Loci identification through SNPs LD information

Question

[alessandrotestori7]

Dear all, I want to define several loci in a genetic region through linkage disequilibrium information of SNPs. I have sorted all SNPs in ascending order according to their association p-values and then I have assigned to a locus all SNPs in linkage with the lead SNP (r^2 >= 0.5). The remaining SNPs have been assigned to other loci applying the same procedure, till any SNP was assigned to a locus. Is this approach commonly used and accepted? How is this procedure called? Please let me know. Thanks, cheers!

Answer 1

[Kevin Blighe]

Yes, you have not done anything incorrect based on what you have written - did you use PLINK? I assume that you are only analysing the statistically significant SNPs.

What you are essentially doing is identifying potential 'haplotype blocks'. Other thresholds that you can use for LD include D and D'. Note that you can visualise these with a program called haploview: https://www.broadinstitute.org/haploview/haploview

Kevin