Genomic copy number variants: evidence for association with antibody response to anthrax vaccine adsorbed

Abstract

Background: Anthrax and its etiologic agent remain a biological threat. Anthrax vaccine is highly effective, but vaccine-induced IgG antibody responses vary widely following required doses of vaccinations. Such variation can be related to genetic factors, especially genomic copy number variants (CNVs) that are known to be enriched among genes with immunologic function. We have tested this hypothesis in two study populations from a clinical trial of anthrax vaccination.

Methods: We performed CNV-based genome-wide association analyses separately on 794 European Americans and 200 African-Americans. Antibodies to protective antigen were measured at week 8 (early response) and week 30 (peak response) using an enzyme-linked immunosorbent assay. We used DNA microarray data (Affymetrix 6.0) and two CNV detection algorithms, hidden markov model (PennCNV) and circular binary segmentation (GeneSpring) to determine CNVs in all individuals. Multivariable regression analyses were used to identify CNV-specific associations after adjusting for relevant non-genetic covariates.

Results: Within the 22 autosomal chromosomes, 2,943 non-overlapping CNV regions were detected by both algorithms. Genomic insertions containing HLA-DRB5, DRB1 and DQA1/DRA genes in the major histocompatibility complex (MHC) region (chromosome 6p21.3) were moderately associated with elevated early antibody response (β = 0.14, p = 1.78×10(-3)) among European Americans, and the strongest association was observed between peak antibody response and a segmental insertion on chromosome 1, containing NBPF4, NBPF5, STXMP3, CLCC1, and GPSM2 genes (β = 1.66, p = 6.06×10(-5)). For African-Americans, segmental deletions spanning PRR20, PCDH17 and PCH68 genes on chromosome 13 were associated with elevated early antibody production (β = 0.18, p = 4.47×10(-5)). Population-specific findings aside, one genomic insertion on chromosome 17 (containing NSF, ARL17 and LRRC37A genes) was associated with elevated peak antibody response in both populations.

Conclusion: Multiple CNV regions, including the one consisting of MHC genes that is consistent with earlier research, can be important to humoral immune responses to anthrax vaccine adsorbed.

Trial registration: ClinicalTrials.gov NCT00119067.

Conflict of interest statement

Competing Interests: One of the co-authors, Dr. Jianming Tang currently serves as an Associate Editor for PLOS ONE. However, this does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials.

Figures

Figure 1. Distribution of insertion and deletion CNVs across chromosome 1 among European Americans: a) CNV calls based on the hidden Markov model calling algorithm PennCNV, b) CNV calls based on the change-point calling algorithm GeneSpring GX 11, and c) CNV calls based on the concordance between PennCNV and GeneSpring.

On the vertical axis, the top peaks (blue) demonstrate the actual count of insertions and the bottom peaks (red) demonstrate the actual count of deletions. The X axis shows chromosome 1 location.

Figure 2. Genome-wide CNV association for early anthrax antibody response among European Americans: a) any insertions at 8 week AbPA titer, b) any deletions at 8 weeks AbPA titer.

Association was assessed using linear regression models adjusted for age, sex, route of administration (SQ vs. IM), and the principal components analysis (PCA) of ancestry. The X axis shows chromosomal locations, and P values were plotted on the Y axis using logarithmic scale.

Figure 3. Genome-wide CNV association for peak anthrax antibody response among European Americans: a) any insertions at 30 week AbPA titer, and b) any deletions at 30 week AbPA titer.

Association was assessed using single linear regression adjusted for age, sex, route of administration (SQ vs. IM), and the principal components analysis (PCA) of ancestry. The X axis shows chromosomal locations, and P values were plotted on the Y axis using a logarithmic scale.