Closed UK: DecodeME updates, was recruitment thread.

[MrMagoo]

Excited!

 

[hotblack]

May be worth reminding everyone of the blog post on the analysis plan.

And here’s a direct link to the delicious pdf with all the details.

I’m not going to pretend I understand it all, but there were bits I understand a bit more about now, compared to when the project started, thanks to my time on these forums.

 

[hotblack]

I’ve been re-listening to some older presentations on DecodeME and going through the analysis plan in more detail and trying to learn more about the processes involved to prepare my brain for whatever comes.

Here’s a few thoughts, hey maybe interesting to others and maybe people with more experience can chip in and answer any questions. Apologies if these are answered elsewhere.

Firstly it just seems incredibly rigorous. Really thorough and deep QC process for the data. Is this normal in all GWAS studies or extra mile stuff? It doesn’t surprise me given the team but still seems impressive.

The imputation steps seem interesting. Would it be fair to say this increases the overall number of variants available to look at? Do we have an idea of the number or scale of increase this will give us? This looks like it would disproportionately increase the resolution in specific areas (of interest) like HLA and mitochondrial dna, is that right?

Replication with other another group is mentioned, is this taking place now or later? Do we have timelines for fingenn?

Will we get the main GWAS results first and then see post GWAS steps taking place later, or will we see everything mentioned in the analysis plan all at once?

 

[V.R.T.]

Replication with other another group is mentioned, is this taking place now or later?

I reckon this is probably the Lipkin study that had funding pulled. Some of the US institutions seem to have won a court case to reinstate funding so maybe that will go ahead eventually.

 

[hotblack]

I reckon this is probably the Lipkin study that had funding pulled. Some of the US institutions seem to have won a court case to reinstate funding so maybe that will go ahead eventually.

Maybe there are mutliple groups I’m not sure. But fingenn is specifically mentioned and they seem to have generic data already, but I don’t know about this bit of the analysis. It could even be concurrent.

 

[V.R.T.]

Maybe there are mutliple groups I’m not sure. But fingenn is specifically mentioned and they seem to have generic data already, but I don’t know about this bit of the analysis. It could even be concurrent.

Oh this is very interesting, i didn't know about this.

Edit: it says in the link that Finngen results are now 'publically available for the whole research community'. So it's entirely possible it's concurrent.

 

[wigglethemouse]

Will we get the main GWAS results first and then see post GWAS steps taking place later, or will we see everything mentioned in the analysis plan all at once?

I assumed the GWAS results would be all at once as Chris Ponting stated in a webinar that funding runs out in August. Follow up studies using the data generated such as the announced projects by Precision Life and University of Glasgow will follow.

 

[hotblack]

I assumed the GWAS results would be all at once as Chris Ponting stated in a webinar that funding runs out in August.

After looking through the plan in more detail I wasn’t sure if we’d see all the steps outlined in section 6 (including things like PheWAS) or get the initial base GWAS results first then followups with the extra detail. It looks like there’s potentially a lot of different and interesting pieces here, not just one result. But you’re probably right and they’ll want/need to finish everything outlined at once.

Edit: PrecisionLife already have the raw genetic data don’t they? They’re not building on top of the GWAS, or at least that was the impression I got from the Genetics Centre of Excellence webinar a couple of weeks ago?