{"paper_id":"539700fa-1c4f-46b7-b87d-fa232b388fcd","body_text":"This may be the author’s version of a work that was submitted/accepted\nfor publication in the following source:\nPainter, Jodie, Nyholt, Dale, Morris, Andrew, Zhao, Zhen Zhen, Hen-\nders, Anjali, Lambert, Ann, Wallace, Leanne, Martin, Nicholas, Kennedy,\nStephen, Treloar, Susan, Zondervan, Krina, & Montgomery, Grant\n(2011)\nHigh-density fine-mapping of a chromosome 10q26 linkage peak suggests\nassociation between endometriosis and variants close to CYP2C19.\nFertility and Sterility, 95(7), pp. 2236-2240.\nThis file was downloaded from: https://eprints.qut.edu.au/91912/\n© Consult author(s) regarding copyright matters\nThis work is covered by copyright. Unless the document is being made available under a\nCreative Commons Licence, you must assume that re-use is limited to personal use and\nthat permission from the copyright owner must be obtained for all other uses. If the docu-\nment is available under a Creative Commons License (or other specified license) then refer\nto the Licence for details of permitted re-use. It is a condition of access that users recog-\nnise and abide by the legal requirements associated with these rights. If you believe that\nthis work infringes copyright please provide details by email to qut.copyright@qut.edu.au\nNotice: Please note that this document may not be the Version of Record\n(i.e. published version) of the work. Author manuscript versions (as Sub-\nmitted for peer review or as Accepted for publication after peer review) can\nbe identified by an absence of publisher branding and/or typeset appear-\nance. If there is any doubt, please refer to the published source.\nhttps://doi.org/10.1016/j.fertnstert.2011.03.062\n\nHigh-density fine-mapping of a chromosome 10q26 linkage peak\nsuggests association between endometriosis and variants close\nto CYP2C19\nJodie N. Painter1, Dale R. Nyholt2, Andrew Morris3, Zhen Z. Zhao4, Anjali K. Henders5, Ann\nLambert6, Leanne Wallace7, Nicholas G. Martin8, Stephen H. Kennedy9, Susan A. Treloar10,\nKrina T. Zondervan11,13, and Grant W. Montgomery12,13\n1Dr Jodie N Painter, PhD. Queensland Institute of Medical Research. Brisbane, Australia\n2Dr Dale R Nyholt, PhD. Queensland Institute of Medical Research. Brisbane, Australia\n3Dr Andrew Morris, PhD, Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for\nHuman Genetics, University of Oxford, Oxford, UK\n4Dr Zhen Z Zhao, M.D., PhD. Queensland Institute of Medical Research. Brisbane, Australia\n5Ms Anjali K Henders, BSc Hons, Queensland Institute of Medical Research. Brisbane, Australia\n6Dr Ann Lambert, PhD. Nuffield Department of Obstetrics and Gynaecology, University of Oxford,\nJohn Radcliffe Hospital, Oxford, UK\n7Mrs Leanne Wallace, MSc, Queensland Institute of Medical Research. Brisbane, Australia\n8Prof. Nicholas G Martin, PhD. Queensland Institute of Medical Research. Brisbane, Australia\n9Dr Stephen H Kennedy, MRCOG, Nuffield Department of Obstetrics and Gynaecology,\nUniversity of Oxford, John Radcliffe Hospital, Oxford, UK\n10Dr Susan A Treloar, PhD, Centre for Military and Veterans' Health, The University of\nQueensland, Mayne Medical School, Brisbane, Australia\n11Krina T Zondervan, PhD, Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for\nHuman Genetics, University of Oxford, Oxford, UK\n12Prof. Grant W Montgomery, PhD, Queensland Institute of Medical Research. Brisbane,\nAustralia\nAbstract\nObjective—To refine a previously reported linkage peak for endometriosis on chromosome\n10q26, and conduct follow-up analyses and a fine-mapping association study across the region to\nidentify new candidate genes for endometriosis.\nDesign—Case-control study.\n© 2011 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.