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Genome-wide assessment of genetic risk for systemic lupus erythematosus and disease severity

By Lingyan Chen, Yong-Fei Wang, Lu Liu, Adrianna Bielowka, Rahell Ahmed, Huoru Zhang, Phil Tombleson, Amy L Roberts, Christopher A Odhams, Deborah S. Cunninghame Graham, Xuejun Zhang, Wangling Yang, Timothy J. Vyse, David L. Morris

Posted 23 Apr 2019
bioRxiv DOI: 10.1101/614867 (published DOI: 10.1093/hmg/ddaa030)

Objective Using three European and two Chinese genome-wide association studies (GWAS), we investigated the performance of genetic risk scores (GRS) for predicting the susceptibility and severity of Systemic lupus erythematosus (SLE), using renal disease as a proxy for severity. Methods We used four GWASs to test the performance of GRS both cross validating within the European population and between European and Chinese populations. The performance of GRS in SLE risk prediction was evaluated by Receiver Operating Characteristic (ROC) curves. We then analyzed the polygenic nature of SLE statistically. We also partitioned patients according to their age-of-onset and evaluated the predictability of GRS in disease severity in each age group. Results We found consistently that the best GRS in the prediction of SLE used SNPs associated at the level of P <1e-05 in all GWAS datasets and that SNPs with P -values above 0.2 were inflated for SLE true positive signals. The GRS results in an area under the ROC curve ranging between 0.64 and 0.72, within European and between the European and Chinese populations. We further showed a significant positive correlation between a GRS and renal disease in two independent European GWAS ( Pcohort1 =2.44e-08; Pcohort2 =0.00205) and a significant negative correlation with age of SLE onset ( Pcohort1 =1.76e-12; Pcohort2 =0.00384). We found that the GRS performed better in prediction of renal disease in the ‘later onset’ compared to the ‘earlier onset’ group. Conclusion The GRS predicts SLE in both European and Chinese populations and correlates with poorer prognostic factors: young age of onset and lupus nephritis.

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