Genetic Susceptibility Loci in Genomewide Association Study of Cluster Headache

Abstract

Objective: Identifying common genetic variants that confer genetic risk for cluster headache.

Methods: We conducted a case-control study in the Dutch Leiden University Cluster headache neuro-Analysis program (LUCA) study population (n = 840) and unselected controls from the Netherlands Epidemiology of Obesity Study (NEO; n = 1,457). Replication was performed in a Norwegian sample of 144 cases from the Trondheim Cluster headache sample and 1,800 controls from the Nord-Trøndelag Health Survey (HUNT). Gene set and tissue enrichment analyses, blood cell-derived RNA-sequencing of genes around the risk loci and linkage disequilibrium score regression were part of the downstream analyses.

Results: An association was found with cluster headache for 4 independent loci (r² < 0.1) with genomewide significance (p < 5 × 10^-8 ), rs11579212 (odds ratio [OR] = 1.51, 95% confidence interval [CI] = 1.33-1.72 near RP11-815 M8.1), rs6541998 (OR = 1.53, 95% CI = 1.37-1.74 near MERTK), rs10184573 (OR = 1.43, 95% CI = 1.26-1.61 near AC093590.1), and rs2499799 (OR = 0.62, 95% CI = 0.54-0.73 near UFL1/FHL5), collectively explaining 7.2% of the variance of cluster headache. SNPs rs11579212, rs10184573, and rs976357, as proxy SNP for rs2499799 (r² = 1.0), replicated in the Norwegian sample (p < 0.05). Gene-based mapping yielded ASZ1 as possible fifth locus. RNA-sequencing indicated differential expression of POLR1B and TMEM87B in cluster headache patients.

Interpretation: This genomewide association study (GWAS) identified and replicated genetic risk loci for cluster headache with effect sizes larger than those typically seen in complex genetic disorders. ANN NEUROL 2021;90:203-216.

FIGURE 1

Manhattan plot and reginal plots for the discovery analysis. (A) Manhattan plot showing the ‐log₁₀ p value for each SNP. Each marker was tested for association using an additive genetic model by logistic regression. The horizontal axis shows the chromosomal position and the vertical axis shows the significance of tested markers from logistic regression. The threshold for genome wide significance (p < 5 × 10⁻⁸) is indicated by a red dotted line. Markers that reach genomewide significance are shown in blue. (B–E) Regional Manhattan plots of the 4 genomewide significant cluster headache loci, with +/− 600 kb‐window. Each dot represents an SNP, the horizontal axis gives the genomic coordinate and the vertical axis the significance level (−log₁₀ p value). The index SNP for each locus is marked with a purple diamond and annotated with its corresponding location number (CRCh37/hg19). SNPs are colored based on their correlation (r ²) with the labeled lead SNP according to the legend. The solid blue line shows the recombination rate from 1000 Genomes (EUR) data (right vertical axis). Gencode genes are shown. Figures were obtained from LocusZoom. (B) Locus: rs11579212 and 1:222072819. (C) Locus: rs6541998 and 2:112785237. (D) Locus: rs10184573 and 2:200448253. (E) Locus: rs2499799 and 6:96851676. SNP = single nucleotide polymorphisms. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 2

Quantile‐quantile (QQ) plot for association with cluster headache (CH). The horizontal axis shows ‐log₁₀ p values expected under the null distribution. The vertical axis shows observed ‐log₁₀ p values. Red = common SNPs (MAF ≥0.05), blue = low frequency SNPs (MAF = 0.005–0.05). Genomic inflation factor (λ) = 1.069. MAF = minor allele frequency; SNPs = single nucleotide polymorphisms. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 3

Gene‐based Manhattan plot. Input SNPs were mapped to 18,795 protein coding genes. The horizontal axis shows the chromosomal position and the vertical axis shows the significance of tested markers. The threshold for genome wide significance (p = 0.05/18,795 = 2.66 × 10⁻⁶) is indicated by a dotted line. SNP = single nucleotide polymorphism. [Color figure can be viewed at www.annalsofneurology.org]