\nCorresponding author: Jodie N Painter, Queensland Institute of Medical Research, Locked Bag 2000, Herston QLD 4029, Australia,\nPh: +61 73362 0124, Fax: +61 73362 0101, jodie.painter@qimr.edu.au.13These authors contributed equally to the work.\nPublisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our\ncustomers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of\nthe resulting proof before it is published in its final citable form. Please note that during the production process errors may be\ndiscovered which could affect the content, and all legal disclaimers that apply to the journal pertain.\nNo conflicts of interest declared.\nNIH Public Access\nAuthor Manuscript\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nPublished in final edited form as:\nFertil Steril. 2011 June ; 95(7): 2236±2240. doi:10.1016/j.fertnstert.2011.03.062.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nSetting—Academic research.\nSubject(s)—Cases = 3,223 women with surgically confirmed endometriosis; Controls = 1,190\nwomen without endometriosis and 7,060 population samples.\nIntervention(s)—Analysis of 11,984 SNPs on chromosome 10.\nMain outcome measure(s)—Allele frequency differences between cases and controls.\nResults—Linkage analyses on families grouped by endometriosis symptoms (primarily\nsubfertility) provided increased evidence for linkage (logarithm of odds (LOD) score = 3.62) near\na previously reported linkage peak. Three independent association signals were found at 96.59 Mb\n(rs11592737, P=4.9 × 10−4), 105.63 Mb (rs1253130, P=2.5 × 10−4) and 124.25 Mb (rs2250804,\nP=9.7 × 10−4). Analyses including only samples from linkage families supported the association\nat all three regions. However, only rs11592737 in the cytochrome P450 subfamily C (CYP2C19)\ngene was replicated in an independent sample of 2,079 cases and 7060 population controls.\nConclusion(s)—The role of the CYP2C19 gene in conferring risk for endometriosis warrants\nfurther investigation.\nKeywords\nEndometriosis; linkage; association; subfertility; CYP2C19\nIntroduction\nEndometriosis, a disease affecting 6–10% of women of reproductive age, is defined as the\npresence of endometrial-like tissue in sites outside of the uterus, most commonly the pelvic\nperitoneum, ovaries and recto-vaginal septum (1). Although symptoms vary, affected\nwomen most commonly experience chronic pelvic pain, severe dysmenorrhea and\nsubfertility. The disease is inherited as a complex genetic trait (1–3), and aggregates within\nfamilies in humans (4,5) and non-human primates (6). Genetic factors accounted for 52% of\nthe variation in liability to endometriosis in an Australian twin study, with a relative-\nrecurrence risk of 2.34 for sibs of endometriosis patients (7).\nWe previously reported significant genetic linkage (logarithm of odds (LOD) score >3) to\nendometriosis on chromosome 10q26 in a study of 1,176 families (8). We have now\nperformed further analyses to refine the linkage peak and extensive fine mapping to identify\nregions associated with risk of developing endometriosis. We used latent class analysis to\ndetermine whether stratification by disease stage and/or symptoms was possible, and the\nrelative contribution of these factors to linkage in the region. Subsequently, we genotyped a\nhigh-density SNP panel in 1,144 familial cases and 1,190 controls. The best association\nsignals were detected at three independent loci although only SNPs at the 96.59 Mb region,\nharbouring the cytochrome P450 family subfamily C (CYP2C19) gene, showed evidence of\nreplication in independent case:control samples.