Forum:Most important International Big Data Projects: Genetics and Epigenetics

Question

[Shicheng Guo]

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

[venu]

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.

[Shicheng Guo]

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

[GenoMax]

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

[Shicheng Guo]

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?

[GenoMax]

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.

[Shicheng Guo]

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

Department of Biostatistics at Vanderbilt University

[grant.hovhannisyan]

GTEX, transcriptomics though.

Answer 1

[GenoMax]

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).

[Garan]

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).

[Shicheng Guo]

Hi genomax, do you know how to access individual-level Million veterans project data?