Dr Krina T Zondervan
| Research Area: | Genetics and Genomics |
|---|---|
| Technology Exchange: | Bioinformatics, Medical statistics, SNP typing, Statistical genetics and Transcript profiling |
| Scientific Themes: | Genetics & Genomics and Clinical Trials & Epidemiology |
| Keywords: | Endometriosis, Epidemiology, Infertility, Women's Health, Genetics and Pelvic pain |
| Web Links: |
My research group focuses on the integration of genetic, molecular, and environmental epidemiological research methods to uncover the aetiology of endometriosis, and related women’s health conditions. We are based both at the Wellcome Trust Centre for Human Genetics (WTCHG) and the Nuffield Dept of Obstetrics & Gynaecology in Oxford, and collaborate with a network of other endometriosis research groups internationally. At NDOG, my group is part of the Endometriosis CaRe centre, of which I am co-Director. At WTCHG, my group forms part of the Genetic and Genomic Epidemiology Unit, together with groups led by Dr Andrew Morris and Dr Cecilia Lindgren.
Endometriosis is a common condition, affecting millions of women worldwide, for which the causes remain unknown. It is characterised by the presence of endometrial-like tissue in sites outside the uterus, causing pelvic pain and subfertility. The need for surgery to confirm diagnosis means exact population prevalence rates are unknown, but estimates vary between 1-10% of women in their reproductive years. Endometriosis has a major impact on health-related quality of life and work productivity, with treatment options limited to hormonal drugs to suppress ovarian function, surgical ablation of endometriotic lesions and, if necessary, removal of the pelvic organs. Our studies and those of other investigators have shown it is a complex disorder, caused by the interplay between genetic and environmental factors that are as yet unknown.
Current projects include:
- Genome-wide association, exome and resequencing studies, to uncover genetic variants associated with endometriosis risk in >5,500 cases and >5,500 controls part of the International Endogene Consortium.
- Sequencing studies following up significant linkage signals found previously on chromosomes 7 and 10 in affected sister-pairs from 1,200 families as well as in the genome-wide association study.
- Targeted gene expression and eQTL studies of genetic regions implicated in the aetiology of endometriosis.
- Genetic linkage and sequencing analyses using information from a multigenerational pedigree of rhesus macaques that develop endometriosis spontaneously.
- Epidemiological studies of endometriosis in 23 clinics worldwide which enrolled ~1800 prospectively collected cases and controls.
- Integrated analyses of genetical genomic and molecular phenotyping data in epidemiological studies of complex diseases.
In addition to the projects above, I am joint Principal Investigator of WERF EPHect (Endometriosis Phenome and Biobanking Harmonisation Project), which has brought together 36 academic and 3 industrial centre to develop a global concensus on 1) phenotypic and epidemiological data collection as well as 2) Standard Operating Protocols for collection, processing and long-term storage of biological samples for research into endometriosis (www.endometriosisfoundation.org/ephect).
Funding: The Wellcome Trust; MRC; NIH; World Endometriosis Research Foundation; European Public Health Programme.
