Genetic overlap between Alzheimer's disease and Parkinson's disease at the MAPT locus.
- Authors
- Desikan, R S; Schork, A J; Wang, Y; Witoelar, A; Sharma, M; McEvoy, L K; Holland, D; Brewer, J B; Chen, C-H; Thompson, W K; Harold, D; Williams, J; Owen, M J; O'Donovan, M C; Pericak-Vance, M A; Mayeux, R; Haines, J L; Farrer, L A; Schellenberg, G D; Heutink, P; Singleton, A B; Brice, A; Wood, N W; Hardy, J; Martinez, M; Choi, S H; DeStefano, A; Ikram, M A; Bis, J C; Smith, A; Fitzpatrick, A L; Launer, L; van Duijn, C; Seshadri, S; Ulstein, I D; Aarsland, D; Fladby, T; Djurovic, S; Hyman, B T; Snaedal, J; Stefansson, H; Stefansson, K; Gasser, T; Andreassen, O A; Dale, A M; ADNI, ADGC, GERAD, CHARGE and IPDGC Investigators
- Year
- 2015
- Journal
- Molecular psychiatry
- PMID
- 25687773
- DOI
- 10.1038/mp.2015.6
- PMCID
- PMC4539304
We investigated the genetic overlap between Alzheimer's disease (AD) and Parkinson's disease (PD). Using summary statistics (P-values) from large recent genome-wide association studies (GWAS) (total n=89 904 individuals), we sought to identify single nucleotide polymorphisms (SNPs) associating with both AD and PD. We found and replicated association of both AD and PD with the A allele of rs393152 within the extended MAPT region on chromosome 17 (meta analysis P-value across five independent AD cohorts=1.65 Γ 10(-7)). In independent datasets, we found a dose-dependent effect of the A allele of rs393152 on intra-cerebral MAPT transcript levels and volume loss within the entorhinal cortex and hippocampus. Our findings identify the tau-associated MAPT locus as a site of genetic overlap between AD and PD, and extending prior work, we show that the MAPT region increases risk of Alzheimer's neurodegeneration.
Forest plot for rs393152. Since rs393152 was not available within the Oslo cohort (*), we used a proxy SNP (rs17690703; r2 = .765, D'=1 in Hapmap2).
LLM interpretation
This is a forest plot showing the odds ratios (OR) and 95% confidence intervals (CI) for the SNP rs393152 across five individual studies (ADGC, GERAD, DeCODE, Oslo, and CHARGE) and a joint analysis. The x-axis represents the Odds Ratio, with a vertical dashed line at 1.0 indicating no effect. The joint analysis result, represented by a red diamond, shows a statistically significant decrease in odds (OR = 0.91, p = 1.65e-07) as the diamond and its CI are entirely to the left of the null line.
(a) Regional linkage disequilibrium (LD) plot demonstrating the relationship between rs393152 on chromosome 17 and loci greater than and less than 1 MB. The bottom panel indicates the location of genes in the region. Linkage Disequilibrium measured in the 1000 genomes European Populations using plink v1.07.(b) Regional association plot illustrating the association signal within the MAPT region on chromosome 17. The bottom panel indicates the location of genes in the region. Linkage Disequilibrium measured in the 1000 genomes European Populations using plink v1.07.
LLM interpretation
This is a regional association plot (Manhattan plot) showing the association signal within the MAPT region on chromosome 17. The y-axis represents $-\log_{10}(p)$ values and the x-axis represents the base pair position in kilobases (kB), with a cluster of highly significant SNPs (red dots, $r^2=1$) centered around the reference SNP rs393152. A bottom panel maps the locations of genes in this region, with the MAPT gene highlighted by a grey shaded vertical bar.
Box plots illustrating the relationship between rs393152 alleles (x-axis) and gene expression levels of MAPT, SYP, and SNCA (y-axis). For each plot, thick black lines show the median value. Regions above and below the black line show the upper and lower quartiles, respectively. The dashed lines extend to the minimum and maximum values with outliers shown as open circles. For MAPT, a proxy SNP was used (please see Results for additional details). As illustrated, the A allele of rs393152 demonstrated a selective dose-dependent effect on the level of intracranial MAPT transcript.
LLM interpretation
This figure consists of three box plots showing the relationship between rs393152 alleles (AA, AG, GG) and the mRNA expression levels of *MAPT*, *SYP*, and *SNCA*. For *MAPT*, there is a visible dose-dependent decrease in expression levels from the AA to the GG genotype. In contrast, *SYP* and *SNCA* expression levels remain relatively stable across the three genotype groups.
Regional association plot demonstrating the relationship between MAPT transcript expression levels (y-axis) and SNPs in LD with rs393152 on chromosome 17. The bottom panel indicates the location of genes in the region. Linkage Disequilibrium measured in the 1000 genomes European Populations using plink v1.07. As illustrated, SNPs in r2 LD =1 with rs393152 constituted the peak of the association signal with MAPT transcript expression levels.
LLM interpretation
This figure is a regional association plot (Manhattan plot) showing the relationship between SNPs on chromosome 17 and *MAPT* transcript expression levels. The top panel plots $-\log_{10}(p)$ against base pair position (kB), with points color-coded by linkage disequilibrium ($r^2$) relative to rs393152, showing a peak of highly significant associations (red dots, $r^2=1$) centered around the *MAPT* gene. The bottom panel provides a genomic map of genes in the region, with the *MAPT* gene location highlighted by a gray shaded vertical bar.
Bar plots demonstrating the relationship between rs393152 alleles (x-axis) and volume loss (annualized percent change β y-axis) of the hippocampus (blue) and entorhinal cortex (gray) among APOE Ξ΅4 carriers (left panel) and APOE Ξ΅4 non-carriers (right panel). As illustrated, the A allele of rs393152 demonstrated a selective dose-dependent relationship with medial temporal lobe atrophy only among APOE Ξ΅4 non-carriers.
LLM interpretation
This figure consists of two side-by-side bar plots showing the annualized percent change in volume for the hippocampus (blue) and entorhinal cortex (gray) across rs393152 genotypes (AA, AG, GG). The left panel represents APOE Ξ΅4 carriers, where volume loss remains relatively consistent across genotypes, while the right panel represents APOE Ξ΅4 non-carriers. In the non-carrier group, there is a visible dose-dependent trend where the GG genotype is associated with less volume loss compared to the AA genotype.
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