geuvadis_rnaseq August 2012

geuvadis_rnaseq@lists.crg.es

2 participants
5 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

11 years, 9 months

[Geuvadis_rnaseq] 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

12 years

[Geuvadis_rnaseq] Geuvadis RNAseq poster at ASHG

by Tuuli Lappalainen

Dear all, For you information, the Geuvadis RNAseq abstracts didn't unfortunately get accepted as platform presentations at the ASHG meeting in San Francisco - I will be presenting a poster on the main project, and Manny Rivas will also have a poster on loss-of-function analyses. 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 -------- Original Message -------- Subject: ASHG 2012: Abstract Assignment/Programming Information Poster Authors Date: Tue, 31 Jul 2012 11:02:09 -0400 From: ASHG Meetings <ashgmeetings(a)ashg.org> Organization: The American Society of Human Genetics To: Tuuli.Lappalainen(a)unige.ch ASHG EMAIL <http://www.ashg.org/cgi-bin/rda.pl?u=100&e=1080> July 31, 2012 Dear Tuuli Lappalainen: This confirms your abstract has been ACCEPTED for a *POSTER* presentation at the 62nd American Society of Human Genetics Annual Meeting in San Francisco, California, November 6-10, 2012. _Please review all information in this email as it contains important details of your assignment_. Please print and bring this e-mail with you to the meeting. _*Accessing Your Poster Assignment*_ You may access your poster presentation assignment day and time by clicking on Abstract Assignment <http://www.ashg.org/cgi-bin/rda.pl?u=101&e=1080> on the ASHG 2012 Web site. All poster presentations will take place inside the Moscone Center, Exhibit Halls ABC on the Lower Level. *We do not accept requests to change the day of presentation* and it is no longer possible to withdraw your abstract. If you are *unable to present* on the day assigned, please ask a co-author or colleague to present on your behalf and notify the ASHG Management Office at ashgmeetings(a)ashg.org <mailto:ashgmeetings@ashg.org> of the presenter change so that a notation can be included in the program addendum. *_Program/Abstract/Board Number:_* The letters *W*, *T*, or *F* of the program/abstract/board number indicates the day (i.e., _W_ednesday, _T_hursday or _F_riday) on which authors present their work. The number indicates the board you are to use for displaying your poster. Posters should remain on the boards for all three days. *_Abstract Availability_* Your abstract and all other 2012 Annual Meeting abstracts will be available to view via the Abstract Search Program on the ASHG 2012 Web site on/after September 6, 2012. *_Registration and Housing_* All poster presenters are required to register for the meeting. If you have not yet registered or made hotel reservations, click on the links below. Registration <http://www.ashg.org/cgi-bin/rda.pl?u=102&e=1080> Hotel Reservations <http://www.ashg.org/cgi-bin/rda.pl?u=103&e=1080> Room Sharing/Bulletin Board <http://www.ashg.org/cgi-bin/rda.pl?u=104&e=1080> *_Poster Mounting and Removal_* *Authors must put up and take down their posters according to the schedule below.* Authors must be present at their boards based on their odd and even abstract/program/board number, and must remain at their boards for the duration of their scheduled presentation times. Posters should remain on the boards for all three days. *Wednesday, November 7* 10:00 am–10:30 am All poster authors (Wednesday, Thursday and Friday) place posters on boards _Note_: Posters should remain on the boards for all three days. 10:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm* *Poster Session I (_W_ednesday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* *Thursday, November 8* 7:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm* *Poster Session II (_T_hursday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* *Friday, November 9* 7:00 am–4:30 pm Posters available for general viewing *2:15 pm–4:15 pm * *Poster Session III (_F_riday Authors Present) * *2:15 pm–3:15 pm (/odd poster board numbers; author must be present/)* *3:15 pm–4:15 pm (/even poster board numbers; author must be present/)* 4:15 pm – 4:30 pm All authors remove posters from boards /You will not have access after 4:30 pm to take down your poster./ 4:30 pm Exhibit Hall and Posters closed. *_Preparation for your Poster Presentation_ * Each poster author will be assigned to _share a poster board_. Each author will have a net useable space in portrait/vertical format that measures _2'10" (86.36 cm) wide x 3'8" (111.76 cm) high_. When creating your poster, please use these dimensions. Please read the _Instructions for Authors of Posters <http://www.ashg.org/cgi-bin/rda.pl?u=105&e=1080>_ and then follow the _Guidelines for Preparing Effective Posters/Poster Size <http://www.ashg.org/cgi-bin/rda.pl?u=106&e=1080>_. *_Important Presenter Information_* * ASHG _requires disclosure of gene names_ as part of your presentation and sharing research data so that findings can be replicated and other investigators with similar data can test findings against their own. Authors who do not provide gene names at the meeting will be subject to sanctions as determined by the Program Committee. * When presenting data and health information (including photos) all presenters must have informed consent compliant with human subjects and applicable HIPAA regulation. * Authors must disclose on their poster whether the abstract has been previously published (prior to November 2012). If the abstract has been previously published, authors should indicate the date and publication. * When preparing your poster, please check the poster size guidelines before printing (see above). * You must register and wear an official ASHG 2012 scientific meeting badge to gain admittance at any time to the poster areas. Unregistered guests (i.e., friends, co-workers, etc.) are not permitted to attend the poster sessions. * All poster boards will be pre-numbered. Please be certain to mount your poster on the correct board. * Remember to bring your own pushpins (in your checked luggage). We will have a very limited number of pushpins available at the meeting. * Do not leave personal materials or belongings under poster boards or in the poster area. ASHG is not responsible for any articles left in the poster area or elsewhere. * There is _no access to the Exhibit Hall_ before 10:00 am on Wednesday or after 4:30 pm on Friday. * Click HERE <http://www.ashg.org/cgi-bin/rda.pl?u=107&e=1080> for a suggested format for _abstract citation._ *_Camera/Recording Policy _* Attendees are _strictly prohibited_ from using cameras and all other recording devices on the Exhibit Hall floor, and in all poster/oral presentations. This means that attendees are _not_ permitted to take pictures or videos of speaker slides, posters or exhibit booths. Attendees not adhering to this policy may be asked to leave the room and will be asked to delete all pictures or videos already taken, and further action may be taken with repeated or egregious offenders. When registering, you indicated that would adhere to this policy. *_Poster Printed, Laminated and Ready for Pickup at the Meeting_ Deadline October 2, 2012* You have the option of printing your poster for pickup when you arrive in San Francisco. A separate e-mail will be sent to poster authors about this service by Mira Digital Printing. You can also e-mail the company directly at ASHG2012(a)mirasmart.com <mailto:ASHG2012@mirasmart.com>. The cost is $50 per poster, plus $25 shipping and the deadline for uploading your poster files is October 2, 2012. We look forward to your participation in the 62nd Annual Meeting of the American Society of Human Genetics. For questions, please contact the ASHG Management Office at ashgmeetings(a)ashg.org <mailto:ashgmeetings@ashg.org>. Sincerely, Joann A. Boughman, PhD Executive Vice President American Society of Human Genetics

