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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
Cancer Epidemiol Biomarkers Prev. Author manuscript; available in PMC 2013 November 1.
Published in final edited form as:
PMCID: PMC3650102

Analysis of Over 10,000 Cases Finds No Association between Previously-Reported Candidate Polymorphisms and Ovarian Cancer Outcome

Kristin L. White,1 Robert A. Vierkant,2 Zachary C. Fogarty,2 Bridget Charbonneau,3 Matthew S. Block,4 Paul D.P. Pharoah,5,6 Georgia Chenevix-Trench,7 Mary Anne Rossing,8,9 Daniel W. Cramer,10,11 C. Leigh Pearce,12 Joellen M. Schildkraut,13,14 Usha Menon,15 Susanne Kruger Kjaer,16,17 Douglas A. Levine,18 Jacek Gronwald,19 Hoda Anton Culver,20 Alice S. Whittemore,21 Beth Y. Karlan,22 Diether Lambrechts,23,24 Nicolas Wentzensen,25 Jolanta Kupryjanczyk,26 Jenny Chang-Claude,27 Elisa V. Bandera,28 Estrid Hogdall,17,29 Florian Heitz,30,31 Stanley B. Kaye,32 Peter A. Fasching,33,34 Ian Campbell,35,36 Marc T. Goodman,37 Tanja Pejovic,38,39 Yukie Bean,38,39 Galina Lurie,40 Diana Eccles,41 Alexander Hein,33 Matthias W. Beckmann,33 Arif B. Ekici,42 James Paul,43 Robert Brown,44 James Flanagan,44 Philipp Harter,30,31 Andreas du Bois,30,31 Ira Schwaab,45 Claus K. Hogdall,16 Lene Lundvall,16 Sara H. Olson,46 Irene Orlow,46 Lisa E. Paddock,47 Anja Rudolph,27 Ursula Eilber,27 Agnieszka Dansonka-Mieszkowska,26 Iwona K. Rzepecka,26 Izabela Ziolkowska-Seta,48 Louise Brinton,25 Hannah Yang,25 Montserrat Garcia-Closas,49 Evelyn Despierre,50 Sandrina Lambrechts,50 Ignace Vergote,50 Christine Walsh,22 Jenny Lester,22 Weiva Sieh,21 Valerie McGuire,21 Joseph H. Rothstein,21 Argyrios Ziogas,20 Jan Lubiński,19 Cezary Cybulski,19 Janusz Menkiszak,51 Allan Jensen,17 Simon A. Gayther,12 Susan J. Ramus,12 Aleksandra Gentry-Maharaj,15 Andrew Berchuck,52 Anna H. Wu,12 Malcolm C. Pike,12,46 David Van Den Berg,12 Kathryn L. Terry,10,11 Allison F. Vitonis,10 Jennifer A. Doherty,53 Sharon Johnatty,7 Anna deFazio,54 AOCS/ACS, Honglin Song,5 Jonathan Tyrer,5 Thomas A. Sellers,55 Catherine M. Phelan,55 Kimberly R. Kalli,4 Julie M. Cunningham,56 Brooke L. Fridley,57 and Ellen L. Goode3



Ovarian cancer is a leading cause of cancer-related death among women. In an effort to understand contributors to disease outcome, we evaluated single-nucleotide polymorphisms (SNPs) previously associated with ovarian cancer recurrence or survival, specifically in angiogenesis, inflammation, mitosis, and drug disposition genes.


Twenty-seven SNPs in VHL, HGF, IL18, PRKACB, ABCB1, CYP2C8, ERCC2, and ERCC1 previously associated with ovarian cancer outcome were genotyped in 10,084 invasive cases from 28 studies from the Ovarian Cancer Association Consortium with over 37,000 observed person-years and 4,478 deaths. Cox proportional hazards models were used to examine the association between candidate SNPs and ovarian cancer recurrence or survival with and without adjustment for key covariates.


We observed no association between genotype and ovarian cancer recurrence or survival for any of the SNPs examined.


These results refute prior associations between these SNPs and ovarian cancer outcome and underscore the importance of maximally powered genetic association studies.


These variants should not be used in prognostic models. Alternate approaches to uncovering inherited prognostic factors, if they exist, are needed.


In 2012, ovarian cancer was estimated to be the seventh leading cause of female cancer-related deaths worldwide (1). Despite standardized treatment approaches, inter-individual variation in outcomes exists; understanding the source of this variation, including potential inherited factors, is of high importance (2). Our prior studies of over 400 candidate genes in biological pathways that are relevant to ovarian cancer suggested association between ovarian cancer outcome and inherited variation in certain genes (35). These include the angiogenesis genes VHL (3) and HGF (4), taxol efflux and metabolism genes ABCB1 and CYP2C8 (5), DNA repair genes ERCC2 and ERCC1 (5), the inflammation gene IL18 (3), and the mitosis gene PRKACB (4). Here, we sought to confirm prior associations (p<0.05) between ovarian cancer outcome and 27 single-nucleotide polymorphisms (SNPs) in these genes using a much larger sample size than the discovery studies.


