Medical Records-Based Genetic Studies of the Complement System
Authors: Khan Atlas , Shang Ning , Petukhova Lynn , Zhang Jun , Shen Yufeng , Hebbring Scott J. , Moncrieffe Halima , Kottyan Leah C. , Namjou-Khales Bahram , Knevel Rachel , Raychaudhuri Soumya , Karlson Elizabeth W. , Harley John B. , Stanaway Ian B. , Crosslin David , Denny Joshua C. , Elkind Mitchell S.V. , Gharavi Ali G. , Hripcsak George , Weng Chunhua , Kiryluk Krzysztof 
Published: May 2021

Significance Statement
The complement pathway represents one of the critical arms of the innate immune system. We combined genome-wide and phenome-wide association studies using medical records data for C3 and C4 levels to discover common genetic variants controlling systemic complement activation. Three genome-wide significant loci had large effects on complement levels. These loci encode three critical complement genes: CFH, C3, and C4. We performed detailed functional annotations of the significant loci, including multiallelic copy number variant analysis of the C4 locus to define two structural genomic variants with large effects on C4 levels. Blood C4 levels were strongly correlated with the copy number of C4A and C4B genes. Lastly, using genome-wide genetic correlations and electronic health records–based phenome-wide association studies in 102,138 participants, we catalogued a spectrum of human diseases genetically related to systemic complement activation, including inflammatory, autoimmune, cardiometabolic, and kidney diseases.

Background
Genetic variants in complement genes have been associated with a wide range of human disease states, but well-powered genetic association studies of complement activation have not been performed in large multiethnic cohorts.

Methods
We performed medical records–based genome-wide and phenome-wide association studies for plasma C3 and C4 levels among participants of the Electronic Medical Records and Genomics (eMERGE) network.

Results
In a GWAS for C3 levels in 3949 individuals, we detected two genome-wide significant loci: chr.1q31.3 (CFH locus; rs3753396-A; β=0.20; 95% CI, 0.14 to 0.25; P=1.52x10-11) and chr.19p13.3 (C3 locus; rs11569470-G; β=0.19; 95% CI, 0.13 to 0.24; P=1.29x10-8). These two loci explained approximately 2% of variance in C3 levels. GWAS for C4 levels involved 3998 individuals and revealed a genome-wide significant locus at chr.6p21.32 (C4 locus; rs3135353-C; β=0.40; 95% CI, 0.34 to 0.45; P=4.58x10-35). This locus explained approximately 13% of variance in C4 levels. The multiallelic copy number variant analysis defined two structural genomic C4 variants with large effect on blood C4 levels: C4-BS (β=−0.36; 95% CI, −0.42 to −0.30; P=2.98x10-22) and C4-AL-BS (β=0.25; 95% CI, 0.21 to 0.29; P=8.11x10-23). Overall, C4 levels were strongly correlated with copy numbers of C4A and C4B genes. In comprehensive phenome-wide association studies involving 102,138 eMERGE participants, we cataloged a full spectrum of autoimmune, cardiometabolic, and kidney diseases genetically related to systemic complement activation.

Conclusions
We discovered genetic determinants of plasma C3 and C4 levels using eMERGE genomic data linked to electronic medical records. Genetic variants regulating C3 and C4 levels have large effects and multiple clinical correlations across the spectrum of complement-related diseases in humans.