| Name | Department | Institution | Country |
|---|---|---|---|
| Prof Grant Montgomery | Dept of Molecular Epidemiology | Queensland Institute for Medical Research, Brisbane | Australia |
| Dr Stacey Missmer | Harvard Medical School | Harvard University | USA |
| Dr Christian Becker | Nuffield Dept of Obstetrics & Gynaecology | University of Oxford | United Kingdom |
| Dr Andrew P Morris | Wellcome Trust Centre for Human Genetics | Oxford University | UK |
| Dr Cecilia Lindgren | Wellcome Trust Centre for Human Genetics | Oxford University | UK |
| Prof Joseph Kemnitz | Dept. of Cell & Regenerative Biology | WNPRC, University of Wisconsin-Madison | USA |
| Dr Jeffrey Rogers | Dept of Molecular and Human Genetics, Human Genome Sequencing Center | Baylor College of Medicine, Houston | USA |
| Prof Stephen Kennedy | Nuffield Dept of Obstetrics & Gynaecology, University of Oxford | UK | |
| Prof Mark McCarthy | Oxford Centre for Diabetes, Endocrinology & Metabolism | Oxford University | UK |
| Prof Tim Spector | Department of Twin Research and Genetic Epidemiology | Kings College, London | UK |
| Prof Chris Holmes | Wellcome Trust Centre for Human Genetics | Oxford University | UK |
| Prof Peter Donnelly FRS | Wellcome Trust Centre for Human Genetics | Oxford University | UK |
| Prof Thomas D'Hooghe | Centre for Reproductive Medicine | University of Leuven | Belgium |
| Prof Peter Rogers | Department of Obstetrics and Gynaecology | University of Melbourne | Australia |
| Prof Paolo Vercellini | Clinica Ostetrica e Ginecologica I | University of Milano School of Medicine | Italy |
2012. Genome-wide association meta-analysis identifies new endometriosis risk loci. Nat Genet, 44 (12), pp. 1355-1359. Read abstract | Read more
We conducted a genome-wide association meta-analysis of 4,604 endometriosis cases and 9,393 controls of Japanese and European ancestry. We show that rs12700667 on chromosome 7p15.2, previously found to associate with disease in Europeans, replicates in Japanese (P = 3.6 × 10(-3)), and we confirm association of rs7521902 at 1p36.12 near WNT4. In addition, we establish an association of rs13394619 in GREB1 at 2p25.1 with endometriosis and identify a newly associated locus at 12q22 near VEZT (rs10859871). Excluding cases of European ancestry of minimal or unknown severity, we identified additional previously unknown loci at 2p14 (rs4141819), 6p22.3 (rs7739264) and 9p21.3 (rs1537377). All seven SNP effects were replicated in an independent cohort and associated at P <5 × 10(-8) in a combined analysis. Finally, we found a significant overlap in polygenic risk for endometriosis between the genome-wide association cohorts of European and Japanese descent (P = 8.8 × 10(-11)), indicating that many weakly associated SNPs represent true endometriosis risk loci and that risk prediction and future targeted disease therapy may be transferred across these populations. Hide abstract
2012. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet, 44 (10), pp. 1084-1089. Read abstract | Read more
Sequence-based variation in gene expression is a key driver of disease risk. Common variants regulating expression in cis have been mapped in many expression quantitative trait locus (eQTL) studies, typically in single tissues from unrelated individuals. Here, we present a comprehensive analysis of gene expression across multiple tissues conducted in a large set of mono- and dizygotic twins that allows systematic dissection of genetic (cis and trans) and non-genetic effects on gene expression. Using identity-by-descent estimates, we show that at least 40% of the total heritable cis effect on expression cannot be accounted for by common cis variants, a finding that reveals the contribution of low-frequency and rare regulatory variants with respect to both transcriptional regulation and complex trait susceptibility. We show that a substantial proportion of gene expression heritability is trans to the structural gene, and we identify several replicating trans variants that act predominantly in a tissue-restricted manner and may regulate the transcription of many genes. Hide abstract
2012. Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes. PLoS Genet, 8 (2), pp. e1002505. Read abstract | Read more
Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS-associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D(ABD-GLU) = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response-related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS-associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10(-4)). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS-related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10(-4)); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10(-4)) and BMI-adjusted waist-to-hip ratio (P = 2.4×10(-4)). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations. Hide abstract
2012. Developing symptom-based predictive models of endometriosis as a clinical screening tool: Results from a multicenter study Fertility and Sterility, 98 (3), Read abstract | Read more
