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
Hello,
A couple of data and analysis updates:
- QC: I've reran the plots of sample correlations and clustering using
the correlation matrices provided by Peter. The total dataset shows
clustering by lab rather than populations (probably because systematical
differences between these populations are not that big), but the
replicate samples look very good with lab effects being less than
biological variation. See
http://sanabre.net/geuvadis/index.php/MRNA#Sample_correlation_and_clusterin…
- Splice junctions for Manny: I've normalized the junctions by total
gene count, to able able to extract splice changes from variation in
overall expression level. The files of these with subsequent
transformation to standard normal are in
/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/quantification/splice_junction-intron
, file names with GeneN.
have a nice weekend,
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
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
Hello,
We'll have our regular Geuvadis RNAseq analysis group call on September
27th at 2pm CET.
Agenda:
- agenda for the whole group call within 2 weeks
- presentations in Santiago de Compostela
- draft of the main paper outline by Tuuli
- we need to come up with a good common statistics (or two) to
describe population variation of different transcriptome features
- Manny will presentation on loff-of-function splice variant effects
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 /
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
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.
I have attached a PDF describing all questions you will face in the survey
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
Hello,
Let's have our weekly Geuvadis analysis group TC on Thursday September
20 at 2pm CET.
On the agenda:
- Analysis updates (that we didn't have time to do last week)
- Matthias's slides on splicing
- 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
/
cheers,
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
Hello all,
I've uploaded normalized miRNA quantifications to the ftp site:
/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables
. See wiki (http://sanabre.net/geuvadis/index.php/Basic_methodology) for
details.
There are files for:
- 363 European QC-passed samples, corrected with 10 PEER factors
(including population and seqlab).
- 89 Yoruba QC-passed samples, corrected with 5 PEER factors (including
seqlab).
These files should be considered slightly preliminary - it is possible
that we'll end up using these in the end, but before freezing this I
want to do some covariate analysis (once I get the fastq QC stats).
We should do eQTL analysis separately for EUR and YRI, but as we
discussed on the call, miRNA-mRNA correlations could maybe be done on
the whole dataset after correcting for population. I'll produce these
files in ~1 week - for this I'll also need to normalize the mRNA data in
a similar manner, and that takes more time to run. In the meanwhile you
can probably use the population-specific data.
cheers,
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
Hello,
We'll have Geuvadis analysis group TC on Thursday 12th of September at
2pm CET.
On the agenda:
- Analysis updates (see below)
- Data visualization and Ensembl collaboration
- Pedro will present on differential expression analysis
- AOB
Call details - different from the usual!
Germany +49 692 573 804 41
Netherlands +31 108 920 271
Spain +34 931 816 661
Sweden +46 840 309 949
Switzerland +41 58 262 07 22
United Kingdom +44 203 370 57 19
United States +1 646 381 08 89
/Access code: 611683 /
For your information, I have my knee surgery scheduled for this Friday.
I'll probably be offline only for a couple of days, but I'm not sure if
I'll be able to work that much next week. Thus, if you need some
feedback or data from me, let me know now so we can try to sort it out
before the surgery.
We need to start wrapping up the analysis soon to put the paper
together. Thus I'd like to ask you to give brief summary on the stage of
your analysis - what you've been doing, are what kind of things are
still pending, and when you would be ready to present the result and
hand results and text over to me. Below is a list of analyses/people
from the paper outline - if your name is there but you won't be on the
call, please send the info to the analysis group mailing list before the
call.
-QC
- Jonas, Olof, Peter, Tuuli
- Differential expression
- Pedro
- mRNA qualitative/quantitative variation
- Jean, Mar
- ASE
- Tuuli
- Splicing variation
- Micha
- Soft splicing
- Matthias
- miRNA-mRNA interactions
- Marc, Henk?
- RNA editing
- Thomas W
- Conjoined genes
- Liliana
- n-TARs
- Daniela
- Transcription of repeats
- Peter/Irina
- QTLs
- Tuuli
- Loss-of-function
- Manny
- Data visualization
- Natalja
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
Hello,
I've done basic QC for miRNA samples. Attached is a sample sheet that
denotes samples to use in analysis. From the total 492 samples, 480
samples from 452 unique individuals pass QC. We end up having 705 genes
quantified in at least 50% of the samples - most of these have low
quantifications though.
Analysis of sample correlation and clustering shows even a clearer
population clustering than mRNA, and very little lab effects.
I've updated the QC section of the wiki with miRNA results: list of
samples to exclude, basic read count and mapping stats, and early
correlation analysis.
The data is on the ftp site:
- sample sheet: /upload/geuvadis/wp4_rnaseq/main_project/analysis_data/qc
- quantifications:
/upload/geuvadis/wp4_rnaseq/main_project/analysis_data/mirna/quantification_tables
I'm now running PEER normalization for miRNAs, and that data will
probably be the best to use for mRNA-miRNA correlations and eQTL
analysis. I'll let you know when this is done.
cheers,
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