Characteristics of invasive EOC cases and those with HGS subtype are described in . To elucidate gene sets related to overall survival, we completed a combined analysis in which the gene set p-values from each survival GWAS were combined using Fisher’s method for meta-analysis. The combined HGS analysis resulted in 43 (1.7%) gene sets with p < 0.005 (), with many of the top GSs from GO. However, this apparent “enrichment” of significant GO GSs is largely due to the fact that the set of GO GSs is much larger than the set of GSs in KEGG or PharmGKB. Assuming independence in GSs, we would have expected only 12.83 GSs to have p < 0.005 out of the 2,566 GSs tested by chance alone. The top gene sets were the intracellular signaling pathway (p = 7.3 × 10−5
), regulation of cell-substrate junction assembly (p = 4.0 × 10−4
), anatomical structure formation involved in morphogenesis (p = 5.3 × 10−4
), and organelle outer membrane (p = 5.8 × 10−4
). Of the 43 gene sets with p < 0.005, 21 had p < 0.10 in both the North American and the UK analyses, including the top gene sets of intracellular signaling pathway (North American p = 1.7 × 10−3
, UK p = 3.3 × 10−3
, combined p = 7.3 × 10−5
) and macrolide binding (North American p = 9.0 × 10−4
, UK p = 6.4 × 10−2
, combined p = 6.2 × 10−4
). Using a conservative Bonferroni adjustment for multiple testing (α = 2.0 × 10−5
), the intracellular signaling pathway was very close to being statistically significant. The top results were similar when adjusting for stage and grade (Supplemental Table 2
Clinical characteristics of epithelial ovarian cancer cases.
Association between gene sets and ovarian cancer survival in cases with high-grade serous (HGS) histological subtype (p < 0.005).
The top gene sets in combined analysis of all cases, regardless of histological subtype, were () meiotic mismatch repair (p = 6.3 × 10−4
), macrolide binding (p = 1.0 × 10−3
), antigen processing and presentation of peptide antigen (p = 1.1 × 10−3
); mismatch repair complex (p = 1.3 × 10−3
); and regulation of cell migration (p = 1.7 × 10−3
). Of the 18 gene sets with combined p < 0.005 (0.7%), eight had p < 0.10 in both the North American and the UK analyses. Similar results were observed in the analysis adjusting for stage and grade (Supplemental Table 2
). After adjusting for multiple testing, none of the gene sets were statistically significant in the combined analysis. To aid in the interpretation of the gene set results, presents the results from hierarchical clustering of gene sets with p < 0.005 (based on proportion of SNPs in common) for both the analysis of all cases and HGS cases.
Association between gene sets and ovarian cancer survival (p < 0.005).
Hierarchical clustering dendrogram of gene sets with p < 0.005 (distance measure based on proportion of SNPs in common between gene sets) for the analysis of (A) all cases and (B) HGS cases.
Next, for the top gene sets (p < 0.01), we examined which particular gene(s) in these gene set may be most associated with overall survival. presents the genes with p < 0.0005 in top gene sets. For the combined analysis the top most significant genes were: HLA-C (p = 1.3 × 10−4), MYH3 (p = 1.7 × 10−4), WNT5A (p = 3.7 × 10−4) and ZSCAN23 (p = 3.8 × 10−4).
Genes with p < 0.0005 in gene sets with p < 0.01 from the combined GSA.
To better interpret the combined GSA results, we also examined the GSA results for the individual GWASes. In the North American GWAS, five gene sets with p-values of association with survival < 0.005 were identified among cases with HGS histological subtype, with the top gene set for analysis of HGS being inflammation related (p = 0.0007), cell migration (p =0.0009) and macrolide binding (p = 0.0009). Similarly, four gene sets were found to be associated with survival (gene set p-value < 0.001; Supplemental Table 3
) in the overall group. Genetic variation in meiotic mismatch repair, as defined in the biological class of GO, and in mismatch repair complex, as defined in the cellular class of GO, were the most significantly associated gene sets (p-values = 2.0 × 10−4
). Of note, the meiotic mismatch repair gene set included only MSH6
and was contained within the mismatch repair complex gene set. Other gene sets with p < 0.001 were positive regulation of cell death (p = 0.0004) and multicellular organismal aging (p = 0.0009). There was no overlap of the top gene sets (p < 0.001) from the analyses of all versus HGS cases. It should be noted that none of these results are statistically significant at the Bonferroni significance level of 2×10−5
GSA of the UK GWAS revealed 11 gene sets with p < 0.001 from the analysis of the HGS cases and three gene sets with p < 0.001 from the analysis of all cases (Supplemental Table 3
). Similar to the North American GSA, there was limited overlap between the top gene sets between the analyses of all individuals and the HGS subgroup. For the analysis of the HGS, the top gene sets were photoreceptor inner segment (p = 0.0002), organelle outer membrane (p = 0.0002), and somatic stem cell maintenance (p = 0.0004). The top gene set in the overall analysis involved regulation of the calcium ion (p = 0.001). However, none of these gene sets were significant at a Bonferroni level of 2 ×10−5
. As Supplemental Table 3
illustrates, there was little agreement in top gene sets between the North American and UK analyses.