Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.

paper Cited Public

Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS) have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls) were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls). These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls). Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27 × 10(-51)) withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible susceptibility gene for ALS.

Figure 1

Study design.For each step, the number of resulting SNP-transcript pairs in cis is shown.

LLM interpretation

This figure is a study design flowchart illustrating a filtering process to identify significant SNP-transcript pairs. It shows a sequential reduction in the number of pairs from eQTL discovery (16,901) through eQTL selection (1,108) and replication (951), resulting in 8 final eQTL results. The process incorporates GWAS discovery (14,167 SNPs with $P_{GWAS} < 0.05$) and GWAS replication (SNPs with $P_{GWAS} < 0.05$ after Bonferroni correction) as integrating steps.

Figure 2

Regional linkage disequilibrium (LD) near the CYP27A1 locus on chromosome 2.Top: the position of GWAS SNPs and RefSeq genes located within the regional LD block are drawn. On the X-axis, genomic position in kb, aligned to NCBI genome build 36 coordinates. On the left Y-axis, −log10(p values) for the strongest cis eQTL association for a gene in the replication data, the vertical position of genes (drawn as arrows) are aligned to this axis and thus represent statistical significance. For one gene (RQCD1), no SNP-transcript pair and, therefore, no eQTL p value was available in our data. This gene is shown as a dashed arrow. On the right Y-axis, −log10(p values) from the replication GWAS analysis for SNPs within the region (black line), SNPs modulating CYP27A1 expression are shown as black dots, other SNPs are grey. Bottom: pairwise linkage disequilibrium for HapMap phase III release 2 SNPs (CEU+TSI populations). The LD plot was created in Haploview v4.2 [50], using the standard D'/LOD color scheme.

LLM interpretation

This figure consists of a genomic plot (top) and a linkage disequilibrium (LD) heat map (bottom) centered on the *CYP27A1* locus on chromosome 2. The top panel displays genomic positions (kb) on the x-axis, with the left y-axis showing $-\log_{10}(p\text{-values})$ for cis-eQTL associations for several genes (represented by arrows) and the right y-axis showing $-\log_{10}(p\text{-values})$ for GWAS SNPs (black line and dots). The bottom panel is a Haploview LD plot using a red-scale D'/LOD color scheme to show pairwise LD between HapMap SNPs across the region.

#	Section	Preview
0	Introduction	Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive…
1	Introduction	Approximately 5% of patients have a family history of ALS [1]. All other cases are considered to…
2	Introduction	Despite these large study samples, GWAS have been able to explain only little of the genetic…
3	Introduction	It has been established that gene expression levels can be mapped to genomic variation as a…
4	Introduction	of gene expression levels has frequently been applied to the fine-mapping of risk loci resulting…
5	Introduction	A schematic overview of our study design is shown in Figure 1. We performed an initial screen for…
6	Methods — Ethics Statement	All participants gave written informed consent and approval was obtained from the Institutional…
7	Methods — GWAS Data	Genome-wide genotype data were derived from a previously published GWAS of sporadic ALS in seven…
8	Methods — GWAS Data	heterozygosity or missing rates between cases and controls were excluded. Duplicate samples, samples…
9	Methods — Expression Data	Genome-wide gene expression data were obtained from 805 Dutch individuals (357 patients and 448…
10	Methods — Expression Data	The R Foundation for Statistical Computing). Using principal components analysis of expression data,…
11	Methods — eQTL Datasets	For the genetic mapping of gene expression, the subset of Dutch individuals with both genome-wide…
12	Methods — Statistical Analysis	For the GWAS data, association with disease was tested in a logistic model using gender, dummy-coded…
13	Methods — Statistical Analysis	For all analyses involving expression data, Surrogate Variable Analysis (SVA) was used to account…
14	Methods — Statistical Analysis	For the eQTL analyses, SNP genotypes coded as an additive genetic model were tested for association…
15	Methods — Statistical Analysis	LD threshold r2 >0.2) were excluded from analysis. Similarly, we removed 24,170 SNP-transcript…
16	Methods — eQTL Selection	In order to link the identified eQTLs to disease, we made a selection of significant cis effects in…
17	Methods — eQTL Selection	Only these SNP-transcript pairs were used for follow-up in the replication data. Patient…
18	Methods — eQTL Selection	Subsequently, association with ALS for SNPs from the replicated cis SNP-transcript pairs was tested…
19	Results — eQTL Discovery	After quality control, eQTL analyses were performed on 162 ALS cases and 207 controls in the eQTL…

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