Question: How To Find All Gwas Studies That A Given Gene Has Been Implicated In?
7
gravatar for Andrew Su
9.1 years ago by
Andrew Su4.8k
San Diego, CA
Andrew Su4.8k wrote:

dbGaP seems to be a primary data repository, but it doesn't store results on the level of genes (or as far as I can tell, even genomic regions).

gene gwas genome • 6.3k views
ADD COMMENTlink modified 9.1 years ago by Andrew Johnson30 • written 9.1 years ago by Andrew Su4.8k

Some definitions from the wikipedia: In genetic epidemiology, a genome-wide association study (GWA study, or GWAS) - also known as whole genome association study (WGA study) - is an examination of genetic variation across a given genome, designed to identify genetic associations with observable traits.

ADD REPLYlink written 9.1 years ago by Istvan Albert ♦♦ 80k

Thank you Istvan for the clarification!

ADD REPLYlink written 9.1 years ago by Andrew Su4.8k

Real bummer that no one's seemed to have tackled this, isn't it?

ADD REPLYlink written 9.1 years ago by Andrew Su4.8k
4
gravatar for Khader Shameer
9.1 years ago by
Manhattan, NY
Khader Shameer18k wrote:

AFAIK, dbGAP is one of the official resource for GWAS studies. A mere gene search may not fetch the exact details about the studies. Dataset from large scale GWAS studies are not available under public access due to sensitive genotype and phenotype data from patients. You have to write to individual investigators to get access to the data. Usually this data will be available only after the Embargo Release date. This is usually after 1year of the submission of the data. I think once you have access to the dataset, you will able to get the p-values of the SNPs genotyped in the whole study with the de-identified case/control and their phenotypes. These SNPs may need further mapping to get the details about the genes.

NHGRI website provides A Catalog of Published Genome-Wide Association Studies: They provide a detailed table of GWAS and their details. As of 03/24/10, this table includes 517 publications and 2443 SNPs. You may map this SNPs to get the respective genes.

Also this manuscript provides results from various GWAS studies.

I am looking forward for other comments to know if there is any public resource that provides GWAS data.

EDIT : I have recently used SCANDB, GWASIntegrator and VARIETAS for integrating GWAS studies around a gene.

ADD COMMENTlink modified 8.7 years ago • written 9.1 years ago by Khader Shameer18k
3
gravatar for Jeff Kiefer
9.1 years ago by
Jeff Kiefer30
United States
Jeff Kiefer30 wrote:

http://www.biomedcentral.com/1471-2350/10/6

See if this helps possibly.

ADD COMMENTlink written 9.1 years ago by Jeff Kiefer30

good link, thanks... not the perfect solution, but a start perhaps...

ADD REPLYlink written 9.1 years ago by Andrew Su4.8k
2
gravatar for Hanif Khalak
8.9 years ago by
Hanif Khalak1.2k
Doha, QA
Hanif Khalak1.2k wrote:

dbGAP as already mentioned lists GWA studies - a search on a gene name, it seems, lists the studies that implicate that gene for a particular phenotype. Regarding data access, doesn't approval from the Data Access Committee of dbGAP give you access to the genotype and phenotype data?

Another NIH site, Genetics Association Database (GAD), lists gene-specific association (GSA?) studies. It also has disease and chromosome region browsing views and searching.

Come to think of it, I'm not sure why someone like NCBI couldn't just provide anonymized SNP/locus-specific raw data from the GWA/GSA studies to get around the "de-identification" issue. I know that ISCB is trying to drum up support for open access to published data and associated software - there's a lot of results buried in journal archives that would bear some mining to integrate in a searchable format.

ADD COMMENTlink written 8.9 years ago by Hanif Khalak1.2k
1

I don't think you can search dbGAP for a gene name directly, unless I'm missing something?

ADD REPLYlink written 8.9 years ago by Andrew Su4.8k

You might be right - typing MYC in the search box yields many studies but that could be because they're all GWA, or a bug..

ADD REPLYlink written 8.9 years ago by Hanif Khalak1.2k
2
gravatar for Chl
8.7 years ago by
Chl180
Paris, France
Chl180 wrote:

Maybe try HuGENavigator which provides sensible results for GWAS studies.

ADD COMMENTlink written 8.7 years ago by Chl180
2
gravatar for Andrew Johnson
8.1 years ago by
Andrew Johnson30 wrote:

I'm the author and architect of http://www.biomedcentral.com/1471-2350/10/6.

We have put substantial effort into an update of this and are fairly far along (there will soon be ~10X the data as in the original publication). It is of course a moving target. We currently see no downward trend in the rate of GWAS publications as some might predict with the increasing focus on sequencing.

We are still trying to assess how we might release a portion (or possibly all) of our work, as well as thinking about our own research priorities in using the accumulated results. For a variety of reasons it may end being a partial release to top results from each study which will still include many more results than currently listed in the NHGRI catalog or other such portals.

If people who have posted on this list have ideas for how they might use such data if released or what information they think would be important to include I'd be glad to hear them. In this pre-publication phase I would also entertain legitimate suggestions for collaboration on a project by project basis (beyond requests to simply share all the data or do wide-ranging queries).

ADD COMMENTlink written 8.1 years ago by Andrew Johnson30
1
gravatar for Will
9.1 years ago by
Will4.5k
United States
Will4.5k wrote:

While I've looked for this sort of information I've never actually found a reasonable database of this sort of information. OMIM is close to what you're looking for but its data is woefully sparse. SNPpedia is a wikipedia-like website trying to annotate the SNPs implicated in diseases but it is also terribly sparse.

Good luck.

ADD COMMENTlink written 9.1 years ago by Will4.5k
1
gravatar for Larry_Parnell
8.7 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Exactly as Khader stated - see this paper's suppl files. However, that paper is rather dated in terms of the life of GWAS. SO much more has been published. The genome.gov site only lists the top SNPs and most robust associations whereas the above referenced paper digs deeper for what may be your definition of "implicated."

We are in conversation with the lead author of the above paper and he is hesitant to update his database/files because it is a mountain of work requiring an assistant.

ADD COMMENTlink written 8.7 years ago by Larry_Parnell16k
1
gravatar for Keith Grimaldi
8.7 years ago by
Keith Grimaldi10 wrote:

Larry - the updating part I get, it's the death of the database! Regarding the question, I have always been using the various functions on HuGENavigator, as mentioned by Khader and chl above - is this a comprehensive resource. Of course it is not specific for just GWAS so I wonder how complete it is - any answers from anyone?

ADD COMMENTlink written 8.7 years ago by Keith Grimaldi10
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