geuvadis_exome August 2012

geuvadis_exome@lists.crg.es

1 participants
3 discussions

by Mathias Brännvall

Dear colleagues, Here at last is the QC-survey for geuvadis. I kindly ask each partner to answer it and send back to me by *11 August* at the latest. As the survey covers both laboratory details and bioinformatics I suggest that each principal investigator at each site delegates the task to the appropriate person(s). For question 11 and 22: You don't have to describe every data analysis pipeline you have, that would be to much to ask. Please choose one or two you use the most and/or one that you have particular expertise in. Please don't hesitate to ask me if there is something that is unclear. Thank you and best summer greetings to all of you. Mathias -- _____________________________________________ Mathias Brännvall, PhD Project coordinator Dept. of Medical Sciences, sect. Molecular Medicine, Uppsala University Akademiska sjukhuset, ing. 70, 3 tr phone: +46-(0)18-6114934 mobile: +46-(0)70-1679446 e-mail: Mathias.Brannvall(a)medsci.uu.se

12 years, 11 months

[Geuvadis_exome] GEUVADIS Meeting and survey to distribute !

by Gabrielle Anne Bertier

Dear all, I remind you that there are just 4 days left before the deadline to register for our next Annual Meeting (preliminary program attached) PS: registration form full link: https://docs.google.com/spreadsheet/viewform?formkey=dEpnY0h6Y2Z3Y291dFhvRz…<https://docs.google.com/spreadsheet/viewform?formkey=dEpnY0h6Y2Z3Y291dFhvRz…> In preparation of the Workshop, and to collect quantitative and qualitative information on the status of NGS in Europe, we have constructed a survey<https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv> to be distributed to all Research and/or clinical institutions using NGS in Europe. The survey covers the following aspects: Technology available (number/type of sequencers, nb of runs, capture method) - Data Use (clinical/research uses) - Patients/participants (origin of samples, consent forms, incidental findings...) - Data storage - Data analysis (general information on analysis pipelines) - Clinical data management - Problems and suggestions. We would highly appreciate if you could distribute this survey to all your relevant colleagues working in such centers, and fill in the survey for your own institution. We'll also send this survey to the European and National Societies of Human Genetics, and the more responses we get the better ! Deadline to respond to the survey: 30th September 2012 Full survey link: https://qtrial.qualtrics.com/SE/?SID=SV_bHJDue550PwdFrv To describe the survey please use freely the following text: ------------------ THE GEUVADIS PROJECT - More information on our website: www.geuvadis.eu<file:///C:\Users\gbertier\Documents\GEUVADIS\Annual%20Meeting%202\www.geuvadis.eu> The latest high-throughput next-generation sequencing technologies allow investigators to sequence entire human genomes and transcriptomes at an affordable price and within a short time frame. An increasing number of research centers in Europe have access to these technologies, in-house or through regional, national and international infrastructures. Storing, disseminating and analysing the large amount of data produced generate major challenges. Tackling these challenges requires extensive exchange of data, information and knowledge between sequencing centers, bio-informatics networks, the medical research community and the industry at the European level. The GEUVADIS (Genetic EUropean VAriation in DISease) Consortium has four main aims: 1. Develop standards in quality control and assessment of sequence data 2. Develop models for sequencing data storage, access and exchange 3. Develop standards for the handling, analysis and interpretation of sequencing data from DNA (and RNA) 4. Develop guidelines on the handling of ethical, legal and social implications of phenotype prediction from sequence variation * PURPOSE OF SURVEY 1. Collect quantitative and qualitative information on the current status of DNA sequence production, storage, exchange and analysis in Europe. 2. Collect feedback from research/clinical centers on their main challenges and difficulties regarding the management of these large data-sets potentially containing important medical information 3. Collect information on local standardization efforts, and avoid duplication of efforts throughout Europe 4. Create a road-map/policy document outlining the necessary steps to take national standards to the European level * POTENTIAL PUBLICATION OF RESULTS 1. Results of this survey will be presented at an internal GEUVADIS workshop, on October 30-31st 2012. 2. We will disseminate the road-map to potential funders (private of public), including the European Commission and other possible national public funders. 3. We will submit an abstract to the Joint Conference of Human Genome Meeting 2013 and 21st International Congress of Genetics. * DEADLINE: 30.09.2012 --------------------- If you have any question or comment regarding the Annual Meeting, the workshop and/or the survey please don't hesitate to contact me. Kind regards, Gabrielle.- Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

