Genome-wide association study identifies novel restless legs syndrome susceptibility loci on 2p14 and 16q12.1

Abstract

Restless legs syndrome (RLS) is a sensorimotor disorder with an age-dependent prevalence of up to 10% in the general population above 65 years of age. Affected individuals suffer from uncomfortable sensations and an urge to move in the lower limbs that occurs mainly in resting situations during the evening or at night. Moving the legs or walking leads to an improvement of symptoms. Concomitantly, patients report sleep disturbances with consequences such as reduced daytime functioning. We conducted a genome-wide association study (GWA) for RLS in 922 cases and 1,526 controls (using 301,406 SNPs) followed by a replication of 76 candidate SNPs in 3,935 cases and 5,754 controls, all of European ancestry. Herein, we identified six RLS susceptibility loci of genome-wide significance, two of them novel: an intergenic region on chromosome 2p14 (rs6747972, P = 9.03 × 10(-11), OR = 1.23) and a locus on 16q12.1 (rs3104767, P = 9.4 × 10(-19), OR = 1.35) in a linkage disequilibrium block of 140 kb containing the 5'-end of TOX3 and the adjacent non-coding RNA BC034767.

Figure 1. Manhattan plot of the GWA.

Association results of the GWA stage. The x-axis represents genomic position along the 22 autosomes and the x-chromosome, the y-axis shows -log10(P) for each SNP assayed. SNPs with a nominal λ-corrected P<10⁻⁴ are highlighted as circles.

Figure 2. Forest plots of the RLS risk loci (1 SNP per locus).

OR and corresponding confidence interval for the GWA sample, all individual replication samples, the combined replication sample as well as the combined GWA and replication sample are depicted. ORs are indicated by squares with the size of the square corresponding to the sample size for the individual populations. (A) rs2300478 in MEIS1; (B) rs9357271 in BTBD9; (C) rs1975197 in PTPRD; (D) rs12593813 in MAP2K5/SKOR1; (E) rs6747972 in intergenic region on chromosome 2; (F) rs3104767 in TOX3/BC034767.

Figure 3. New genome-wide significant RLS loci.

a) Risk locus on chromosome 2p14, showing the best-associated SNP rs6747972 and ±200 kb of surrounding sequence. b) Risk locus on chromosome 16p21, showing the best-associated SNP rs3104767 and ±200 kb of surrounding sequence. The left-hand x-axis shows the negative log10 of the nominal λ-corrected P-values of the GWA stage for all SNPs genotyped in the respective region. The right-hand x-axis shows the recombination frequency in cM/Mb. The y-axis shows the genomic position in Mb based on the hg18 assembly. The r²-based LD between SNPs is colour-coded, ranging from red (r²>0.8) to dark blue (r²<0.2) and uses the best-associated SNP as reference. This SNP is depicted as a violet diamond. Recombination frequency and r² values are calculated from the HapMap II (release 22) CEU population. Plots were generated with LocusZoom 1.1 (http://csg.sph.umich.edu/locuszoom/).