Changes between Initial Version and Version 1 of BIOS_bios


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Timestamp:
Sep 19, 2016 2:12:50 PM (8 years ago)
Author:
rick
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  • BIOS_bios

    v1 v1  
     1== BIOS ==
     2The 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]]
     3The 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.
     4
     5== Access to BIOS data ==
     6There are two ways to access BIOS data:
     7
     8=== 1.  Download of selected data through EGA ===
     9RNA-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.
     10
     11=== 2.  Analyze all data on a centralized computational facility ===
     12For 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.
     13
     14== Publications acknowledging BIOS ==
     15Latest update: [http://www.bbmri.nl/wp-content/uploads/2015/10/BIOSpapersacknowledging.pdf September 2015]
     16
     17=== Management team ===
     18Bastiaan T. Heijmans (chair)^1^, Peter A.C. ’t Hoen^2^, Joyce van Meurs^3^, Rick Jansen^5^, Lude Franke^6^.
     19=== Cohort collection ===
     20Dorret 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).
     21=== Data Generation ===
     22Joyce 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^.
     23=== Data management and computational infrastructure ===
     24Hailiang 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^.
     25=== Data Analysis Group ===
     26Lude 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]]
     271.      Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
     282.      Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
     293.      Department of Internal Medicine, ErasmusMC, Rotterdam, The Netherlands
     304.      Department of Genetic Epidemiology, ErasmusMC, Rotterdam, The Netherlands
     315.      Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
     326.      Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
     337.      Department of Biological Psychology, VU University Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, The Netherlands
     348.      Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, The Netherlands
     359.      Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, The Netherlands
     3610.     Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
     3711.     Department of Epidemiology, ErasmusMC, Rotterdam, The Netherlands
     3812.     Sequence Analysis Support Core, Leiden University Medical Center, Leiden, The Netherlands
     3913.     SURFsara, Amsterdam, the Netherlands
     4014.     Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
     4115.     Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
     42