13 years, 3 months

[Geuvadis_exome] GEUVADIS - Summer annoucements

by Gabrielle Anne Bertier

Dear all, here are a few announcements for the summer: 1) Report I uploaded and officially sent the new version of the mid-term report to the EC. Let's see if they accept it this time ! 2) Annual Meeting -As you know, our next Annual Meeting will take place in Santiago de Compostela on October 29-31. All information is now available on the dedicated page<http://www.geuvadis.org/group/geuvadis/annual-meeting-2011> of our intranet. Don't forget to register here<https://docs.google.com/spreadsheet/viewform?formkey=dEpnY0h6Y2Z3Y291dFhvRz…> before the end of the month. Note that all labs should be represented by at least one person. - Please note that we will have two Special attendees to our meeting and workshop: - Pui-Yan Kwok (USF) as our Scientific Advisor - Patrik Kolar, head of the personalized medicine unit at the Health directorate of the EC. - We are setting up the workshop on day 2 and 3 of the annual meeting on the following theme: Exome seq data storage, sharing and analysis: from National to European standards. To collect quantitative and qualitative data on NGS data use in Europe, we have set up a survey (word file attached), to be distributed to a maximum of institutions using NGS for research/clinical purposes. We plan to distribute this survey before the end of the month, so please let me know if you have any comment on the content, and if you want access to the online version to have an idea of the format. 3) Events announcements - GEUVADIS/ENGAGE Course announcement, to be passed on to your labs: With sponsoring from the ENGAGE and GEUVADIS consortia, partners EBI and LUMC are organizing a course on RNA-seq data analysis for participants from both EU consortia. The course will be held from December 4-6, 2012 at the EBI campus, in Hinxton, UK. It involves a three-day program with lectures and many hands-on sessions covering the following topics: introduction to RNA-seq technology, quality assessment, alignment tools, statistical analysis of differential expression, eQTL analysis, miRNA-seq and archiving of RNA-seq data. For a full program and speakers, please visit the website: http://www.ebi.ac.uk/training/onsite/121204_ENGAGE.html The course is aimed at PhD students and postdocs that have familiarity with the technology and the biological use cases of high throughput sequencing . Experience in R is desirable. Registration costs including housing and meals are £150. You can register here: http://www.ebi.ac.uk/training/events/121204_Engage.html - ENGAGE Workshop announcement, to be passed on to your labs: We are organizing a scientific conference "From Genetic Discovery to Future Health" as a closure highlight for our EU-funded project the 'European Network for Genetic and Genomic Epidemiology' (ENGAGE Consortium, website: www.euengage.org<http://www.euengage.org/>) to be held on November 15th, 2012 in Rotterdam, the Netherlands. This scientific conference is open to the wider scientific community with aims to (a) share ENGAGE experiences through presenting the project results and (b) involve leaders from related fields in dialogue to maximise the translational opportunities afforded by basic science discovery. Please find attached the conference flyer for details. The participation is free of charge but registration is required prior to the deadline. - Note that I will be out of office until the August 20th, and then from August 31st to September 12th. I wish you a very nice summer, Kind regards, Gabrielle Gabrielle Bertier Scientific Project Manager International and Scientific Affairs CRG, Center for Genomic Regulation Carrer Dr. Aiguader, 88 08003 Barcelona, España Tel: +34933160374 Mobile: +34639960656 email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es> web: www.geuvadis.eu; www.fliact.eu

13 years, 4 months

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geuvadis_exome August 2012