A total of 10,084 women with invasive epithelial ovarian cancer (over 37,000 person-years follow-up) including 5,248 high-grade serous cases were examined. Participants from 28 studies (Table 1) in the Ovarian Cancer Association Consortium (OCAC) were genotyped on a custom Illumina iSelect BeadArray using centralized genotype calling and quality control procedures, as previously described (6). In brief, we excluded SNPs and samples with call rate < 95%; we restricted to women with > 90% predicted European ancestry and estimated principal components (PCs) representing European substructure (6).

Table 1
Participating Invasive Epithelial Ovarian Cancer Studies

Cox proportional hazards regression modeling accounting for left truncation and censoring at 10 years following diagnosis was used to estimate per-allele hazard ratios (HRs) and 95% confidence intervals (CIs) for associations with death from any cause for all cases and for high-grade serous cases. Two models were assessed: a minimally adjusted model including covariates for age at diagnosis, five population substructure PCs, and study site, and a fully adjusted model which additionally included histology (for analyses of all cases only), tumor stage, tumor grade, and oral contraceptive use as these covariates were associated with survival in these data (p<0.05). Analyses were also conducted with a recurrence endpoint defined by time to disease recurrence or death (377 additional events, including 273 among women with high-grade serous disease).


Overall, there were no associations between SNPs and ovarian cancer survival in either the minimally or fully adjusted models; Table 2 shows HRs, 95% CIs, and p-values for all cases and high-grade serous cases. No heterogeneity across studies was observed (p-values>0.05). SNP rs2214825 in HGF was significantly associated with survival in the minimally adjusted model (p=0.03), although not in the fully adjusted model (Table 2). After excluding 2,015 women who contributed to the original report (4), no association was seen at p<0.05 (minimally adjusted HR=1.04, 95% CI=0.98–1.10, p=0.19). Additionally, in ERCC2, SNP rs50872 conferred a slightly increased risk of death among women with high-grade serous disease (p=0.03) in the fully adjusted model, but this association was not statistically significant at α=0.05 in the minimally adjusted model, and, after excluding 497 women in the original report (5), no statistically significant association was seen (fully adjusted HR=1.06, 95% CI=1.00–1.14, p=0.06). Near identical results were seen for these SNPs in analysis of time to recurrence. On the whole, while these candidates showed promise with large effect sizes (i.e., HRs >1.23 or <0.82) in earlier reports (35), our very large scale study refutes association at these loci with 95% CIs excluding prior risk estimates.

Table 2
Association between SNPs and Ovarian Cancer Survival


Here, we aimed to confirm the relationship between previously-associated SNPs and ovarian cancer outcome using a sample of over 10,000 women from 28 studies participating in the OCAC. Results of this analysis did not confirm the associations originally observed (35). While associations with other SNPs may exist, we report no consistent associations between these 27 SNPs and ovarian cancer outcome and believe it critical to disseminate results to reduce the possibility of publication bias. These null results highlight the necessity of large-scale replication of initial SNP associations, as the most likely explanation for non-replication is that initial false positive findings resulted from chance in smaller studies.

Studies of SNPs and cancer outcome have been less fruitful than cancer susceptibility studies (7). This may be due to several challenges: lack of a large collection of homogeneous cases due to missing baseline clinical data, inability to verify chemotherapeutic or surgical data to evaluate whether SNP effects arise only in certain clinical contexts, and inconsistent follow-up methods leading to variable completeness of endpoints (8). Although ovarian cancer has high mortality rate and a generally uniform treatment compared to other cancers, there is a trade-off in expected power between the larger sample sizes of observational studies and the detailed data available from clinical trials. We propose that utilization of both study designs, including detailed tumor characteristics and coordination with animal and mechanistic studies, is the best path forward for the identification of predictive and prognostic factors in ovarian cancer outcomes.


