Once a set of associated variants is identified from a genomewide scan, an assessment of their potential function is needed to move forward toward biological insight. It would be useful to leverage the GTEx and MODs (Alliance) data to assess: 1) for GTEx: if the intergenic variants have evidence of regulatory function and, if known, what genes are they regulating? 2) for MODS: if a target gene is identified (eg the... more »
Apologies - this feature request is captured within existing user narratives. I don't see a way to delete the idea, though!
Detecting GxE interactions often requires amassing large sample sizes, but identifying cohorts with similar phenotype and environmental exposure data is often cumbersome. dbGaP provides some opportunity for identifying such cohorts, but the complete set of phenotype and environmental variables as well as availability of multi-omics data are often not included. STAGE could provide a venue for aligning cohorts with harmonizable... more »
PIs have responsibility for the data they generate, including information about subject consent. Such data and consent information may change over time, so dataSTAGE should have tools for PIs to ensure that study data and information is accurate and up to date. It may be useful to develop an interface with documentation, training, and support infrastructure similar to the dbGaP submission tools, documented here: https://www.ncbi.nlm.nih.gov/gap/docs/submissionguide/... more »
A novice user (grad student) can log into DataSTAGE and access teaching data sets from BioLINCC (link: https://biolincc.nhlbi.nih.gov/teaching/). She can find material (FAQs, videos, etc.) that will explain what kind of data elements exist within the datasets. She can also find pre-scripted Jupyter notebooks that walk her through how to run standard epidemiological analyses.
DataSTAGE should curate all available GWAS scan results available in GWAS catalog (https://www.ebi.ac.uk/gwas/), the NCBI archie (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639349/), and other privately held repositories (eg GIANT and T2D portal , Broad Inst) to enable PheWAS analysis. Biological insight can be gained in looking at the pleiotropic effects of specific variants that can suggest appropriate functional... more »