\nMaterial and Methods\nRefining the linkage peak\nLatent class analysis—The linkage study included 931 affected sister pair families\ncollected by the Queensland Institute of Medical Research (QIMR) and 245 collected by the\nUniversity of Oxford (8,9). To refine the published linkage peak we sought to increase the\ngenetic homogeneity of the sample by examining endometriosis subtypes using information\nabout self-rated symptoms of pelvic pain (ever experiencing severe pelvic pain) and\nsubfertility (failure to conceive after trying for 12 months) and physician-diagnosed disease\nPainter et al. Page 2\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nstage (based on the revised American Fertility Society (rAFS) classification system) (10). As\nit can be difficult to stage disease accurately using clinical records alone, a simplified two-\nstage system was used (9,10): stage A (rAFS I–II or some ovarian disease plus a few\nadhesions) and stage B (rAFS III–IV). Latent class analysis (LCA), a method to find\nsubtypes of related cases from multivariate categorical data, was used to investigate the\npresence and composition of endometriosis subgroups using the Bayes Information Criterion\n(BIC) (11) as the index of model goodness-of-fit. The null hypothesis of a one-class (group)\nsolution (i.e. all individuals belong to the same class or group) is rejected if models with\nmore parameters (groups) provide a smaller BIC value.\nLinkage and ordered subset analyses—To investigate whether stratifying on\nsubfertility provided a more phenotypically homogenous sample, the approach of Cox et. al.\n(12) was adapted to conduct linkage analyses with families weighted according to reported\nsubfertility (0=subfertility, 1=no subfertility). Non-parametric, multipoint, affected-only\nLOD scores were calculated on the basis of the S-pairs scoring function and an exponential\nallele-sharing model (exponential LOD (expLOD) scores) using the ALLEGRO analysis\npackage (13). Ordered subset analyses (OSA) (14) were performed to assess the increased\nevidence of linkage in subsets of families ordered by their subfertility value relative to the\nentire sample.\nAssociation mapping sample selection\nFor the fine-mapping association analyses we genotyped unrelated cases mostly from the\nfamilies included in the linkage study (8). Subject to DNA availability, cases were chosen to\ninclude individuals with the most severe disease, i.e. the highest disease stage or the\nyoungest age at onset if both sisters had the same disease stages. There were 871 such cases\nfrom the 931 QIMR families and 231 from Oxford. A further 40 QIMR cases were chosen\nfrom families not included in the original linkage analysis but containing a proband plus at\nleast 2 affected relatives using the same criteria.\nQIMR controls (N=952) were chosen from female twin pairs originally recruited for a study\nof gynaecological health (15), including one sample from pairs where neither sister had self-\nreported endometriosis. Oxford controls (N=238) were unrelated women recruited in\ncollaborating hospitals who were: 1) undergoing laparoscopy for pelvic pain, subfertility or\nother gynaecological complaints, hysterectomy or sterilisation; 2) free of endometriosis at\nsurgery, and 3) without a previous surgical diagnosis of endometriosis. All study\nparticipants were volunteers, had signed written informed consent and had provided a blood\nsample for DNA extraction. Ethics approval was obtained from the QIMR Human Research\nEthics Committee, and the UK Regional Multi-centre and local Research Ethics\nCommittees.