geuvadis_rnaseq October 2012

geuvadis_rnaseq@lists.crg.es

7 participants
6 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, 5 months

[Geuvadis_rnaseq] Geuvadis RNAseq author list: proposal

by Manolis Dermitzakis

Dear all, Please find attached a proposal for the author list of the main RNAseq paper. Please let me know your comments/additions/objections Many thanks, Manolis ------------------------------------------ Emmanouil (Manolis) Dermitzakis, PhD Louis-Jeantet Professor Department of Genetic Medicine and Development University of Geneva Medical School 1 Rue Michel-Servet (CMU office 9088) Geneva 1211 Switzerland Email: emmanouil.dermitzakis(a)unige.ch Tel: +41 (0) 22 379 5483 Fax: +41 (0) 22 379 5706 website: http://funpopgen.unige.ch/ Admin assistant: Ancilla Stefani, Tel: +41 22 379 5551 e-mail: Ancilla.Stefani(a)unige.ch ------------------------------------------ Tuuli Lappalainen wrote: > Hello, > > Here are the minutes of the call. The next call will be in one week, > November 1st. > > - deadline to send text and figures is *this Friday, *so Tuuli is > expecting a lot of emails. Thanks to those of you who have already > sent material. > - Tuuli presented the draft of the ASHG poster; discussion of recent > analyses. The miRNA analysis is challenging - there are some signals > that are interesting but few very strong and expected genome-wide trends. > - Jean presented slides of sQTL analysis; plenty of interesting > signals and ideas how to take this forward. His sQTLs are running for > the Europeans combined, and they will be then compared to > gene-RPKM-eQTLs that Tuuli calculated. > > best, > Tuuli > > Tuuli Lappalainen, PhD > Department of Genetic Medicine and Development > University of Geneva Medical School > CMU / Rue Michel-Servet 1 > 1211 Geneva 4 > Switzerland > Tel. +41-(0)22-3795550 > tuuli.lappalainen(a)unige.ch > On /25/1012 12:54 PM, Tuuli Lappalainen wrote: >> Hello, >> >> We'll have a Geuvadis analysis group call today Oct 25th at 2pm CET. >> Apologies for the late reminder. >> >> On the agenda: >> - ASHG poster >> - analysis updates >> - sQTL presentation from Jean >> >> best, >> Tuuli >> >> Call details: >> Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> >> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> >> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> >> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> >> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> >> United Kingdom +44 203 370 57 19 >> <tel:%2B44%20203%20370%2057%2019> >> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> >> /Access code: 611683 / >> >> >> >> -- >> Tuuli Lappalainen, PhD >> Department of Genetic Medicine and Development >> University of Geneva Medical School >> CMU / Rue Michel-Servet 1 >> 1211 Geneva 4 >> Switzerland >> Tel. +41-(0)22-3795550 >> tuuli.lappalainen(a)unige.ch >> >> >> _______________________________________________ >> Geuvadis_rna_analysis mailing list >> Geuvadis_rna_analysis(a)lists.crg.es >> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis >> > > ------------------------------------------------------------------------ > > _______________________________________________ > Geuvadis_rna_analysis mailing list > Geuvadis_rna_analysis(a)lists.crg.es > http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis >

12 years, 7 months

[Geuvadis_rnaseq] Please forward - Petition to protect EU science budget

by Gabrielle Anne Bertier

Dear GEUVADIS partners, I would like to draw your attention to the petition from Anna Leptin. We highly encourage everybody to sign up and to forward it to colleagues at your institute and outside. http://www.no-cuts-on-research.eu Thanks Best 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 -----Original Message----- From: Maria Leptin [mailto:maria.leptin@embo.org] Sent: martes, 23 de octubre de 2012 02:13 p.m. Subject: Please forward - Petition to protect EU science budget Dear colleagues, The discussions at the next summit of the European Union heads of state or government, which is scheduled for 22 and 23 November, will be decisive in determining the EU research budget for the next seven years. Several Member States are demanding severe cuts on the total EU budget and research will have to compete with other policy priorities. This is a time when we, the scientific community, should act together and make our case to protect research funding, including that of the European Research Council (ERC), from cuts. Decisions will be prepared in discussions among politicians at the national level. All of us must look for opportunities to affect these decisions and send a strong signal to the heads of state or government. An open letter signed by European Nobel laureates has been published in top European newspapers this week. The impact of this letter will be increased if it is followed by a mobilization of the national scientific communities. To keep the momentum going, an online petition has been launched: http://www.no-cuts-on-research.eu I would like to ask you to sign it and to encourage all your colleagues to do likewise. Note that in the past, less than 30 000 scientists signed the largest petition for a European scientific cause compared to the hundreds of thousands of signatures on petitions from other groups of society. We must do better than that. This action is coordinated by the Initiative for Science in Europe (ise(a)i-se.org<mailto:ise@i-se.org>; www.initiative-science-europe.org<http://www.initiative-science-europe.org>), of which EMBO is a member. Please contact Wolfgang Eppenschwandtner, Executive Coordinator of the ISE if you have any questions or suggestions. Best regards, Maria Leptin Director EMBO - excellence in life sciences Meyerhofstr. 1 69117 Heidelberg, Germany tel +49-6221-8891-102 fax +49-6221-8891-202 maria.leptin(a)embo.org<mailto:maria.leptin@embo.org>

