Citations

Abstract Many germline genetic variants have been found to be associated with susceptibility to epithelial ovarian cancer (EOC), but currently few associations have been identified for EOC outcomes such as overall survival. In the absence of evidence for common germline markers, it is possible that rare variants not captured in GWAS arrays may be associated with overall survival. We hypothesize that rare variants, either individually or combined across a gene, may be associated with overall survival in EOC. We utilized data from two genotyping projects of the Ovarian Cancer Association Consortium (OCAC) that used commercial exome-based arrays. The primary sample, genotyped on the Affymetrix Axiom Exome Array at 227,892 standard and custom variants, consisted of 14 independent EOC studies (4293 cases; 2257 deaths). The secondary sample, genotyped on the Illumina Infinium HumanExome BeadChip at 114,620 variants, consisted of six additional EOC studies (1744 cases; 1027 deaths). Both sets were analyzed using Cox proportional hazards regression to determine the association of each variant with overall survival time. Meta-analysis was conducted across samples at 73,203 overlapping variants. Gene-level tests of over 18,000 genes were also conducted using burden tests and Sequencing Kernel Association Tests (SKAT) adapted for Cox proportional hazards models. Gene-level tests were conducted separately for the primary and secondary cases and then were meta-analyzed. Models were adjusted for age, site, and three principle components. Six individual variants had meta-analysis p-values < 1.0E-4, five of which were rare (MAF < 0.003). Common variant rs8170 (MAF = 0.2) in BABAM1 encoding BRISC and BRCA1 A complex member 1 - previously reported to be associated with EOC risk_showed evidence of association with overall survival (Pmeta = 1.5E-5) and consistent estimates of effect size across both samples (HR1 = 1.18, HR2 = 1.19). In imputed genotype data from over 18,000 subjects from OCAC genotyped on the COGS array, this association reaches genome-wide significance (HR = 1.15, P = 4.7E-9). Five genes had gene-level meta-analysis p-values < 1.0E-4, including top ranked ATG2B (p = 1.1E-6), an autophagy gene important for apoptosis; zinc finger protein PEG3 (p = 1.8E-5), playing a role in autophagy and down-regulated in EOC; helicase-like transcription factor HLTF (p = 1.9E-5), involved in post-replication DNA repair; mitochondrial fission regulator 1-like gene FAM54B (p = 3.1E-5); and T-cell surface glycoprotein CD1E (p = 8.8E-5). With over 6000 EOC cases in the primary and secondary samples, this is the largest genome-wide assessment of rare variant genetic associations with EOC overall survival. Variant rs8170 in BABAM1, a necessary component of the BRCA1 complex, is associated with overall survival. Single variant and gene-level analyses provide complementary approaches, suggesting additional candidates that warrant follow-up study. Citation Format: Stacey J. Winham, Brooke L. Fridley, Melissa C. Larson, Zachary Fogarty, Andrew Berchuck, Yian Ann Chen, Hui-Yi Lin, Georgia Chenevix-Trench, Jenny Permuth-Wey, Thomas A. Sellers, Ailith Pirie, Ellen L. Goode, Ovarian Cancer Association Consortium. Investigation of exome variants associated with overall survival in ovarian cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4636. doi:10.1158/1538-7445.AM2015-4636

Abstract Background: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. Methods: We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). Results: Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. Conclusion: We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. Impact: Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization. Cancer Epidemiol Biomarkers Prev; 24(10); 1574–84. ©2015 AACR.

Abstract Purpose: Chemotherapy resistance remains a major challenge in the treatment of ovarian cancer. We hypothesize that germline polymorphisms might be associated with clinical outcome. Experimental Design: We analyzed approximately 2.8 million genotyped and imputed SNPs from the iCOGS experiment for progression-free survival (PFS) and overall survival (OS) in 2,901 European epithelial ovarian cancer (EOC) patients who underwent first-line treatment of cytoreductive surgery and chemotherapy regardless of regimen, and in a subset of 1,098 patients treated with ≥4 cycles of paclitaxel and carboplatin at standard doses. We evaluated the top SNPs in 4,434 EOC patients, including patients from The Cancer Genome Atlas. In addition, we conducted pathway analysis of all intragenic SNPs and tested their association with PFS and OS using gene set enrichment analysis. Results: Five SNPs were significantly associated (P ≤ 1.0 × 10−5) with poorer outcomes in at least one of the four analyses, three of which, rs4910232 (11p15.3), rs2549714 (16q23), and rs6674079 (1q22), were located in long noncoding RNAs (lncRNAs) RP11-179A10.1, RP11-314O13.1, and RP11-284F21.8, respectively (P ≤ 7.1 × 10−6). ENCODE ChIP-seq data at 1q22 for normal ovary show evidence of histone modification around RP11-284F21.8, and rs6674079 is perfectly correlated with another SNP within the super-enhancer MEF2D, expression levels of which were reportedly associated with prognosis in another solid tumor. YAP1- and WWTR1 (TAZ)-stimulated gene expression and high-density lipoprotein (HDL)-mediated lipid transport pathways were associated with PFS and OS, respectively, in the cohort who had standard chemotherapy (pGSEA ≤6 × 10−3). Conclusions: We have identified SNPs in three lncRNAs that might be important targets for novel EOC therapies. Clin Cancer Res; 21(23); 5264–76. ©2015 AACR.

