Linkage disequilibrium used by Open Targets

Community Feedback
1

I understand that OpenTargets applied a LD map developed by randomly selected 10,000 samples. Recently, TOPMED created a fantastic LD map for 5 ancestry which can be considered for Open Targets for next or future update so that we are more consistent with academic community.

TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data

The final dataset included 1,335 unrelated individuals of African, 844 of East Asian, 13,160 of European, and 239 of South Asian ancestry for pairwise LD inference. Regarding variants, we started with all TOPMed freeze 8 polymorphic variants that passed quality control and retained multi-allelic variants or multiple entries at the same position, resulting in a total of 23.0–153.0 million SNVs in each of the ancestral groups

https://www.cell.com/ajhg/fulltext/S0002-9297(22)00154-9?dgcid=raven_jbs_aip_email

Shicheng

2

Thanks for sharing. This sounds like a useful resource that could help us to conduct some of the downstream work (i.e. fine-mapping/coloc) for non-European GWAS sumstats.