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We sought to comprehensively and systematically characterize the relationship between genetic variation, miRNA expression, and mRNA expression. Genome-wide expression profiling of samples of European and African ancestry identified in each population hundreds of miRNAs whose increased expression is correlated with correspondingly reduced expression of target mRNAs. We scanned 3' UTR SNPs with a potential functional effect on miRNA binding for cis-acting expression quantitative trait loci (eQTLs) for the corresponding proximal target genes. To extend sequence-based, localized analyses of SNP effect on miRNA binding, we proceeded to dissect the genetic basis of miRNA expression variation; we mapped miRNA expression levels-as quantitative traits-to loci in the genome as miRNA eQTLs, demonstrating that miRNA expression is under significant genetic control. We found that SNPs associated with miRNA expression are significantly enriched with those SNPs already shown to be associated with mRNA. Moreover, we discovered that many of the miRNA-associated genetic variations identified in our study are associated with a broad spectrum of human complex traits from the National Human Genome Research Institute catalog of published genome-wide association studies. Experimentally, we replicated miRNA-induced mRNA expression inhibition and the cis-eQTL relationship to the target gene for several identified relationships among SNPs, miRNAs, and mRNAs in an independent set of samples; furthermore, we conducted miRNA overexpression and inhibition experiments to functionally validate the miRNA-mRNA relationships. This study extends our understanding of the genetic regulation of the transcriptome and suggests that genetic variation might underlie observed relationships between miRNAs and mRNAs more commonly than has previously been appreciated.

Purpose Utilizing cell-based approaches to identify genetic markers predictive of patients’ risk for poor response prior to chemotherapy. Experimental Design We performed genome-wide association studies (GWASs) to identify SNPs associated with cellular sensitivity to carboplatin through their effects on mRNA expression using International HapMap lymphoblastoid cell lines (LCLs) and replicated them in additional LCLs. SNPs passing both stages of the cell-based study were tested for association with progression free survival (PFS) in patients. Phase-1 validation was based on 377 ovarian cancer patients receiving at least 4-cycle of carboplatin and paclitaxel from the Australian Ovarian Cancer Study (AOCS). Positive associations were then assessed in the phase-2 validation analysis of 1,326 patients from the Ovarian Cancer Association Consortium and The Cancer Genome Atlas. Results In the initial GWAS, 342 SNPs were associated with carboplatin-induced cytotoxicity, of which 18 unique SNPs were retained after assessing their association with gene expression. One SNP (rs1649942) was replicated in an independent LCL set (p-valueBonferroni adjusted=9×10−3). It was found to be significantly associated with decreased PFS in phase-1 AOCS patients (Pper-allele=2×10−2), with a stronger effect in the subset of women with optimally debulked tumours (Pper-allele=4×10−3). rs1649942 was also associated with poorer overall survival in women with optimally debulked tumours (Pper-allele=9×10−3). However, this SNP was not significant in the phase-2 validation with patients from numerous cohorts. Conclusion This study demonstrates the potential of cell-based, genome-wide approaches to identify germ-line predictors of treatment outcome and highlights the need for extensive validation in patients to assess their clinical effect.