Abstract Background: Common genetic variants identified by genome-wide association studies and follow-up genotyping initiatives only explain a small proportion of the heritability of epithelial ovarian cancer (EOC). We hypothesized that some of the missing heritability may be explained by rare (minor allele frequency (MAF) <0.5%) and low-frequency (MAF 0.5-5%) protein-coding variants that are not well captured by genotyping arrays that focus on common variants. Methods: To examine the association between uncommon variants and EOC susceptibility, we genotyped 7,060 EOC cases and 6,712 controls from the Ovarian Cancer Association Consortium using the Affymetrix Axiom Exome Genotyping Array. This platform contains 300,785 putative functional coding variants selected from exome sequences of 12,000+ individuals representing multiple ethnicities and complex traits. After performing quality control (QC), we used unconditional logistic regression treating the number of minor alleles carried as an ordinal variable (log-additive model) to evaluate SNP-EOC risk associations. Genotype cluster plots were visually inspected for top-ranking variants to determine assay success, and allele frequencies of samples from the 1000 Genomes Project and other cohorts were evaluated for QC purposes. Results: A total of 13,318 samples (97%) passed QC, and 12,779 eligible samples (6,293 invasive serous and endometrioid cases and 6,486 controls) were included in the analyses. 280,737 (93%) of the 300,785 attempted markers were successfully genotyped and had call rates >90%. After removing 31,436 monomorphic markers, the 249,301 remaining markers were included in association analyses. We confirmed variants at previously reported EOC susceptibility loci (9p22, 3q25, 17cen-q21.3, and 8q24), with p-values between 10-5 and 10-11. Several correlated low-frequency non-synonymous variants (MAF=5%) residing in a novel EOC susceptibility gene at 3q25.31 were risk-associated. The most significant variant at 3q25.31 had an OR=1.36 and p = 5.58x10-8. Also noteworthy is a rare variant at 15q15.1-q21.1 (MAF=0.5%) that introduces a stop codon in a gene belonging to the tyrosine kinase family (OR=0.39, CI=0.26-0.58, p = 4.52x10-6). We also identified a more common synonymous coding variant in a phosphatase at 6q21.3 that was associated with increased risk (OR=1.22, CI=1.13-1.33, p = 1.84x10-6, MAF=9.6%). Population stratification and gene-based analyses are underway to further examine the impact of the newly-identified variants on EOC risk. A meta-analysis to include data from an additional 2104 EOC cases and 2516 controls genotyped with Illumina's HumanExome Beadchip rare variant array is also underway. Functional analysis of the most promising variants will follow. Conclusions: Preliminary data from this large-scale study reveals novel rare and low-frequency variants that may influence susceptibility to epithelial ovarian cancer. Citation Format: Jennifer Permuth-Wey, Y. Ann Chen, Zhihua Chen, Andrew Berchuck, Georgia Chenevix-Trench, Jennifer Doherty, Simon Gayther, Ellen L. Goode, Edwin Iversen, Alvaro N.A. Monteiro, Leigh Pearce, Paul D.P. Pharoah, Catherine M. Phelan, Ailith Pirie, Susan Ramus, Mary Ann Rossing, Joellen M. Schildkraut, Thomas A. Sellers, on behalf of the Ovarian Cancer Association Consortium. Exome genotyping array identifies rare and low-frequency variants that may be associated with ovarian cancer risk. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 946. doi:10.1158/1538-7445.AM2014-946

