SLE is a complex autoimmune disease with high genetic heretabilty. During my Ph.D. study, I have been involved in mutlitple SLE common variants GWAS analysis projects. I have identified 3 novel loci associated with SLE, and replicated known chrX SLE associated loci and higher trisomy X ratio in East Asian population. Currently, I am preparing a manuscript about a extra novel SLE associated loci by meta-analyze multiple SNP array and WGS cohorts (Manuscript preparing, not shown here). In addition, I am replicating known SLE associated loci using whole-genome sequencing (WGS) techonolgy, trying to boost depolying of WGS in complex trait analysis (Manuscript preparing, not shown here).

More than 330 common variants loci have been identified associated with systemic lupus erythematosus (SLE), but their causal mechanisms are rarely well-explained. Many GWAS downstream analysis ideas were proposed, including fine-mapping, colocalization, Mendelian randomization causal inference, and multi-omics integrated analysis. But it is easy to get confused as there are many statisics hypotheses and caveat before using these tools. In this article, I will present my GWAS downstream analysis pipeline using a SLE signal as example.

SLE is a complex autoimmune disease with high genetic heretabilty. Although many common variants have been identified in SLE, the contribution of rare variants to SLE pathogenesis remains largely unexplored. Genetic heritability analysis shown that the contribution of currentyl identified common variants is limited. Therefore, we performed a whole-genome sequencing (WGS) analysis of SLE patients to identify rare variants associated with SLE.