600 dorsolateral prefrontal cortex** samples, and DNA methylation QTL summary output on **258 prefrontal cortex** samples (age >13)[18]. The reference genotypes were based on the Health and Retirement Study, imputed to the 1000 Genomes phase 1 reference panel. SNP exclusions included: imputation score <0.3, Hardy?Weinberg P-value 600 samples," but in the dataset [syn4622659](https://www.synapse.org/#!Synapse:syn4622659), they say that the Gene-level eQTL (and isoQTL) were derived from: "**n=467** genetically-inferred Caucasian samples (209 SCZ cases, 206 Controls, and 52 AFF cases)". I need to know the sample size, so I would be grateful if someone could clarify this, please. Also, I wanted to know if the eQTL data is based on the reference genome Hg38? I want to use it for colocalization analysis and need to know if I should apply liftover. I'll very gratefull for your help. Kind regards :) " />

Hi all! While looking for eQTL data from brain tissues to do a colocalization analysis to study Alzheimer's disease I found this great article: https://www.nature.com/articles/s41398-018-0150-6 They talk about the two sets of eQTL summary data that they used (one with adjustments and another with more adjustments): """ **Summary data-based Mendelian randomisation** To test for pleiotropic associations between SNPs and AD and gene expression/DNA methylation in the brain, summary data-based Mendelian randomisation (SMR) was performed17. GWAS summary output from the meta-analysis of UK Biobank and IGAP (sample size specified as 314,278?+?74,046?=?388,324) were included along with expression Quantitative Trait Loci (QTL) summary output from the Common Mind Consortium, which contains data on **>600 dorsolateral prefrontal cortex** samples, and DNA methylation QTL summary output on **258 prefrontal cortex** samples (age >13)[18]. The reference genotypes were based on the Health and Retirement Study, imputed to the 1000 Genomes phase 1 reference panel. SNP exclusions included: imputation score <0.3, Hardy?Weinberg P-value 600 samples," but in the dataset [syn4622659](https://www.synapse.org/#!Synapse:syn4622659), they say that the Gene-level eQTL (and isoQTL) were derived from: "**n=467** genetically-inferred Caucasian samples (209 SCZ cases, 206 Controls, and 52 AFF cases)". I need to know the sample size, so I would be grateful if someone could clarify this, please. Also, I wanted to know if the eQTL data is based on the reference genome Hg38? I want to use it for colocalization analysis and need to know if I should apply liftover. I'll very gratefull for your help. Kind regards :)

Created by Lila Maciel Rodríguez Pérez Lila_Maciel2024
@Lila_Maciel2024 You should reach out to the manuscript authors for clarity on their manuscript and analyses. The eQTL were imputed to 1000 Genomes phase 1, which is Hg37. You might also be interested in this eQTL meta-analysis, which includes more samples and is in Hg38: https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage/StudyDetails?Study=syn25398075

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