A Genome-Wide Screen for Large-Effect Alloimmunization Susceptibility Loci among Red Blood Cell Transfusion Recipients with Sickle Cell Disease

Abstract

Background: A selective susceptibility of certain individuals to form multiple alloantibodies in response to red cell transfusion is well-recognized in clinical practice, and is a particular problem in persons with sickle cell disease (SCD). The reason for this differential susceptibility is unclear, but inter-individual genetic differences are likely to contribute.

Methods: We conducted a pilot case-control genome-wide association study using 1,000,000 SNPs in 94 alloimmune responders (cases) and non-responders (controls) with SCD in order to identify loci of large effect size associated with alloimmunization.

Results: No loci showed evidence of association at a genome-wide significance cut-off (p < 0.5 × 10(-8)). SNPs in the ARAP1/STARD10 region showed suggestive association (p < 1 × 10(-6)), but no association was observed at previously implicated loci TRIM21 or HLA. In analyses of the number of accumulated antibodies, a modest association was found with SNPs in the Toll-like receptor gene TLR10 (p < 1 × 10(-4)).

Conclusions: Alloimmunization in persons with SCD is unlikely to be mediated by loci of very large effect size; however, larger and more comprehensive studies are required to fully evaluate loci with more moderate effects. This study provides a working approach to such future studies in SCD.

Keywords: African American; GWAS; Genome-wide association studies; Genomics; Responders.

Fig. 1

Sample quality control (QC); Samples were removed from analysis if they i) failed to meet the minimum DNA concentration for the assay according to manufacturer's recommendations (DNA conc); ii) were successfully genotyped at less than 95% of included SNPs (Genotyping); iii) had an inbreeding coefficient (F) suggestive of an excess of homozygotes; iv) had evidence of close-familial pairing (identify by-decent (IBD) or were ancestry population outliers on principal components analysis (see fig. 2).

Fig. 2

Multidimensional scaling (MDS) cluster plot of study participants for principal components C1 and C2. A Clustering of SCD pilot cohort with HapMap African Americans from Oklahoma and in relation to major continental HapMap groups (YRI = Yoruba from Nigeria; CEU = Ceph from Utah). B MDS clustering of cases (black circles) and controls (red triangles) in the pilot cohort. PCA study outliers are circled.

Fig. 3

Case control GWAS of responder status. A Manhattan plot showing no SNPs below genome-wide significance (red line, p = 0.5 × 10^–8), but suggestive SNPs (blue line, p = 1 × 10^–4) in the ARAP1/STARD10 gene region (green dots). B Local Manhattan plot of 250 kb region around ARAP1/ STARD10 including genotyped and imputed SNPs. Pairwise LD (r²) is derived from the HapMap YRI population. C GWAS results for genotyped and imputed (shaded) SNPs in the ARAP1/STARD10 region. OR = Odds ratio; Perm P = permuted p value.

Fig. 4

Local Manhattan plots for previously associated loci TRIM21 (A) and the MHC (B). In each figure the highlighted SNP (purple diamond) is the strongest association in the region. In A pairwise LD (r²) is derived from the Hapmap YRI population. In B the gene list is restricted for space considerations.

Fig. 5

Suggestive association between SNPs across TLR10 and number of alloantibodies formed. A Local Manhattan plot of SNPs within 250 kb of TLR10. B SNPs showing suggestive association.