I want to follow up some GWAS hits for obesity by doing some eQTL analysis in fat and liver tissue. I found this paper by Eric Schadt's group that did something similar, and I found their expression data on ArrayExpress, and on GEO here, here, and here.
Assuming this study was funded by NIH they are required to deposit their data onto dbGaP. Given a publication and an author list, how can I search dbGaP to see if the data mentioned in this paper is in dbGaP? It seems that you need to know the title of the study to find a dataset, and knowing a paper or author list doesn't help you much. Any help is appreciated.
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Stephen
1 answer
Raw genotype/phenotype data from dbGAP data is not readily available for download.
Datasets may have embargo release dates, also the user (in the level of PI) need to send a request to the corresponding author of study and need to wait for the approval. See the manuscript, data request procedure and tutorial to access data for more details.
To download diseases related to specific phenotype you may use one of the resources:
- dbGAP search interface: See the hits for the keyword "obesity" here
- NHGRI GWAS database - Filter using keyword or pre-defined traits to get list of studies.
- Phenotype Association Browser - Filter using chromosome, p-value or trait. When I searched for 'obesity', I got 23 Result(s) match selected current query.
- Phenopedia - You can query using phenotype and retrieve direct dbGAP links. For example: Obesity, Obesity abdominal, Obsesity, Morbid
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