How to generate genetics risk score with linkage disequilibrium?

Question

[xinhui.wang]

Dear all, I am working on genetics risk score generation with many SNPs on certein diseases. Our previousl algorithm is based on weight GRS, however, without considering linkage disequilibrium. I would like to check the linkage disequilibrium between these SNPs and calculate the GRS with considering linkage disequilibrium. Is there any algorithm or paper could give me some idea on how to deal with this problem? Thanks and with best regards, Xinhui

Answer 1

[Denise CS]

If you are talking about human diseases, regarding linkage disequilibrium data you can get the information from Ensembl. LD is also available through their Perl and REST APIs. Ensembl keeps adding more and more REST endpoints, so definitely having a look at that option.