12 years, 7 months

[Geuvadis_rnaseq] Geuvadis TC October 19th at 4pm CET

by Tuuli Lappalainen

Dear all, We will have a Geuvadis RNAseq workpackage call on Friday October 19th at 4pm CET. Agenda: - Update on the analysis - Outlines of the papers: - main paper - QC companion - splicing companion - loss-of-function companion - Publication and authorship - AOB Call details: Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022> United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089> /Access code: 611683 /People calling from CRG: Recently there have been some problems in calling to the Spanish number above. The problem seems to be in your end, and Gabrielle is checking what can be done. If it doesn't work, please call e.g. to the German number. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetic Medicine and Development University of Geneva Medical School CMU / Rue Michel-Servet 1 1211 Geneva 4 Switzerland Tel. +41-(0)22-3795550 tuuli.lappalainen(a)unige.ch

12 years, 7 months

[Geuvadis_rnaseq] REMINDER: GEUVADIS survey DEADLINE tomorrow

by Gabrielle Anne Bertier

This is to remind you that the deadline for the survey is tomorrow. Here are the results so far per country: Denmark 1 Estonia 1 France 2 Germany 4 Ireland 1 Slovenia 1 Spain 8 Sweden 6 Switzerland 7 the Netherlands 5 Turkey 4 We still have no response from many European countries, which lowers the value of our survey. Please get in touch with me if you know specific people who have not filled in the survey and can do so quickly. You'll find the names of the institutes who have answered below, Kind regards, Gabrielle Dept. Medical Sciences, Molecular Medicine national centre for medical genetics The EStonian Genome Center of University of Tartu Diagnostikcentrum, Clinical Pathology and Clinical Genetics University of Lausanne CHUV Uppsala University; SNP&SEQ Technology platform + Uppsala Genome Center University Hospital Copenhagen Institute of Medical Genetics at the University of Zurich Kantonsspital Olten Division of Human Genetics Leiden University Medical Center Center for Human Genetics and Laboratory Medicine Institut Central des Hopitaux Valaisans-RSV Humangenetics İstanbul University Institute of Experimental Medicine Max Planck Institute for Molecular Genetics UMC Utrecht Leiden University Medical Center TUBITAK, MAM, Genetic Engineering and Biotechnology Institute VUMC Lund University Diabetes Centre Science For Life Laboratory Department of Medical genetics & Inserm U 910 Helmholtz Zentrum Zentrum München Hôpital Timone Enfants et faculté de Médecine Center for Genomic Regulation INGEMM Fundacion Investigación Clínico de Valencia-INCLIVA Instituto de Salud Carlos III Uppsala University. Immunology, Genetics and Pathology / SciLifeLab Hospital Universitario Ramon y Cajal Hospital de Terrassa Complexo Hospitalario Universitario de Santiago Clinical institute of medical genetics Ljubljana Maastricht UMC+, Department of Clinical Genetics Sabanci University Institute of Medical Genetics and Applied Genomics, University of Tuebingen Hospital San Pedro de Alcántara TUBITAK-BILGEM From: Gabrielle Anne Bertier Sent: 28 September, 2012 18:12 PM To: 'geuvadis_partners(a)lists.crg.es'; 'geuvadis_exome(a)lists.crg.es'; 'geuvadis_wpl(a)lists.crg.es'; 'geuvadis_rnaseq(a)lists.crg.es'; 'geuvadis_rna_analysis(a)lists.crg.es' Cc: Xavier Estivill; Michela Bertero; 'Bea Sobrino' Subject: IMPORTANT NOTICE: GEUVADIS survey DEADLINE EXTENDED Dear all, I remind you that we would highly appreciate if you could fill in, and distribute our survey on NGS to all your relevant colleagues. Note that we've extended the deadline to the 10th October 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

12 years, 7 months

[Geuvadis_rnaseq] GEUVADIS RNAseq paper -- TC doodle

by Gabrielle Anne Bertier

Dear all, Please fill in the following doodle for the next GEUVADIS RNAseq TC on the project's publication: http://www.doodle.com/pdeyynfz3rnwvtaf?lt=2<http://www.doodle.com/pdeyynfz3rnwvtaf?lt=1> Preliminary agenda would be: - outlines of the main paper and the QC companion paper - practicalities of publication - other companion papers 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

12 years, 7 months

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geuvadis_rnaseq October 2012