Abstract Background Genome-wide association studies (GWAS) previously identified 8 new risk loci for all subtypes of epithelial ovarian carcinoma (EOC) and one specific to invasive serous EOC. One locus, at 2q31, was also associated with invasive mucinous EOC (mEOC) at P=7.3 x 10-7 (Nat Genet 2010:874). Here, we report new risk loci for mEOC, which is thought to develop from a borderline mucinous tumor. These loci may provide clues to the molecular basis of the disease. Methods We used genotype data from 4 GWAS of EOC and from multiple case-control studies in the Ovarian Cancer Association Consortium that had been genotyped using the iCOGS custom SNP panel (210k SNPs) developed for the Collaborative Oncological Gene-environment Study. We imputed genotypes of common variation across the genome using the 1000 Genomes Project reference panel and tested for association using log-additive unconditional regression models. Results Genotypes were available for 1,643 combined invasive and borderline mEOC and for 1,002 invasive-only mEOC of European ancestry. Three loci in new regions, and one locus in a previously published region, with minor allele frequency (MAF) > 1% and P ≤ 10-7 were found. The imputed SNP rs72831838 (imputation r2=0.67, MAF=0.15) is located at 2q13 in an intron of the PAX8 (paired box 8) gene (all mEOC OR=1.35, P=4.2 x 10-8 and invasive-only OR=1.43, P=9.6 x 10-8). PAX8 is a transcription factor and may be a Müllerian lineage marker that distinguishes carcinomas of gynecologic origin from other sites. The imputed variant at chr19:39745695 (imputation r2=0.61, MAF=0.32) is an insertion/deletion polymorphism located at 19q13.2 and falls within the MSRB1P1 (methionine sulfoxide reductase B1 pseudogene 1). This locus was associated with decreased risk (all mEOC OR=0.74, P = 2.1 x 10-9 and invasive-only OR=0.79, P = 8.1 x 10-5) and is enriched with the H3K27Ac histone mark that identifies active enhancers of gene expression. The imputed SNP rs6425050 (imputation r2=0.45, MAF=0.19) is located at 1q25 (all mEOC OR=1.38, P=4.7 x 10-8 and invasive-only OR=1.41, P=1.6x10-6). This SNP is intronic to PLA2G4A (phospholipase A2, group IVA), which encodes an enzyme that hydrolyzes membrane phospholipids for eicosanoid metabolism and signaling. None of these loci were associated with other EOC histological subtypes at P ≤ 10-7. The genotyped SNP, rs711830 (MAF=0.32), is located at 2q31.1 in the 3′ region of the HOXD3 homeobox gene (all mEOC OR=1.30, P=7.5 x 10-12 and invasive-only OR=1.26, P=7.8 x 10-7). This SNP is highly correlated (r2=0.99) with rs2072590, which is located 5.3kb upstream and previously reported by us to be associated with mEOC and invasive serous EOC (Nat Genet 2010:874). The HOXD3 locus is highly conserved and may also be a marker of Müllerian cell type origin. Conclusions The 3 new loci for mEOC require confirmation by genotyping. Fine mapping and functional analysis of all loci is needed in order to determine their likely target genes. Citation Format: Linda E. Kelemen, Jonathan Tyrer, Catherine M. Phelan, Susan J. Ramus, Andrew Berchuck, Simon A. Gayther, Ellen L. Goode, Celeste L. Pearce, Joellen M. Schildkraut, Georiga Chenevix-Trench, Alvaro N. Monteiro, Marc T. Goodman, Thomas A. Sellers, Paul PD Pharoah. GWAS identifies risk variants for mucinous ovarian carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3283. doi:10.1158/1538-7445.AM2014-3283

