Beyond Endometriosis Genome-Wide Association Study: From Genomics to Phenomics to the Patient

Abstract

Endometriosis is a heritable, complex chronic inflammatory disease, for which much of the causal pathogenic mechanism remains unknown. Genome-wide association studies (GWAS) to date have identified 12 single nucleotide polymorphisms at 10 independent genetic loci associated with endometriosis. Most of these were more strongly associated with revised American Fertility Society stage III/IV, rather than stage I/II. The loci are almost all located in intergenic regions that are known to play a role in the regulation of expression of target genes yet to be identified. To identify the target genes and pathways perturbed by the implicated variants, studies are required involving functional genomic annotation of the surrounding chromosomal regions, in terms of transcription factor binding, epigenetic modification (e.g., DNA methylation and histone modification) sites, as well as their correlation with RNA transcription. These studies need to be conducted in tissue types relevant to endometriosis-in particular, endometrium. In addition, to allow biologically and clinically relevant interpretation of molecular profiling data, they need to be combined and correlated with detailed, systematically collected phenotypic information (surgical and clinical). The WERF Endometriosis Phenome and Biobanking Harmonisation Project is a global standardization initiative that has produced consensus data and sample collection protocols for endometriosis research. These now pave the way for collaborative studies integrating phenomic with genomic data, to identify informative subtypes of endometriosis that will enhance understanding of the pathogenic mechanisms of the disease and discovery of novel, targeted treatments.

Figure 1

Regional ‘locuszoom’ chromosomal plots showing contrasting evidence of association for individual SNPs with stage A (left column; 1,686 cases) vs. stage B (right column; 1,364 cases) endometriosis vs. 7,060 controls. Data were from the International Endogene Consortium GWAS dataset after imputation to the 1000 Genomes panel version 3. Each data point signifies a variant (SNP), and SNPs are colour coded according to their correlation (r2) with the top associated genotyped SNP (purple diamond) from meta-analysis (Table 1).The x-axis shows the genomic location, relative to gene locations. The y-axis shows the significance of association (-log10 of p-value).