\nFine-mapping\nSNP selection—The 95% confidence interval for both the published (region 112–129 Mb)\nand ‘fertility-related’ (region 94–107 Mb) linkage peaks extends over 36 Mb (NCBI build\n36; http://www.ensembl.org). Assays for 13,589 SNPs were manufactured and the\ngenotyping and initial quality control performed at Illumina Inc (San Diego, CA, USA) on\nan Illumina Infinium iSelect custom platform. Across the entire 36 Mb region, gene-based\nSNPs were included in all exons and 5’ and 3’ untranslated regions for approximately 250\ngenes, and under the published and fertility-related linkage peaks SNPs tagged to a\nminimum pair-wise r2 of 0.97. In an attempt to capture information from rare SNPs (minor\nallele frequencies (MAFs) <1%)) we did not exclude loci with MAFs of 0 in the HapMap\n(www.hapmap.org) although most variants were common in our dataset: only 6% of SNPs\nhad MAFs <1% (range 0.0002–0.0098; Table 1).\nPainter et al. Page 3\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nQuality control and association analyses—Additional quality control was performed\non genotype data from 2,369 (1,158 cases, 1,211 controls) individuals and 12,537\npolymorphic SNPs using PLINK (16). We detected and removed individuals with non-\nCaucasian ancestry and SNPs with >5% missing genotypes or Hardy-Weinberg P-values <1\n× 10−4 in control samples. Thereafter, 1,144 cases (911 QIMR; 233 Oxford), 1,190 controls\n(952 QIMR; 238 Oxford) and 11,984 SNPs remained in the dataset. Cochran-Mantel-\nHaenszel (CMH) tests of association were performed using PLINK including QIMR and\nOxford data as different strata to account for any subtle differences between populations in\nbaseline effect (17). Breslow-Day (BD) tests were conducted to check that the assumptions\nof the CMH test (i.e. similar effect size across strata) were true. The significance of the\nassociation signals was assessed by permutation (10,000 replicates).\nInvestigation of association in a replication data set\nWe attempted to replicate the results from the ‘discovery’ sample in an independent set of\n2,079 cases (1,383 QIMR; 696 Oxford), all surgically confirmed, without a family history,\nrecruited within the QIMR and Oxford studies. Each was genotyped on Illumina\nHuman670Quad Beadarrays for a genome-wide association (GWA) study (17). There were\n7,060 population controls genotyped using: a) Human610Quad (QIMR controls: 1,870\nunrelated individuals recruited within the Brisbane Adolescent Twin Study (18,19)) or b)\nHuman1M-Duo beadchips (Oxford controls: 5,190 UK unrelated population controls\nprovided by The Wellcome Trust Case Control Consortium 2). Association analysis, and\nmeta-analysis of the P-values for both datasets, were performed using PLINK (16).\nResults\nLinkage\nLatent class analysis—Comparative fits of LCA models determined a two-class solution\nas the most parsimonious with a minimum BIC of −247.50 (one-class BIC −237.30; three-\nclass BIC −220.81). The main phenotypic measure discriminating between the two classes\nwas subfertility. Class 1 families (CL1: 51.7% of the linkage families; 663 QIMR, 138\nOxford) represented an endometriosis type typically without subfertility (91%), a slightly\nlower proportion with stage B disease (27%), but more common experience of pelvic pain\n(80.3%). Class 2 (CL2; 48.3%; 268 QIMR, 107 Oxford) families represented a form\ntypically seen with subfertility (89%), a slightly higher proportion with stage B disease\n(40%) and less common experience of pelvic pain (72.3%).\nThe results of linkage analyses, performed using the subfertility weighting, did not change\nsubstantially by including CL2 families only. Restricting the analysis to CL1 families\nproduced an expLOD=3.62 at approximately 98 Mb, 27 Mb closer to the centromere than\nthe published significant linkage peak (expLOD=3.08 at 125 Mb) (Fig. 1). These results\nwere confirmed by the ordered subset analysis, with an increased expLOD=3.58 when\nfamilies ranked by fertility scores were successively added to the linkage analysis. The\nincreased evidence for linkage in the fertile subset relative to the entire sample (assessed via\n10,000 permutations) was significant (P=0.02).