Objective: To generate and validate symptom-based models to predict endometriosis among symptomatic women prior to undergoing their first laparoscopy. Design: Prospective, observational, two-phase study, in which women completed a 25-item questionnaire prior to surgery. Setting: Nineteen hospitals in 13 countries. Patient(s): Symptomatic women (n = 1,396) scheduled for laparoscopy without a previous surgical diagnosis of endometriosis. Intervention(s): None. Main Outcome Measure(s): Sensitivity and specificity of endometriosis diagnosis predicted by symptoms and patient characteristics from optimal models developed using multiple logistic regression analyses in one data set (phase I), and independently validated in a second data set (phase II) by receiver operating characteristic (ROC) curve analysis. Result(s): Three hundred sixty (46.7%) women in phase I and 364 (58.2%) in phase II were diagnosed with endometriosis at laparoscopy. Menstrual dyschezia (pain on opening bowels) and a history of benign ovarian cysts most strongly predicted both any and stage III and IV endometriosis in both phases. Prediction of any-stage endometriosis, although improved by ultrasound scan evidence of cyst/nodules, was relatively poor (area under the curve [AUC] = 68.3). Stage III and IV disease was predicted with good accuracy (AUC = 84.9, sensitivity of 82.3% and specificity 75.8% at an optimal cut-off of 0.24). Conclusion(s): Our symptom-based models predict any-stage endometriosis relatively poorly and stage III and IV disease with good accuracy. Predictive tools based on such models could help to prioritize women for surgical investigation in clinical practice and thus contribute to reducing time to diagnosis. We invite other researchers to validate the key models in additional populations. © 2012 by American Society for Reproductive Medicine. Hide abstract
2011. Impact of endometriosis on quality of life and work productivity: a multicenter study across ten countries. Fertil Steril, 96 (2), pp. 366-373.e8. Read abstract | Read more
To assess the impact of endometriosis on health-related quality of life (HRQoL) and work productivity. Hide abstract
2011. Coding regions of INHBA, SFRP4 and HOXA10 are not implicated in familial endometriosis linked to chromosome 7p13-15. Mol Hum Reprod, 17 (10), pp. 605-611. Read abstract | Read more
Endometriosis is a common, chronic gynaecological disease affecting up to 10% of women in their reproductive years. Its aetiology still remains unclear, but evidence indicates genetic factors play a role. We previously identified a region of significant linkage on chromosome 7 in 52 families comprising at least three affected women, stretching ∼6.4 Mb. We screened coding regions and parts of the regulatory regions of three candidate genes with a known role in endometrial development and function-INHBA, SFRP4 and HOXA10-located under or very near the linkage peak, for potential causal mutations using Sanger sequencing. Sequencing was conducted in 47 cases from the 15 families contributing most to the linkage signal (Z(mean) ≥ 1). Minor allele frequencies (MAFs) of observed variants were compared with MAFs from two publicly available reference populations of European ancestry: 60 individuals in HapMap and 150 individuals in the 1000 Genomes Project. A total of 11 variants were found, 5 (45%) of which were common (MAF > 0.05) among the 15 case families and the reference populations (P-values for MAF difference: 0.88-1.00). The remaining six were rare and unlikely to be individually or cumulatively responsible for the linkage signal. The results indicate that the coding regions of these three genes do not harbour mutations responsible for linkage to endometriosis in these families. Hide abstract
2011. High-density fine-mapping of a chromosome 10q26 linkage peak suggests association between endometriosis and variants close to CYP2C19. Fertil Steril, 95 (7), pp. 2236-2240. Read abstract | Read more
To refine a previously reported linkage peak for endometriosis on chromosome 10q26, and conduct follow-up analyses and a fine-mapping association study across the region to identify new candidate genes for endometriosis. Hide abstract
2011. Basic statistical analysis in genetic case-control studies. Nat Protoc, 6 (2), pp. 121-133. Read abstract | Read more
This protocol describes how to perform basic statistical analysis in a population-based genetic association case-control study. The steps described involve the (i) appropriate selection of measures of association and relevance of disease models; (ii) appropriate selection of tests of association; (iii) visualization and interpretation of results; (iv) consideration of appropriate methods to control for multiple testing; and (v) replication strategies. Assuming no previous experience with software such as PLINK, R or Haploview, we describe how to use these popular tools for handling single-nucleotide polymorphism data in order to carry out tests of association and visualize and interpret results. This protocol assumes that data quality assessment and control has been performed, as described in a previous protocol, so that samples and markers deemed to have the potential to introduce bias to the study have been identified and removed. Study design, marker selection and quality control of case-control studies have also been discussed in earlier protocols. The protocol should take ~1 h to complete. Hide abstract
