Inquiry regarding PsychENCODE eQTL resource


Was the eQTLs calculated on 1,886 unique individuals?

No, the eQTLs were calculated on 1387 filtered adult samples with matching gene expression and genotypes.

In Fig S34, it mentions only 1,432 individuals have genotyped. How was the genotype information determined for the remaining 454 individuals?

We didn’t have genotype information determined for the remaining 454 individuals. So we didn’t include these 454 individuals in any QTL analysis.

The # of samples with genotypes enumerated in Table S1 and Table S11 do not appear to match. For example, Table S1 reports 450 GTEx samples (97 DFC), but Table S11 reports 25 GTEx genotypes from the pre-frontal cortex. There might be some subtlety between these two tables I have missed, could you please clarify how to properly interpret these tables?

The Genotypes column in Table S11 only includes the filtered high genotyping quality samples (for example, genotype imputation accuracy score R2>0.3) which have matched RNA-seq data.

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