\nFine-mapping association analyses in the discovery sample\nNominal signals of association (P<1×10−3), supported by multiple SNPs, were seen in three\nregions (Table 2, Fig. 2). The SNPs with the smallest P-values were under the fertility-\nrelated linkage peak: at ~96.59 Mb (top SNP rs11592737, P=4.9 × 10−4, OR=0.78) in intron\n7 of the CYP2C19 gene, and at ~105.63 Mb (rs12573103, P=2.5 × 10−4, OR=1.24) upstream\nof the SH3 and PX domain-containing adaptor (SH3PXD2A) gene. The next smallest P-\nvalue was for rs2250804 at 124.25 Mb (P=9.7 × 10−4; OR=1.22) under the published\nPainter et al. Page 4\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nlinkage peak, in intron 3 of the HtrA serine peptidase 1 precursor (HTRA1) gene. All three\nsignals were independent, with no linkage disequilibrium between the SNPs. However, the\npermutation analysis showed that none of association signals was significant at a study-wide\nlevel (P<0.05), with corrected empirical P-values of 0.92, 0.75 and 0.99 for rs11592737,\nrs12573103 and rs2250904, respectively.\nExploratory analyses were performed limiting cases to those from the previously published\nlinkage families (1,105 cases) and CL1 families only (755 cases). P-values for the SNPs at\n96.59 Mb, 105.63 Mb and 124.25 Mb remained the smallest in these analyses. For\nrs11592737 at 96.59 Mb, a P=9.0 × 10−4 (OR=1.26) was obtained including only linkage\nfamily cases but was below background levels including only CL1 family cases (P=5.0 ×\n10−2; OR=1.18). For rs12573103 at 105.63 Mb, a P=1.0 × 10−4 (OR=1.25) was obtained\nincluding only linkage family cases and P=5.3 × 10−5 (OR=1.31) for CL1 cases. The signal\nfor rs2250804 at 124.25 Mb was reduced by including only linkage family (P=1.1 × 10−3,\nOR=1.23) and CL1 (P=1.2 × 10−2, OR=1.19) cases.\nReplication analyses in an independent case-control sample\nThe SNPs with the smallest P-values in the 96.59 Mb, 105.63 Mb and 124.25 Mb regions\nwere not present on the commercial Illumina arrays typed in the replication samples.\nHowever, additional SNPs that were in moderate linkage disequilibrium (LD: pairwise\nr2>0.5) were included in our Illumina iSelect panel, allowing a direct comparison of P-\nvalues for the discovery and replication datasets. All three SNPs in LD (r2≥0.98) with\nrs11592737 at 96.59 Mb showed nominal evidence of association (P=4.0 × 10−2 for\nrs7085745 and 5.0 × 10−2 for rs12243416 and rs11188067; ORs=1.10) in the replication\ndataset (Table 2), with corresponding P-values between 3.1–4.5 × 10−4 (ORs=1.14) in the\nmeta-analysis of the fine-mapping discovery and replication datasets (Table 2).\nThere was no replication signal for SNPs at either 105.63 Mb or 124.25 Mb. The SNP in\nhighest LD with rs12573103 at 105.63 Mb (rs1980653, r2=0.94) had a P=0.60 (OR=1.02) in\nthe replication dataset. The two SNPs in highest LD with rs2250804 at 124.25 Mb\n(rs2300433 and rs2253755, r2=0.50) had P-values of 0.44 and 0.47 in the replication dataset\n(Table 2).\nDiscussion\nAnalysis of endometriosis stage and pelvic pain and subfertility symptoms identified two\nclasses of families, distinguished primarily by the presence or absence of subfertility.\nSeparate linkage analyses with the two classes produced significantly increased evidence for\nlinkage amongst families without subfertility, shifting the linkage peak approximately 27\nMb. We genotyped SNPs at high density across the region covered by both the published\nand fertility-related linkage peaks and found evidence of association at three independent\nloci. Although this was not significant at a study-wide level, there was evidence for\nreplication of the signal(s) at 96.59 Mb within the CYP2C19 gene in the independent set of\nendometriosis cases.