| Literature DB >> 32157568 |
Michael Strupp1, Stephan Maul2, Bettina Konte2, Annette M Hartmann2, Ina Giegling3, Sophia Wollenteit3, Katharina Feil3, Dan Rujescu3,2.
Abstract
Downbeat nystagmus (DBN) is a frequent form of acquired persisting central fixation nystagmus, often associated with other cerebellar ocular signs, such as saccadic smooth pursuit or gaze-holding deficits. Despite its distinct clinical features, the underlying etiology of DBN often remains unclear. Therefore, a genome-wide association study (GWAS) was conducted in 106 patients and 2609 healthy controls of European ancestry to identify genetic variants associated with DBN. A genome-wide significant association (p < 5 × 10-8) with DBN was found for a variation on chromosome 13 located within the fibroblast growth factor 14 gene (FGF14). FGF14 is expressed in Purkinje cells (PCs) and a reduction leads to a decreased spontaneous firing rate and excitability of PCs, compatible with the pathophysiology of DBN. In addition, mutations in the FGF14 gene cause spinocerebellar ataxia type 27. Suggestive associations (p < 1 × 10-05) could be detected for 15 additional LD-independent loci, one of which is also located in the FGF14 gene. An association of a region containing the dihydrofolate reductase (DHFR) and MutS Homolog 3 (MSH3) genes on chromosome 5 was slightly below the genome-wide significance threshold. DHFR is relevant for neuronal regulation, and a dysfunction is known to induce cerebellar damage. Among the remaining twelve suggestive associations, four genes (MAST4, TPPP, FTMT, and IDS) seem to be involved in cerebral pathological processes. Thus, this GWAS analysis has identified a potential genetic contribution to idiopathic DBN, including suggestive associations to several genes involved in postulated pathological mechanisms of DBN (i.e., impaired function of cerebellar PCs).Entities:
Keywords: Cerebellum; Dihydrofolate reductase (DHFR); Downbeat nystagmus; Fibroblast growth factor 14 (FGF14); Genome-wide association study
Year: 2020 PMID: 32157568 PMCID: PMC7198638 DOI: 10.1007/s12311-020-01113-x
Source DB: PubMed Journal: Cerebellum ISSN: 1473-4222 Impact factor: 3.847
Batch distribution of cases and controls
| Post-imputation | GWAS | ||
|---|---|---|---|
| Batch | |||
| 1 | 319 | 0 | 0 |
| 2 | 709 | 262 | 0 |
| 3 | 954 | 925 | 0 |
| 4 | 287 | 99 | 0 |
| 5 | 607 | 578 | 0 |
| 6 | 352 | 267 | 0 |
| 7 | 1347 | 478 | 106 |
| Combined | 4575 | 2609 | 106 |
Fig. 1Scatterplot of the first two principal components (PC) derived by EIGENSTRAT
Fig. 2Manhattan plot of the genome-wide association analysis of 106 DBN cases and 2609 controls. The x-axis shows the chromosomal position, and the y-axis shows the significance of association (−log10(p)). The red line shows the genome-wide significance level (5 × 10−8)
Fig. 3Quantile-quantile plot of GWAS analysis. The area shaded in gray indicates the 95% confidence interval under the null
LD-independent SNV associations for DBN
| Chr. (region) | SNV | A1/2 | Info | Frqcon | Frqcase | OR (95% CI) | Gene (dist.) | |
|---|---|---|---|---|---|---|---|---|
Chr. 13 102,703,679–103,052,397 | rs72665334 | T/C | 0.720 | 0.074 | 0.189 | 4.30 (2.60–7.13) | FGF14 (0) | |
| chr13_103023008_D | TAAC/− | 0.956 | 0.945 | 0.840 | 0.31 (0.19–0.51) | 4.52E-06 | ||
Chr. 1 30,238,075–30,238,075 | rs147830437 | T/C | 0.928 | 0.223 | 0.343 | 2.36 (1.65–3.38) | 2.98E-06 | LINC01648 (246982) |
Chr. 2 79,338,772–79,338,772 | rs140798366 | A/G | 0.725 | 0.022 | 0.065 | 7.25 (3.03–17.38) | 8.85E-06 | REG1A (8812) |