2011. The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits. PLoS One, 6 (7), pp. e22070. Read abstract | Read more
The integrated analysis of genotypic and expression data for association with complex traits could identify novel genetic pathways involved in complex traits. We profiled 19,573 expression probes in Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from 299 twins and correlated these with 44 quantitative traits (QTs). For 939 expressed probes correlating with more than one QT, we investigated the presence of eQTL associations in three datasets of 57 CEU HapMap founders and 86 unrelated twins. Genome-wide association analysis of these probes with 2.2 m SNPs revealed 131 potential eQTLs (1,989 eQTL SNPs) overlapping between the HapMap datasets, five of which were in cis (58 eQTL SNPs). We then tested 535 SNPs tagging the eQTL SNPs, for association with the relevant QT in 2,905 twins. We identified nine potential SNP-QT associations (P<0.01) but none significantly replicated in five large consortia of 1,097-16,129 subjects. We also failed to replicate previous reported eQTL associations with body mass index, plasma low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides levels derived from lymphocytes, adipose and liver tissue. Our results and additional power calculations suggest that proponents may have been overoptimistic in the power of LCLs in eQTL approaches to elucidate regulatory genetic effects on complex traits using the small datasets generated to date. Nevertheless, larger tissue-specific expression data sets relevant to specific traits are becoming available, and should enable the adoption of similar integrated analyses in the near future. Hide abstract
2011. Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis. Nat Genet, 43 (1), pp. 51-54. Read abstract | Read more
Endometriosis is a common gynecological disease associated with pelvic pain and subfertility. We conducted a genome-wide association study (GWAS) in 3,194 individuals with surgically confirmed endometriosis (cases) and 7,060 controls from Australia and the UK. Polygenic predictive modeling showed significantly increased genetic loading among 1,364 cases with moderate to severe endometriosis. The strongest association signal was on 7p15.2 (rs12700667) for 'all' endometriosis (P = 2.6 × 10⁻⁷, odds ratio (OR) = 1.22, 95% CI 1.13-1.32) and for moderate to severe disease (P = 1.5 × 10⁻⁹, OR = 1.38, 95% CI 1.24-1.53). We replicated rs12700667 in an independent cohort from the United States of 2,392 self-reported, surgically confirmed endometriosis cases and 2,271 controls (P = 1.2 × 10⁻³, OR = 1.17, 95% CI 1.06-1.28), resulting in a genome-wide significant P value of 1.4 × 10⁻⁹ (OR = 1.20, 95% CI 1.13-1.27) for 'all' endometriosis in our combined datasets of 5,586 cases and 9,331 controls. rs12700667 is located in an intergenic region upstream of the plausible candidate genes NFE2L3 and HOXA10. Hide abstract
2010. Data quality control in genetic case-control association studies. Nat Protoc, 5 (9), pp. 1564-1573. Read abstract | Read more
This protocol details the steps for data quality assessment and control that are typically carried out during case-control association studies. The steps described involve the identification and removal of DNA samples and markers that introduce bias. These critical steps are paramount to the success of a case-control study and are necessary before statistically testing for association. We describe how to use PLINK, a tool for handling SNP data, to perform assessments of failure rate per individual and per SNP and to assess the degree of relatedness between individuals. We also detail other quality-control procedures, including the use of SMARTPCA software for the identification of ancestral outliers. These platforms were selected because they are user-friendly, widely used and computationally efficient. Steps needed to detect and establish a disease association using case-control data are not discussed here. Issues concerning study design and marker selection in case-control studies have been discussed in our earlier protocols. This protocol, which is routinely used in our labs, should take approximately 8 h to complete. Hide abstract
2009. Priorities for endometriosis research: recommendations from an international consensus workshop. Reprod Sci, 16 (4), pp. 335-346. Read abstract | Read more
Endometriosis is an estrogen-dependent disorder where endometrial tissue forms lesions outside the uterus. Endometriosis affects an estimated 10% of women in the reproductive-age group, rising to 30% to 50% in patients with infertility and/or pain, with significant impact on their physical, mental, and social well-being. There is no known cure, and most current medical treatments are not suitable long term due to their side-effect profiles. Endometriosis has an estimated annual cost in the United States of $18.8 to $22 billion (2002 figures). Although endometriosis was first described more than 100 years ago, current knowledge of its pathogenesis, spontaneous evolution, and the pathophysiology of the related infertility and pelvic pain, remain unclear. A consensus workshop was convened following the 10th World Congress on Endometriosis to establish recommendations for priorities in endometriosis research. One major issue identified as impacting