\nThe most significantly associated SNP at 96.59 Mb is in intron 7 of CYP2C19, which\nparticipates in the metabolism of drugs and oestrogen including conversion of oestradiol\n(E2) to oestrone (E1), and the production of E1 and E2 2α- and 16α-hydroxylation\nmetabolites (20,21). The key SNP rs11592737 is in complete LD with rs12248560 (the\nsecond best SNP in the region), a functional variant located in the CYP2C19 promoter. The\nrs12248560 “T” allele (CYP2C19*17; http://www.cypalleles.ki.se/cyp2c19.htm) increases\nthe rate of CYP2C19 transcription and was initially thought to produce an ‘ultra-rapid’\nPainter et al. Page 5\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nmetaboliser form of the CYP2C19 protein (22), although a recent review found drug\nmetabolic rates within the ranges seen for wild-type homozygotes (23).\nFurther evidence for a role for CYP2C19 in diseases influenced by oestrogen comes from a\nrecent study showing a decreased risk of breast cancer in rs12248560 carriers, possibly\nthrough increased catabolism resulting in lower overall oestrogen levels (24). CYP2C19 has\nalso been associated with endometriosis in a small study of 50 cases and 50 controls\nsuggesting that affected women were significantly more likely (P=0.023; OR=3.12) to be\nheterozygous carriers of rs4244285, a splice site defect that abrogates gene expression (25).\nHowever, these findings were not replicated in another small study of 46 cases and 39\ncontrols (26). While both studies were clearly under-powered, the initial study adds further\nsupport to CYP2C19 as a plausible endometriosis candidate gene. The P-value for\nrs4244285 in our discovery sample was only nominally significant (P=0.011; OR=1.23),\nindicating this SNP is not driving our association signal in the region. Several lines of\nevidence now point to a role for CYP2C19 either through the effect on transcription of the\nrs12248560 variant or additional rare and low frequency alleles in LD with this SNP. The\nassociation result does not account for the linkage signal. Linkage to this region could result\nfrom a combination of a common variant like the one described here in CYP2C19 and rare\nvariants of larger effect that might be observed in only a few families.\nThere was no evidence for replication of the 105.63 Mb or 124.25 Mb signals. The\ndirections of the effects were the same for both the fine-mapping and replication datasets,\nand both regions harbour plausible candidate genes for endometriosis: SH3PXD2A is an\ninteraction partner of ADAM metallopeptidase domain 12 (ADAM12), which has a role in\nuterine decidualization in mice (27, 28). HTRA1 is upregulated in human decidual cells,\nsuggesting a role in preparing the endometrium for embryo implantation (29). It is likely that\nthese associations represent false positive signals, although we were unable to test the key\nSNPs directly in the replication study. Additionally, the discovery sample used familial\ncases but these were not available for the replication sample, and non-familial cases may\nhave different underlying disease aetiology.\nWe detected evidence of genetic association in a region of significant linkage to\nendometriosis on chromosome 10. This signal does not fully account for the previously\nreported or fertility-related linkage peaks. However, the finding of suggestive association,\nand the presence of an extremely plausible candidate gene in the region of association,\nsuggest that further investigation is warranted. Future studies should include replication in\nother samples, a search for rare and novel genetic variants and gene expression studies.