Forum: Most important International Big Data Projects: Genetics and Epigenetics
6
gravatar for Shicheng Guo
23 months ago by
Shicheng Guo8.2k
Shicheng Guo8.2k wrote:

Here, I summarized the most important international bigdata project which need to be followed. All of them have large number of genetics and epigeneitcs data to be downloaded and to be used for next model building and knowledge achievement.

International Human Epigenome Consortium (IHEC)

NIH Roadmap Epigenomics Mapping consortium

The Canadian Epigenetics, Environment and Health research Consortium (CEEHRC)

CREST / IHEC - Team Japan

The ENCODE project

The German Epigenome Program - DEEP

International Cancer Genome Consortium

EpiGeneSys - Network of Excellence

Blueprint Epigenome Project

International cancer Genome Consortium Project

Pan Cancer Analysis of Whole Genomes (PCAWG) Project

Human Epigenome Atlas

Recount2: analysis-ready RNA-seq gene and exon counts datasets

forum bigdata • 915 views
ADD COMMENTlink modified 20 months ago • written 23 months ago by Shicheng Guo8.2k
4

What about TCGA?

P.S. A one line description of what type of data one can find in each of the project would be helpful.

ADD REPLYlink written 23 months ago by venu6.6k
1

I will follow All of US project. Just want to know when they will publish some preliminary data.

ADD REPLYlink written 23 months ago by Shicheng Guo8.2k
2

It may not be for some time. That project just got off to a start a couple of months ago.

ADD REPLYlink written 23 months ago by genomax85k
1

As your estimation, how long time they need to publish the first paper? I guess Nature again, right? 3 years or 5 years? Which group will be charge of 'Data Analysis' section?

ADD REPLYlink modified 23 months ago • written 23 months ago by Shicheng Guo8.2k
2

Your guess is as good as mine. It will all depend on enrollment and when they can actually start doing the analysis. Vanderbilt University Med Center, Verily (Google's life science arm) and Broad Institute have been named data centers but there may be additional ones as project gets underway.

ADD REPLYlink written 23 months ago by genomax85k
1

Miss the big train again. Big project has been totally monopolized by these big organization.

Department of Biostatistics at Vanderbilt University

ADD REPLYlink modified 23 months ago • written 23 months ago by Shicheng Guo8.2k

GTEX, transcriptomics though.

ADD REPLYlink written 20 months ago by grant.hovhannisyan2.0k
3
gravatar for genomax
23 months ago by
genomax85k
United States
genomax85k wrote:

Would be good to indicate public data availability. Probably others that are larger but not public.

Genomics England (10000 genomes from UK)
All of US from NIH - Just starting, million participants eventually.
Million veterans project in US.

Model organisms:
1001 Arabidopsis genomes
Collaborative cross Mice genomes.
E. coli evolution (50000 generations).

ADD COMMENTlink modified 23 months ago • written 23 months ago by genomax85k

I would add UK Biobank to that list since it's being Exome sequenced and Whole Genome sequenced. I think Tempus RNA stabilisation tubes were collected from participants in addition to samples for DNA sequencing (for phase 2 at least).

ADD REPLYlink modified 21 months ago • written 21 months ago by Garan620
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