on the capacity to undertake endometriosis research is the need for multidisciplinary expertise. A total of 25 recommendations for research have been developed, grouped under 5 subheadings: (1) diagnosis, (2) classification and prognosis, (3) treatment and outcome, (4) epidemiology, and (5) pathophysiology. Endometriosis research is underfunded relative to other diseases with high health care burdens. This may be due to the practical difficulties of developing competitive research proposals on a complex and poorly understood disease, which affects only women. By producing this consensus international research priorities statement it is the hope of the workshop participants that researchers will be encouraged to develop new interdisciplinary research proposals that will attract increased funding support for work on endometriosis. Hide abstract
2009. Marker selection for genetic case-control association studies. Nat Protoc, 4 (5), pp. 743-752. Read abstract | Read more
Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of study design. The abundant single nucleotide polymorphisms (SNPs) are the markers of choice in genetic case-control association studies. The genotypes of neighboring SNPs are often highly correlated ('in linkage disequilibrium', LD) within a population, which is utilized for selecting specific 'tagSNPs' to serve as proxies for other nearby SNPs in high LD. General guidelines for SNP selection in candidate genes/regions and genome-wide studies are provided in this protocol, along with illustrative examples. Publicly available web-based resources are utilized to browse and retrieve data, and software, such as Haploview and Goldsurfer2, is applied to investigate LD and to select tagSNPs. Hide abstract
2008. The search for genes contributing to endometriosis risk. Hum Reprod Update, 14 (5), pp. 447-457. Read abstract | Read more
Genetic variation contributes to the risk of developing endometriosis. This review summarizes gene mapping studies in endometriosis and the prospects of finding gene pathways contributing to disease using the latest genome-wide strategies. Hide abstract
2007. Significant evidence of one or more susceptibility loci for endometriosis with near-Mendelian inheritance on chromosome 7p13-15. Hum Reprod, 22 (3), pp. 717-728. Read abstract | Read more
Endometriosis is a common disease with a heritable component. The collaborative International Endogene Study consists of two data sets (Oxford and Australia) comprising 1176 families with multiple affected. The aim was to investigate whether the apparent concentration of cases in a proportion of families could be explained by one or more rare variants with (near-)Mendelian autosomal inheritance. Hide abstract
2007. Designing candidate gene and genome-wide case-control association studies. Nat Protoc, 2 (10), pp. 2492-2501. Read abstract | Read more
This protocol describes how to appropriately design a genetic association case-control study, either focusing on a candidate gene (CG) or region or implementing a genome-wide approach. The steps described involve: (i) defining the case phenotype in adequate detail; (ii) checking the heritability of the disease in question; (iii) considering whether a population-based study is the appropriate design for the research question; (iv) the appropriate selection of controls; (v) sample size calculations and (vi) giving due consideration to whether it is a de novo or replication study. General guidelines are given, as well as specific examples of a CG and a genome-wide association study into type 2 diabetes. Software and websites used in this protocol include the International HapMap Consortium website, Genetic Power Calculator, CaT, and SNPSpD. Running each of the programs takes only a few seconds; the rate-limiting steps involve thinking through the designs and parameters in the disease models. Hide abstract
2004. Familial aggregation of endometriosis in a large pedigree of rhesus macaques. Hum Reprod, 19 (2), pp. 448-455. Read abstract | Read more
Endometriosis occurs in several non-human primate species that have menstrual cycles. This study investigated the prevalence and familial aggregation of endometriosis in one of those species, the rhesus macaque. Hide abstract
2004. The complex interplay among factors that influence allelic association. Nat Rev Genet, 5 (2), pp. 89-100. Read abstract | Read more
Small effect sizes, common-disease/common-variant versus rare variant influences, biased single nucleotide polymorphism ascertainment and low linkage disequilibrium have recently been discussed as impediments to association studies. Such a focus on the individual factors that highlight their maximum potential effect (whether positive or deleterious) is often optimistic as, in practice, they do not operate in isolation. Instead, they work jointly to generate the disease gene architecture and to determine the ability of a study to discover it. Here, we consider how the effect size of the susceptibility locus, the frequency of the disease allele(s), the frequency of the marker allele(s) that are correlated with the disease allele(s) and the extent of linkage disequilibrium together influence genetic association studies. Hide abstract
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