Abstract Introduction The epithelial-mesenchymal transition (EMT) pathway contributes to epithelial ovarian cancer (EOC) progression. Previously we identified associations of single nucleotide polymorphisms (SNPs) in EMT-related genes and EOC risk (data not shown). To further investigate the role of EMT-related gene variants in EOC and to derive more reliable risk estimates, we evaluated associations for 795 SNPs from 278 EMT-related genes in a replication study of 43 studies within the Ovarian Cancer Association Consortium (OCAC). Methods The study population included 14,736 cases and 23,448 controls of European ancestry, 89 cases and 200 controls of African ancestry, and 249 cases and 1574 controls of Asian ancestry. The 795 SNPs were genotyped using an Illumina Infinium iSelect BeadChip as part of the Collaborative Oncological Gene-environment Study (COGS). For women of European ancestry, both invasive cancers combined and the four main histological subtypes (serous [n=8,372], endometroid [n=2,068], clear cell [n=1,025] and mucinous [n=943] were analyzed, while for women of African and Asian ancestries only the serous subtype was analyzed. SNP analyses were conducted using unconditional logistic regression under a log-additive model separately for women of each ancestry. All analyses were adjusted for study site and population substructure within each ancestry. Results For women of European ancestry, the strongest evidence of an association for invasive cancers combined was observed for IGF1R rs10794486 (OR=1.05, 95%CI=1.02-1.09, P=0.002), which was also associated with serous (P=0.019), but not the other histological subtypes. In the histological subtype-specific analysis, the most significant association for serous was observed at NRP2 rs3771044 (OR=1.09, 95%CI=1.03-1.15, P=0.00014), for endometroid at rs1770247 (13q31.3, OR=1.16, 95%CI=1.07-1.25, P=0.00028), for clear cell at rs4848300 (2q13, OR=0.84, 95%CI=0.76-0.93, P=0.00099) and for mucinous at SEMA4B rs8030039 (OR=1.09, 95%CI=1.01-1.17, P=0.00019). For women of African ancestry, the strongest association for serous histological subtype was observed at F9 rs6048 (OR=1.71, 95%CI=1.17-2.50, P=0.006). This SNP was not significant in women of European or Asian ancestry. The strongest association for women of Asian ancestry was IGF1R rs10794486 (OR=1.68, 95%CI=1.16-2.45, P=0.007), which was also significant in women of European, but not African, ancestry. Conclusion Findings from this large study provide additional evidence that variants in EMT-related genes may be associated with ovarian cancer risk and that EMT susceptibility loci may differ by ovarian cancer histological subtypes. Furthermore, the findings suggest that susceptibility locus for the serous subtype may be different for women of African ancestry. Future studies are warranted to confirm these findings. Citation Format: Ernest K. Amankwah, Jonathan Tyrer, Hui-Yi Lin, Ya-Yu Tsai, Zhihua Chen, Gang Han, Xiaotao Qu, Ellen Goode, Julie Cunninghan, Edward Iverson, Susan Ramus, Andrew Berchuck, Joellen Schildkraut, Alvaro Monteiro, Simon Gayther, Steven Narod, Paul Pharoah, Thomas A. Sellers, Catherine Phelan. Epithelial-mesenchymal transition (EMT) gene variants influence epithelial ovarian cancer risk in women of European, African and Asian ancestry. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1352. doi:10.1158/1538-7445.AM2013-1352

Abstract Background: Circadian rhythms of biological processes are regulated by endogenous clock genes and clock-controlled genes. Aberrant expression of circadian clock genes may have important consequences on the transactivation of downstream targets that control the cell cycle and cellular proliferation potentially promoting carcinogenesis. Animal models indicate that several circadian rhythm genes are expressed in the ovaries, where they influence and are influenced by estrous cycles. The goal of the current study was to examine the association of circadian gene variants and epithelial ovarian cancer (EOC) risk. Methods: Thirty-one SNPs from five circadian genes (i.e., ARNTL, CRY2, KLF10, NPAS2, PER3, TIMELESS) were genotyped in 14,736 cases and 23,448 control women of European ancestry from 43 studies in the Ovarian Cancer Association Consortium (OCAC), on a custom Illumina iSelect designed for the Collaborative Oncological Gene-Environment Study (COGS). Both invasive cancers combined and the four main histological subtypes (serous [n=8,372], endometroid [n=2,068], clear cell [n=1,025] and mucinous [n=943] were analyzed, SNP analyses were conducted using unconditional logistic regression under a log-additive model. All analyses were adjusted for study site and population substructure. Results: Eleven SNPs were found to be associated with ovarian cancer risk. The SNPs most associated with serous cancer risk were KLF10 rs2513928 (OR=.95 p=6.1x10−3), rs2513927 (OR=1.05 p=6.1x10−3), rs2511703 (OR=1.05 p=9.8x10−3), rs3191333 (OR=1.05, p=1.5x10−2) and NPAS2 rs13012930 (OR=.95, p=3.5x10−2). Endometroid cancer risk was significantly associated with ARNTL SNPs rs10732458 (OR=1.3, p=1.0x10−2) and rs7117836 (OR=1.2, p=4.6x10−2), while clear cell cancer risk was associated with ARNTL rs1562438 (OR=.88, p=1.5x10−2), rs1026071 (OR=.89, p=1.8x10−2), and rs3816360 (OR=.91, p=4.8x10−2) and KLF10 rs2388232 (OR=1.1, p=3.3x10−2). No variants were significantly associated with mucinous cancer risk. Four SNPs in KLF10 were associated with cancer invasiveness; they were rs2513928 (OR=.95, p=1.8x10−3), rs3191333 (OR=1.04, p=1.4x10−2), rs2513927 (OR=1.04, p=1.9x10−2), and rs2511703 (OR=1.03, p=2.8x10−2). Conclusions: Data from the current study suggest that polymorphisms in circadian genes ARNTL, KLF10, and NPAS2 are significantly associated with ovarian cancer histopathologic subtypes and invasiveness. These findings merit further investigation and replication. Funding: R01 CA149429 Citation Format: Heather Jim, Jonathan Tyrer, Hui-Yi Lin, Gang Han, Xiaotao Qu, Ellen L. Goode, Zhihua Chen, Ya-Yu Tsai, Julie M. Cunningham, Edward Iversen, Susan Ramus, Andrew Berchuck, Joellen Schildkraut, Alvaro Monteiro, Simon Gayther, Steven A. Narod, Thomas A. Sellers, Paul Pharoah, Catherine M. Phelan. Variation in circadian rhythm genes influence epithelial ovarian cancer risk and invasiveness. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4850. doi:10.1158/1538-7445.AM2013-4850 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