Chr. 3 63,595,461–63,595,461 | rs113612577 | T/C | 0.872 | 0.014 | 0.053 | 6.38 (2.81–14.5) | 9.44E-06 | SYNPR (0) |
Chr. 3 175,540,277–175,540,538 | rs113420566 | C/G | 0.732 | 0.954 | 0.908 | 0.21 (0.11–0.42) | 9.06E-06 | NAALADL2 (16849) |
Chr. 4 8,190,987–8,190,987 | rs148323050 | T/C | 0.666 | 0.013 | 0.046 | 12.49 (4.16–37.53) | 6.82E-06 | SH3TC1 (10073) |
Chr. 5 662,547–676,768 | rs12516404 | A/G | 0.814 | 0.133 | 0.244 | 2.57 (1.69–3.91) | 9.45E-06 | TPPP (0) |
Chr. 5 66,364,063–66,455,108 | rs74495954 | T/C | 0.998 | 0.985 | 0.953 | 0.15 (0.06–0.34) | 6.51E-06 | MAST4 (0) |
Chr. 5 79,902,336–80,171,134 | rs245100 | A/G | 0.966 | 0.747 | 0.557 | 0.45 (0.32–0.61) | 5.03E-07 | DHFR (0) MSH3 (0) |
| rs33003 | A/G | 0.985 | 0.345 | 0.170 | 0.39 (0.26–0.58) | 3.87E-06 | ||
Chr. 5 120,836,941–120,894,696 | rs111326090 | C/G | 1.025 | 0.814 | 0.680 | 0.47 (0.33–0.65) | 8.85E-06 | FTMT (303199) |
Chr. 5 160,104,068–160,104,068 | rs151003482 | A/G | 0.947 | 0.017 | 0.064 | 6.04 (2.77–13.21) | 6.43E-06 | ATP10B (0) |
Chr. 11 133,618,819–133,657,216 | rs34790786 | A/G | 0.959 | 0.816 | 0.701 | 0.43 (0.30–0.61) | 3.49E-06 | SPATA19 (53301) |
Chr. 21 39,418,784–39,541,479 | rs138188997 | C/G | 0.754 | 0.972 | 0.931 | 0.17 (0.08–0.37) | 6.56E-06 | DSCR4 (7529) |
Chr. X 148,510,680–148,532,290 | rs187733794 | T/C | 1.001 | 0.020 | 0.078 | 4.89 (2.48–9.65) | 4.49E-06 | IDS (28005) |
Genome-wide significant association is shown on top (p value in bold); otherwise, SNVs are sorted by genomic position according to UCSC hg19/NCBI build 37. The deletion variant is given in the form “chromosome_position_deletion.” Column A12 contains the SNV alleles, with the first allele (A1) depicting the reference allele for the frequency (Frq) and odds ratio (OR) of A1. CI is the confidence interval, gene is the next gene, dist. is the distance to index SNV in bp. Chromosome (Chr.) and position denote the associated region surrounding the index SNV containing SNVs in LD (r > 0.6) with the index SNV. Two LD-independent regions were merged on account of a distance below 250 kb (shaded in gray)
Fig. 4Regional association plots for loci associated with DBN. In order to highlight the statistical strength of the association in the context of the surrounding markers, gene annotations and estimated recombination rates (NCBI build 37) of the SNPs in the specific regions are plotted against their corresponding p values (as −log10 values, left-hand y-axis). A purple diamond represents the SNP with the highest association signal in each locus. All other SNPs are represented as single dots, where dot colors indicate the LD with the associated SNP. Color coding represents the r value, and respective categories are shown on the upper left hand side. Estimated recombination rates (cM/Mb) are plotted to reflect the local LD structure surrounding the associated SNP and are shown as vertical light blue lines, marked on the right-hand y-axis. Genes in the region are displayed below. The orientation of the genes is indicated by arrows. a Regional association plot of the FGF14 variations on chromosome 13q33.1 associated with DBN. The genome-wide–associated SNP (rs72665334, purple diamond) is localized in intron 9, the suggestive hit chr13_103023008_D (yellow circle) in intron 1 of the fibroblast growth factor 14 gene (FGF14). LD structure refers to the genome-wide associated variant rs72665334. b Regional association plot of the merged region on chromosome 5 containing the overlapping genes DHFR and MSH3 and the respective hits (rs245100, purple; rs33003, yellow). LD structure refers to the associated variant localized in DHFR (rs245100)