Recombination rate cut off values

Question

[Floris Brenk]

Dear all,

I'm having some trouble interpreting some GWAS and eQTL results and was hoping someone could help me out. In the genome there are haploblocks which are present in individuals and usually these haploblocks are separated by recombination hotspots (as far as I know). Using locuszoom it is possible to create very nice plots that are commonly used to plot GWAS data for example http://www.nature.com/ng/journal/v45/n7/images/ng.2637-F1.jpg. I'm looking for a method to identify whether eQTL variants fall into the same haploblock of the gene or that the eQTL variant is more distant of the influenced gene and in another haploblock. So is there a cut off value of cM/Mb that I can use that is commonly accepted as a indicator for a new haploblock? or is there a way how I can change the cM/Mb number to another number that indicated the chance of a new haploblock?

Thanks in advance for any help.

Answer 1

[Adam]

Rather than thinking in terms of haploblocks or recombination rate, you might want to think in terms of genetic distance. For example, you might decide to only consider variants within, say, 0.5 cM. In terms of physical distance, this threshold would correspond to approximately 500kb on average, but by using genetic distance instead of physical distance you are accounting for the fact that some regions are more recombinogenic than others.

[Floris Brenk]

Hmm how would I do that? Convert all basepairs to centimorgans like here How To Convert Centimorgan To Base Pair and do the eQTL analysis again?