Question: Publicly Available, Individual-Level, Gwas Data?
3
gravatar for Mohammed Alquraishi
7.9 years ago by
Mohammed Alquraishi60 wrote:

Does anyone know of a publicly available data set that contains genotype-phenotype associations? All studies that I have seen seem to require an official request process through the NIH or some other body. The closest thing I've seen is the Personal Genome Project, but that only has information on 10 individuals. I'm looking for something a little larger.

gwas • 5.7k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Mohammed Alquraishi60
1

I think you should also check this question: biostar.stackexchange.com/questions/4610/… I think yours is essentially a duplicate. The answers to that question mention both privacy issues involved and some sources that might be useful (even though you normally indeed have to make a request, precisely because of these privacy issues).

ADD REPLYlink written 7.9 years ago by Chris Evelo10.0k

I think you should also check this question: http://biostar.stackexchange.com/questions/4610/dataset-with-snps-linked-to-phenotype, I think yours is essentially a duplicate. The answers that question mention both privacy issues involved and some sources that might be useful (even though you normally indeed have to make a request, precisely because of these privacy issues).

ADD REPLYlink written 7.9 years ago by Chris Evelo10.0k

You will find that the developing standard is to go through a data access committee (DAC). That is (and will probably remain) the standard way of accessing genotypic information derived both from sequencing technologies as well as microarrays. So, that is the equivalent of publicly available data.

ADD REPLYlink written 7.9 years ago by Sean Davis25k
1
gravatar for Paul
7.9 years ago by
Paul750
United States
Paul750 wrote:

This is the most well known large GWAS I think (by the Wellcome Trust Case Control Consortium):

http://www.ncbi.nlm.nih.gov/pubmed/17554300 http://www.wtccc.org.uk/info/070606.shtml

ADD COMMENTlink written 7.9 years ago by Paul750

this data is available to anyone, but to access it you need to get permission from its Data Access Committee.

ADD REPLYlink written 7.9 years ago by Giovanni M Dall'Olio26k
0
gravatar for Jeroen Van Goey
7.9 years ago by
Jeroen Van Goey2.2k
Ghent, Belgium
Jeroen Van Goey2.2k wrote:

The 1000 Genomes Project is the first project to sequence the genomes of a large number of people, to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype.

As with other major human genome reference projects, data from the 1000 Genomes Project is made available quickly to the worldwide scientific community through freely accessible public databases.

Publication in Nature: A map of human genome variation from population-scale sequencing (pdf).

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Jeroen Van Goey2.2k
3

Thanks for the reply. I did see the 1000 Genomes Project, but unfortunately it does not as of yet provide any phenotype-genotype associations (correct me if I'm wrong). It's only genotypes.

ADD REPLYlink written 7.9 years ago by Mohammed Alquraishi60
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