\nAcknowledgments\nWe thank the women who participated in the QIMR, OXEGENE studies, and Endometriosis Associations for\nsupporting study recruitment. The QIMR Study was supported by grants from the National Health and Medical\nResearch Council (NHMRC) of Australia (241944, 339462, 389927,389875, 389891, 389892, 389938, 443036,\n442915, 442981, 496610, 496739, 552485, 552498), the Cooperative Research Centre for Discovery of Genes for\nCommon Human Diseases (CRC), Cerylid Biosciences (Melbourne), and donations from Neville and Shirley\nHawkins, the Endometriosis Associations of Queensland and Western Australia, and the family of the late Kim\nGoodwin. The fine-mapping genotyping was funded by the National Institutes of Health (NIH, USA) grant number\nR01HD50537. DRN is supported by the NHMRC Fellowship (339462 and 613674) and ARC Future Fellowship\n(FT0991022) schemes. GWM is supported by the NHMRC Fellowships Scheme (339446, 619667). We thank B.\nHaddon, D. Smyth, H. Beeby, O. Zheng, B. Chapman and additional research assistants and interviewers for project\nand database management, sample processing, and genotyping. We thank Brisbane gynaecologist Dr Daniel T\nO’Connor for confirmation of diagnosis and staging of disease for some Australian patients. We also thank the\nmany hospital directors and staff, gynaecologists, general practitioners, and pathology services in Australia who\nprovided assistance with confirmation of diagnoses. We thank Sullivan Nicolaides and Queensland Medical\nLaboratory for pro bono collection and delivery of blood samples and other pathology services for assistance with\nblood collection.\nPainter et al. Page 6\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nThe genome-wide association study was supported by a grant from the Wellcome Trust (WT084766/Z/08/Z), and\nmakes use of WTCCC2 control data generated by the Wellcome Trust Case-Control Consortium. A full list of the\ninvestigators who contributed to the generation of these data is available from www.wtccc.org.uk. Funding for the\nWTCCC project was provided by the Wellcome Trust under award 076113 and 085475. APM is supported by a\nWellcome Trust Senior Research Fellowship (WT081682/Z/06/Z). SK is supported by the Oxford Partnership\nComprehensive Biomedical Research Centre with funding from the Department of Health NIHR Biomedical\nResearch Centres funding scheme. KTZ is supported by a Wellcome Trust Research Career Development\nFellowship (WT085235/Z/08/Z). We thank Louise Cotton, Lesley Pope, Gillian Chalk, Gail Farmer (University of\nOxford). We also thank Philippe Koninckx, (Leuven, Belgium), Martin Sillem (Heidelberg, Germany), Colm\nO’Herlihy and Mary Wingfield (Dublin, Ireland), Mette Moen (Trondheim, Norway), Leila Adamyan (Moscow,\nRussia), Enda McVeigh (Oxford, UK), Christopher Sutton (Guildford, UK), David Adamson (Palo Alto, USA), and\nRonald Batt (Buffalo, USA), for providing diagnostic confirmation.\nFinancial support\nQueensland Institute of Medical Research:\nNational Institutes of Health (NIH, USA): R01HD50537.\nNational Health and Medical Research Council (NHMRC) of Australia: 241944, 339446, 339462, 389927,389875,\n389891, 389892, 389938, 443036, 442915, 442981, 496610, 496739, 552485, 552498, 613674, 619667.\nAustralian Research Council (ARC) Future Fellowship scheme: (FT0991022.\nOxford University:\nWellcome Trust: 084766, 081682, 085235, 076113 and 085475.\nReferences\n1. Giudice LC, Kao LC. Endometriosis. Lancet. 2004; 364:1789–1799. [PubMed: 15541453]\n2. Simpson JL, Bischoff FZ. 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Justenhoven C, Hamann U, Pierl CB, Baisch C, Harth V, Rabstein S, et al. CYP2C19*17 is\nassociated with decreased breast cancer risk. Breast Cancer Res Treat. 2009; 115:391–396.\n[PubMed: 18521743]\n25. Cayan F, Ayaz L, Aban M, Dilek S, Gumus LT. Role of CYP2C19 polymorphisms in patients with\nendometriosis. Gynecol Endocrinol. 