12 years, 1 month

[Geuvadis_rnaseq] New Geuvadis wiki

by Tuuli Lappalainen

Hello all, The new Geuvadis wiki is now functional, and can be accessed in http://sanabre.net/geuvadis. Your personal user names can be found in the attached file, and the password is 'franciscrick'. I've only taken a quick look at the new wiki, but it looks a lot better, seems to be more flexible and is easier to use. I'll be doing a bunch of updates and maintenance during this week. If you have further questions, comments or requests, feel free to email me and/or Gabrielle. 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 -------- Original Message -------- Subject: FW: Geuvadis MediaWiki e-mail address confirmation Date: Fri, 03 Aug 2012 17:10:49 +0200 From: Gabrielle Anne Bertier <gabrielle.bertier(a)crg.eu> To: Tuuli Lappalainen <Tuuli.Lappalainen(a)unige.ch> CC: Michael Sammeth <micha(a)sammeth.net> Hi Tuuli, normally it should be better now. whenever you judge it good enough you can send the access to all participants. (usernames attached) I'm going on holidays now but I'll be connected, if you have more comments I can pass it on to the company, but I think we can start working with this new version ! If so let me know and I'll de activate the old version of the Wiki Thanks ! Ciao, Gabrielle Wiki link: http://sanabre.net/geuvadis. Usernames attached password: 'franciscrick'

12 years, 1 month

[Geuvadis_rnaseq] 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

12 years, 1 month

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geuvadis_rnaseq August 2012