Rare variants at 16p11.2 are associated with common variable immunodeficiency

Abstract

Background: Common variable immunodeficiency (CVID) is characterized clinically by inadequate quantity and quality of serum immunoglobulins with increased susceptibility to infections, resulting in significant morbidity and mortality. Only a few genes have been uncovered, and the genetic background of CVID remains elusive to date for the majority of patients.

Objective: We sought to seek novel associations of genes and genetic variants with CVID.

Methods: We performed association analyses in a discovery cohort of 164 patients with CVID and 19,542 healthy control subjects genotyped on the Immuno BeadChip from Illumina platform; replication of findings was examined in an independent cohort of 135 patients with CVID and 2,066 healthy control subjects, followed by meta-analysis.

Results: We identified 11 single nucleotide polymorphisms (SNPs) at the 16p11.2 locus associated with CVID at a genome-wide significant level in the discovery cohort. The most significant SNP, rs929867 (P = 6.21 × 10(-9)), is in the gene fused-in-sarcoma (FUS), with 4 other SNPs mapping to integrin CD11b (ITGAM). Results were confirmed in our replication cohort. Conditional association analysis suggests a single association signal at the 16p11.2 locus. A strong trend of association was also seen for 38 SNPs (P < 5 × 10(-5)) in the MHC region, supporting that this is a genuine CVID locus. Interestingly, we found that 80% of patients with the rare ITGAM variants have reduced switched memory B-cell counts.

Conclusion: We report a novel association of CVID with rare variants at the FUS/ITGAM (CD11b) locus on 16p11.2. The association signal is enriched for promoter/enhancer markers in the ITGAM gene. ITGAM encodes the integrin CD11b, a part of complement receptor 3, a novel candidate gene implicated here for the first time in the pathogenesis of CVID.

Keywords: ITGAM; Immunodeficiency; genome-wide association study; immunogenetics; rare variants.

Figure 1

Manhattan plot of genome-wide association results for CVID in the Caucasian discovery cohort. Red line indicates the genome-wide significance threshold.

Figure 2

Regional association plot at the 16p11.2 (ITGAM) locus. SNPs are plotted by chromosomal position in a 400-kb window against their −log10 transformed P values for association with CVID phenotype in the discovery cohort. The color of each SNP reflects their LD with the most significant rs929867. The r² values were calculated from the discovery cohort in PLINK.