A genome-wide association study of chronic otitis media with effusion and recurrent otitis media identifies a novel susceptibility locus on chromosome 2

Abstract

Chronic otitis media with effusion (COME) and recurrent otitis media (ROM) have been shown to be heritable, but candidate gene and linkage studies to date have been equivocal. Our aim was to identify genetic susceptibility factors using a genome-wide association study (GWAS). We genotyped 602 subjects from 143 families with 373 COME/ROM subjects using the Illumina Human CNV370-Duo DNA Bead Chip (324,748 SNPs). We carried out the GWAS scan and imputed SNPs at the regions with the most significant associations. Replication genotyping in an independent family-based sample was conducted for 53 SNPs: the 41 most significant SNPs with P < 10(-4) and 12 imputed SNPs with P < 10(-4) on chromosome 15 (near the strongest signal). We replicated the association of rs10497394 (GWAS discovery P = 1.30 × 10(-5)) on chromosome 2 in the independent otitis media population (P = 4.7 × 10(-5); meta-analysis P = 1.52 × 10(-8)). Three additional SNPs had replication P values < 0.10. Two were on chromosome 15q26.1 including rs1110060, the strongest association with COME/ROM in the primary GWAS (P = 3.4 ×10(-7)) in KIF7 intron 7 (P = 0.072), and rs10775247, a non-synonymous SNP in TICRR exon 2 (P = 0.075). The third SNP rs386057 was on chromosome 5 in TPPP intron 1 (P = 0.045). We have performed the first GWAS of COME/ROM and have identified a SNP rs10497394 on chromosome 2 is significantly associated with COME/ROM susceptibility. This SNP is within a 537 kb intergenic region, bordered by CDCA7 and SP3. The genomic and functional significance of this newly identified locus in COME/ROM pathogenesis requires additional investigation.

FIG. 1.

COME/ROM genome-wide scan association results using the QLS_W method (GC = genomic control value). The circled SNPs represent the SNPs in Table 2 (replication P < 0.10). The SNP circled in red is rs10497394, the significantly replicated SNP. X chromosome analyses were not presented since they were analyzed using a different method (GDT; Chen et al. 2009).

FIG. 2.

Genomic characteristics of the chromosome 2 region of high LD (chr2: 174286992–174307309) from UCSC Genome Browser build hg19 which includes a processed pseudogene with 89 % sequence identity to the coding sequence of the hematological and neurological expressed 1 (HN1) gene; an H3K27Ac mark and an H3K4Me1 mark from ENCODE; DNaseI hypersensitive regions including those discovered in relevant cell lines (lung, non-pigment ciliary epithelial, and small airway epithelial cell lines); a conserved CTCF insulator binding site; and numerous predicted transcription factor binding sites (The ENCODE Project Consortium ; Rosenbloom et al. 2012). Conservation in this region is measured using Multiz Alignments of eight vertebrates.

FIG. 3.

Locus Zoom plots of the chromosome 2 region using UMN GWAS data and HapMap3 imputation. SNP shown in purple is our replicated SNP rs10497394, and linkage disequilibrium (LD) is in relation to this SNP.