We thank all the individuals who took part in this study and all the researchers, clinicians and technical and administrative staff who have made possible the many studies contributing to this work. In particular, we thank: D. Bowtell, A. deFazio, D. Gertig, A. Green, P. Parsons, N. Hayward, P. Webb and D. Whiteman (AUS); G. Peuteman, T. Van Brussel and D. Smeets (BEL); the staff of the genotyping unit, S. LaBoissière and F. Robidoux (Genome Quebec); T. Koehler (GER); G.S. Keeney, S. Windebank, C. Hilker and J. Vollenweider (MAY); L. Rodriquez, M. King, U. Chandran, D. Gifkins, and T. Puvananayagam (NJO); M. Sherman, A. Hutchinson, N. Szeszenia- Dabrowska, B. Peplonska, W. Zatonski, A. Soni, P. Chao and M. Stagner (POL); C. Luccarini, P. Harrington, the SEARCH team, and ECRIC (SEA); the Scottish Gynaecological Clinical Trails group and SCOTROC1 investigators (SRO); I. Jacobs, M. Widschwendter, E. Wozniak, N. Balogun, A. Ryan and J. Ford (UKO); C. Pye (UKR); A. Amin Al Olama, K. Michilaidou, and K. Kuchenbäker (COGS). The Australian Ovarian Cancer Study (AOCS) Management Group (D Bowtell, G. Chenevix-Trench, A. deFazio, D. Gertig, A. Green, and P.M. Webb) gratefully acknowledges the contribution of all the clinical and scientific collaborators (see reference 9). The Australian Cancer Study (ACS) Management Group comprises A. Green, P. Parsons, N. Hayward, P.M. Webb, and D. Whiteman.

The COGS project is funded through a European Commission's Seventh Framework Programme grant (agreement number 223175 - HEALTH-F2-2009-223175). The Ovarian Cancer Association Consortium is supported by a grant from the Ovarian Cancer Research Fund thanks to donations by the family and friends of Kathryn Sladek Smith (PPD/RPCI.07). The scientific development and funding for this project were in part supported by the Genetic Associations and Mechanisms in Oncology (GAME-ON): a NCI Cancer Post-GWAS Initiative (U19-CA148112). G.C.-T. and P.M.W. are supported by the National Health and Medical Research Council. B.K. holds an American Cancer Society Early Detection Professorship (SIOP-06-258-01-COUN).

Funding of the constituent studies was provided by the American Cancer Society (CRTG-00-196-01-CCE); the California Cancer Research Program (00-01389V-20170, N01-CN25403, 2II0200); the Canadian Institutes for Health Research; Cancer Council Victoria; Cancer Council Queensland; Cancer Council New South Wales; Cancer Council South Australia; Cancer Council Tasmania; Cancer Foundation of Western Australia; the Cancer Institute of New Jersey; Cancer Research UK (C490/A6187, C490/A10119, C490/A10124, C536/A13086, C536/A6689); the Celma Mastry Ovarian Cancer Foundation; the Danish Cancer Society (94-222-52); the ELAN Program of the University of Erlangen-Nuremberg; the Eve Appeal; the Helsinki University Central Hospital Research Fund; Helse Vest; Imperial Experimental Cancer Research Centre (C1312/A15589); the Norwegian Cancer Society; the Norwegian Research Council; the Ovarian Cancer Research Fund; Nationaal Kankerplan of Belgium; the L & S Milken Foundation; the Polish Ministry of Science and Higher Education; the US National Cancer Institute (K07-CA095666, K07-CA143047, K22-CA138563, N01-CN55424, N01-PC067010, N01-PC035137, P01-CA017054, P01-CA087696, P30-CA072720, P30-CA15083, P50-CA105009, P50-CA136393, R01-CA014089, R01-CA016056, R01-CA017054, R01-CA049449, R01-CA050385, R01-CA054419, R01-CA058598, R01-CA058860, R01-CA061107, R01-CA061132, R01-CA063682, R01-CA064277, R01-CA067262, R01-CA071766, R01-CA074850, R01-CA076016, R01-CA080742, R01-CA080978, R01-CA083918, R01-CA087538, R01-CA092044, R01-095023, R01-CA106414, R01-CA122443, R01-CA61107, R01-CA112523, R01-CA114343, R01-CA126841, R01-CA136924, R01-CA149429, R03-CA113148, R03-CA115195, R37-CA070867, R37-CA70867, U01-CA069417, U01-CA071966 and Intramural research funds); the US Army Medical Research and Material Command (DAMD17-98-1-8659, DAMD17-01-1-0729, DAMD17-02-1-0666, DAMD17-02-1-0669, W81XWH-10-1-0280); the National Health and Medical Research Council of Australia (199600 and 400281); the German Federal Ministry of Education and Research of Germany Programme of Clinical Biomedical Research (01 GB 9401); the state of Baden-Württemberg through Medical Faculty of the University of Ulm (P.685); the Minnesota Ovarian Cancer Alliance; the Mayo Foundation; the Fred C. and Katherine B. Andersen Foundation; the Lon V. Smith Foundation (LVS-39420); the Polish Committee for Scientific Research (4P05C 028 14 and 2P05A 068 27); the Oak Foundation; the OHSU Foundation; the Mermaid I project; the Rudolf-Bartling Foundation; the UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge, Imperial College London, University College Hospital “Womens Health Theme” and the Royal Marsden Hospital; and WorkSafeBC.


The authors have no financial conflicts of interest.


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