Population genomics in a disease targeted primary cell model

Abstract

The common genetic variants associated with complex traits typically lie in noncoding DNA and may alter gene regulation in a cell type-specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an expression quantitative trait loci (eQTL) study of primary human osteoblasts (HOb) derived from 95 unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. We combined our data with publicly available information from a genome-wide association study (GWAS) of bone mineral density (BMD). The top 2000 BMD-associated SNPs (P < ;10 À3 ) were tested for cisassociation of gene expression in HObs and in lymphoblastoid cell lines (LCLs) using publicly available data and showed that HObs have a significantly greater enrichment (threefold) of converging cis-eQTLs as compared to LCLs. The top 10 BMD loci with SNPs showing strong cis-effects on gene expression in HObs (P = 6 3 10 À10 À 7 3 10 À16 ) were selected for further validation using a staged design in two cohorts of Caucasian male subjects. All 10 variants were tested in the Swedish MrOS Cohort (n = 3014), providing evidence for two novel BMD loci (SRR and MSH3). These variants were then tested in the Rotterdam Study (n = 2090), yielding converging evidence for BMD association at the 17p13.3 SRR locus (P combined = 5.6 3 10 À5 ). The cis-regulatory effect was further fine-mapped to the proximal promoter of the SRR gene (rs3744270, r 2 = 0.5, P = 2.6 3 10 À15 ). Our results suggest that primary cells relevant to disease phenotypes complement traditional approaches for prioritization and validation of GWAS hits for follow-up studies.

Global miRNA expression and correlation with mRNA levels in primary human bone cells

“…mRNA-expression profiling of the 95 samples, each with three biological replicates, was performed using the Illumina HumRef-8v2 BeadChips (Illumina, Inc.) where 200 ng of total RNA was processed according to the protocol supplied by Illumina as previously reported (Grundberg et al 2009) The biological replicates were always separated and hybridized on different BeadChips in order to avoid that results are confounded by technical effects. Any sample or array that showed an abnormal distribution of signal intensities as visualized in box plots was removed or rehybridized.…”

“…Specimens were collected from 104 donors from a cohort of patients with osteoarthritis undergoing total hip or knee replacement, with no other bone-related pathologies reported (Grundberg et al 2009(Grundberg et al , 2011. The bone chips obtained from each donor were thoroughly minced and washed with PBS.…”

Correction for hidden confounders in the genetic analysis of gene expression

“…From the perspective of dissecting the genetics of a complex disease, eQTL studies can provide insight into how a disease-associated locus might be contributing to the disease of interest by providing information about which gene-expression pathway(s) the locus is affecting (2,4). From a statistical perspective, one can use the results of an eQTL study to prioritize a list of disease-associated loci to follow up on; that is, one can use the existence of a SNP-gene-expression association as prior evidence that variation at the locus is more likely to have disease consequences (2,6). Furthermore, eQTL studies can infuse causal information into gene-gene and protein-protein correlation networks by making use of the fact that DNA can affect gene expression, but not the other way around (1,(7)(8)(9).…”

ATP2C2andDYX1C1are putative modulators of dyslexia‐related MMR

“…To identify eQTL effects, eQTL databases were analyzed (Borel et al., 2011; Dimas et al., 2009; Dixon et al., 2007; Fehrmann et al., 2011; Greenawalt et al., 2011; Grundberg et al., 2009; GTEx Consortium, 2015; Kim, Cho, Lee, & Webster, 2012; Kirsten et al., 2015; Mehta et al., 2013; Myers et al., 2007; Ramasamy et al., 2014; Schadt et al., 2008; Schröder et al., 2011; Veyrieras et al., 2008; Westra et al., 2013; Xia et al., 2012; Zeller et al., 2010). We only considered SNPs identified in brain or blood tissue and eQTLs had to be replicated in at least one study.…”