2009; 25:530–535. [PubMed: 19499406]\n26. Bozdag G, Alp A, Saribas Z, Tuncer S, Aksu T, Gurgan T. CYP17 and CYP2C19 gene\npolymorphisms in patients with endometriosis. Reprod Biomed Online. 2010; 20:286–290.\n[PubMed: 20113968]\n27. Zhang L, Guo W, Chen Q, Fan X, Zhang Y, Duan E. Adam12 plays a role during uterine\ndecidualization in mice. Cell Tissue Res. 2009; 338:413–421. [PubMed: 19841944]\n28. Kim J, Kim H, Lee SJ, Choi YM, Lee JY. Abundance of ADAM-8, -9, -10, -12, -15 and -17 and\nADAMTS-1 in mouse uterus during the oestrous cycle. Reprod Fertil Dev. 2005; 17:543–555.\n[PubMed: 15907280]\n29. Nie G, Hale K, Li Y, Manuelpillai U, Wallace EM, Salamonsen LA. Distinct expression and\nlocalization of serine protease HtrA1 in human endometrium and first-trimester placenta. Dev\nDyn. 2006; 235:3448–3455. [PubMed: 17072861]\nPainter et al. Page 8\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nFigure 1.\nChromosome 10 linkage peaks for endometriosis\nPainter et al. Page 9\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nFigure 2.\nFine-mapping association analysis results across the 36 Mb region under the published and\nfertility-related linkage peaks for endometriosis.\nPainter et al. Page 10\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\n\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\nPainter et al. Page 11\nTable 1\nMinor allele frequency ranges for 11,984 polymorphic SNPs included in the fine-mapping association\nanalyses.\nMinor allele frequencies SNPs per frequency class\nCommon\n    MAF > 5% 10,245 (85.5%)\nLow frequency\n    MAF 1–5% 1008 (8.4%)\nRare\n    MAF < 1% 731 (6.1%)\nFertil Steril. Author manuscript; available in PMC 2012 June 1.\n\nNIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author Manuscript\nPainter et al. Page 12\nTable 2\nAssociation signal in the 96.5 Mb and 105.6 Mb regions for the fine-mapping (discovery), replication, and combined datasets. Results are shown for the\nmost significant SNP in each region, and for the replication and meta-analysis for SNPs in moderate LD (r2 > 0.5) for which the replication samples had\nbeen genotyped.\nLinkage peak Fine-mapping Replication Meta-analysis\nSNP Position r2* RAF** P OR*** P OR P OR\n96.59 Mb\nrs11592737 96593404 0.79 (A) 4.9 × 10−4 1.28 (1.11–1.47) -- -- -- --\n   rs12243416 96444146 0.99 0.79 (G) 7.6 × 10−4 1.28 (1.11–1.47) 5.0 × 10−2 1.10 (1.00–1.20) 8.4 × 10−4 1.14 (1.05–1.22)\n   rs11188067 96483699 0.99 0.79 (A) 6.7 × 10−4 1.28 (1.11–1.47) 5.0 × 10−2 1.10 (1.00–1.20) 8.4 × 10−4 1.14 (1.05–1.22)\n   rs7085745 96672504 0.98 0.79 (T) 1.0 × 10−3 1.28 (1.11–1.47) 4.0 × 10−2 1.10 (1.00–1.20) 7.6 × 10−4 1.14 (1.05–1.22)\n105.63 Mb\nrs12573103 105629231 0.48 (A) 2.5 × 10−4 1.24 (1.10–1.39) -- -- -- --\n   rs10748858 105629504 0.68 0.41 (G) 3.2 × 10−4 1.24 (1.10–1.39) 0.60 1.02 (0.95–1.10) 6.0 × 10−3 1.09 (1.02–1.15)\n   rs1980653 105644154 0.94 0.49 (T) 1.8 × 10−3 1.20 (1.07–1.34) 0.11 1.06 (0.99–1.14) 1.3 × 10−3 1.01 (1.04–1.17)\n   rs11191865 105662832 0.93 0.49 (G) 1.5 × 10−3 1.20 (1.07–1.35) 0.13 1.06(0.98–1.14) 1.7 × 10−3 1.01 (1.04–1.17)\n124.25 Mb\nrs2250804 124254868 0.33 (C) 9.7 × 10−4 1.23 (1.09–1.39) --- --- --- ---\n   rs2300433 124233447 0.50 0.31 (G) 4.8 × 10−2 1.13 (1.00–1.28) 0.44 0.96 (0.89–1.05) 0.53 1.04 (0.96–1.14)\n   rs2253755 124231547 0.50 0.31 (G) 4.5 × 10−2 1.13 (1.00–1.28) 0.47 0.97 (0.89–1.05) 0.50 1.02 (0.96–1.09)\n*r2 values between the best SNPs in each region (in bold) to those included both in the fine-mapping dataset and on the Illumina 610 K chips, calculated using the fine-mapping data.\n**Risk allele frequency\n***Odds ratios were calculated for the risk allele, indicated in parentheses\nFertil Steril. Author manuscript; available in PMC 2012 June 1.","source_license":"CC0","license_restricted":false}