf BIOS Code Of Conduct]. [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSrequestsoverview2015-Sep.pdf Click here] for an overview of current data requests.
+
+== Publications acknowledging BIOS == 
+Latest update: [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSpapersacknowledging.pdf September 2015]
+
+=== Management team ===
+Bastiaan T. Heijmans (chair)^1^, Peter A.C. ’t Hoen^2^, Joyce van Meurs^3^, Rick Jansen^5^, Lude Franke^6^.
+=== Cohort collection ===
+Dorret I. Boomsma^7^, René Pool^7^, Jenny van Dongen^7^, Jouke J. Hottenga^7^ (Netherlands Twin Register); Marleen MJ van Greevenbroek^8^, Coen D.A. Stehouwer^8^, Carla J.H. van der Kallen^8^, Casper G. Schalkwijk^8^ (Cohort study on Diabetes and Atherosclerosis Maastricht); Cisca Wijmenga^6^, Lude Franke^6^, Sasha Zhernakova^6^, Ettje F. Tigchelaar^6^ (!LifeLines Deep); P. Eline Slagboom^1^, Marian Beekman^1^, Joris Deelen^1^, Diana van Heemst^9^ (Leiden Longevity Study); Jan H. Veldink10, Leonard H. van den Berg10(Prospective ALS Study Netherlands); Cornelia M. van Duijn4, Bert A. Hofman11, Aaron Isaacs4, André G. Uitterlinden3 (Rotterdam Study).
+=== Data Generation ===
+Joyce van Meurs (Chair)^3^, P. Mila Jhamai^3^, Michael Verbiest^3^, H. Eka D. Suchiman^1^, Marijn Verkerk^3^, Ruud van der Breggen^1^, Jeroen van Rooij^3^, Nico Lakenberg^1^.
+=== Data management and computational infrastructure ===
+Hailiang Mei (Chair)^12^, Maarten van Iterson^1^, Michiel van Galen^2^, Jan Bot^13^, Dasha V. Zhernakova^6^, Rick Jansen^5^, Peter van ’t Hof^12^, Patrick Deelen^6^, Irene Nooren^13^, Peter A.C. ’t Hoen^2^, Bastiaan T. Heijmans^1^, Matthijs Moed^1^.
+=== Data Analysis Group ===
+Lude Franke (Co-Chair)^6^, Martijn Vermaat^2^, Dasha V. Zhernakova^6^, René Luijk^1^, Marc Jan Bonder^6^, Maarten van Iterson^1^, Patrick Deelen^6^, Freerk van Dijk^14^, Michiel van Galen^2^, Wibowo Arindrarto^12^, Szymon M. Kielbasa^15^, Morris A. Swertz^14^, Erik. W van Zwet^15^, Rick Jansen^5^, Peter-Bram ’t Hoen (Co-Chair)^2^, Bastiaan T. Heijmans (Co-Chair)^1^.[[BR]]
+1.      Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
+2.      Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
+3.      Department of Internal Medicine, ErasmusMC, Rotterdam, The Netherlands
+4.      Department of Genetic Epidemiology, ErasmusMC, Rotterdam, The Netherlands
+5.      Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
+6.      Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
+7.      Department of Biological Psychology, VU University Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
+8.      Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, The Netherlands
+9.      Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
+10.     Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
+11.     Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
+12.     Sequence Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
+13.     SURFsara, Amsterdam, the Netherlands
+14.     Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
+15.     Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
+