The Post Genome-Wide Association Initiative has recently launched a nice initiative: they are writing a perspective on how to functionally characterize the variants identified by a GWAS, and they made the draft of their paper publicly editable, so anybody interested is able to contribute or review it before the publication.
Over the last years, many GWAS have identified variants involved in cancer or other congenital diseases; however, too frequently these GWAS are not followed by a proper analysis to characterize the mechanism that relate the variant with the disease (the etiology), or to identify the real causal variant.
So, the paper will be a perspective to describe methods and best practices to characterize the functions of a SNP or variant identified by a GWAS.
The paper is well written and is already most complete, but I believe it lacks a chapter on the characterization of the function of a variant using computational tools. For example, a gene prediction tool can be used to predict whether the variant identified lays into a non-annotated gene or pseudogene, and other software can predict whether it is in a regulatory position; or, in the case that a variant falls into a coding sequence, there are many tools to determine its effect on the structure of the protein.
So, you can find an editable version of the draft into the WikiGenes page. However, I propose you to do the following: write here, in Biostar, about any computational method that you know of or that you could apply, so we will be able to vote the best contributions and discuss them here, avoiding confusion in the wiki. The deadline for the manuscript is December 20th, so we will choose the best answers a week before that, and put the in the draft. The authorship will be recognized, and the posts on biostar will be always stay here to testify your contribution. Edit: I meant that your authorship on the wiki will be recognized, and we will tell the original authors of the draft to look at this question in biostar. However, whether to include you or anybody as authors of the paper is a decision that depends from the corresponding author.
p.s. I am also putting down some notes on my blog. If you want to contribute to the paper, look also at the Discussion page.
"a GWAS study" is the same as HIV virus or LCD display ;)
I want to share some of my recent experiences in post-GWAS analysis and would love to share it here for comments from BioStar members. But it is not clear to me how collaborative contribution is possible in this particular case ? I think the Wiki will only recognize individual contribution by distinct username. Is there a way to inform the coordinators that the content is a group effort ?
@Khader: the best way is to talk to the corresponding authors and tell him to look here.
I will write to the authors and check this.
ok!! remember that you can also contribute to the document at WikiGenes directly. I was just proposing to create a discussion on computational methods here at Biostar, to involve the Biostar community, but if you have something that could be submitted into the original document directly you should better go to WikiGenes and edit there.
ARRGGHHH!! We bumped into each other editing over there. I really liked the idea of editing here and then bringing it over...alas...
don't worry, I reintegrated my previous changes... did you loose something in the process?
No, I'm fine....I am just easily frustrated by wikis...
I am not able to submit the sections to the article I am getting "Text exceeds maximum length The text you are attempting to submit is too long. Please shorten and save it again." error - any idea why this is happening or is there any limit on inserting text ?