Osteoclast-specific eQTL results for osteoporosis risk variants (co-localised loci)

This dataset contains osteoclast-specific
expression quantitative trait locus (eQTL) summary statistics for 21 genetic
loci demonstrating co-localisation with estimated bone mineral density (eBMD)
genome-wide association study (GWAS) association signals from Morris et al.
(PMID 30598549). The data is provided in a single .xlsx file. The complete osteoclast eQTL dataset is publicly available on the GEnetic Factors for OSteoporosis Consortium (GEFOS) website (http://www.gefos.org/?q=content/human-osteoclast-eqtl-2018-2020).

The
eQTL results were generated from a study of 158 osteoclast cell cultures (PMID 32216834, 29473973, 30705363). Genome-wide array genotyping was performed on genomic
DNA samples from the study participants using the Illumina Infinium
OmniExpress-24 BeadChip array, with imputation performed using the Haplotype
Reference Consortium (HRC) release 1.1 reference panel. Transcriptome-wide
quantitation of gene expression was performed on the osteoclast RNA samples
using 50 bp single-end RNA-Seq on an Illumina HiSeq 2500. Trimmed mean of
M-values (TMM) normalisation and correction for total read count by conversion
to counts per million (CPM) was performed on the gene expression data using the
edgeR package. The eQTL analysis was performed on the TMM-normalised CPM gene
expression values using the FastQTL software, implementing quantile
normalisation. Only variants with a MAF≥5% were included in the analysis, which
was adjusted for the covariates patient age, RNA-Seq batch and 10 genomic
principal components.