ScopeWe reevaluated previously reported associations between variants in pathways of one‐carbon (1‐C) (folate) transfer genes and ovarian carcinoma (OC) risk, and in related pathways of purine and pyrimidine metabolism, and assessed interactions with folate intake.Methods and resultsOdds ratios (OR) for 446 genetic variants were estimated among 13 410 OC cases and 22 635 controls, and among 2281 cases and 3444 controls with folate information. Following multiple testing correction, the most significant main effect associations were for dihydropyrimidine dehydrogenase (DPYD) variants rs11587873 (OR = 0.92; p = 6 × 10−5) and rs828054 (OR = 1.06; p = 1 × 10−4). Thirteen variants in the pyrimidine metabolism genes, DPYD, DPYS, PPAT, and TYMS, also interacted significantly with folate in a multivariant analysis (corrected p = 9.9 × 10−6) but collectively explained only 0.2% of OC risk. Although no other associations were significant after multiple testing correction, variants in SHMT1 in 1‐C transfer, previously reported with OC, suggested lower risk at higher folate (pinteraction = 0.03–0.006).ConclusionVariation in pyrimidine metabolism genes, particularly DPYD, which was previously reported to be associated with OC, may influence risk; however, stratification by folate intake is unlikely to modify disease risk appreciably in these women. SHMT1 SNP‐by‐folate interactions are plausible but require further validation. Polymorphisms in selected genes in purine metabolism were not associated with OC.

Abstract Survival in epithelial ovarian cancer (EOC) is influenced by the host immune response, yet the key genetic determinants of inflammation and immunity that affect prognosis are not known. The nuclear factor-κB (NF-κB) transcription factor family plays an important role in many immune and inflammatory responses, including the response to cancer. We studied common inherited variation in 210 genes in the NF-κB family in 10,084 patients with invasive EOC (5,248 high-grade serous, 1,452 endometrioid, 795 clear cell, and 661 mucinous) from the Ovarian Cancer Association Consortium. Associations between genotype and overall survival were assessed using Cox regression for all patients and by major histology, adjusting for known prognostic factors and correcting for multiple testing (threshold for statistical significance, P < 2.5 × 10−5). Results were statistically significant when assessed for patients of a single histology. Key associations were with caspase recruitment domain family, member 11 (CARD11) rs41324349 in patients with mucinous EOC [HR, 1.82; 95% confidence interval (CI), 1.41–2.35; P = 4.13 × 10−6] and tumor necrosis factor receptor superfamily, member 13B (TNFRSF13B) rs7501462 in patients with endometrioid EOC (HR, 0.68; 95% CI, 0.56–0.82; P = 2.33 × 10−5). Other associations of note included TNF receptor–associated factor 2 (TRAF2) rs17250239 in patients with high-grade serous EOC (HR, 0.84; 95% CI, 0.77–0.92; P = 6.49 × 10−5) and phospholipase C, gamma 1 (PLCG1) rs11696662 in patients with clear cell EOC (HR, 0.43; 95% CI, 0.26–0.73; P = 4.56 × 10−4). These associations highlight the potential importance of genes associated with host inflammation and immunity in modulating clinical outcomes in distinct EOC histologies. Cancer Epidemiol Biomarkers Prev; 23(7); 1421–7. ©2014 AACR.