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@article{Eriksson2018b,
abstract = {Results: Variants in/near CYP19A1 demonstrated the strongest evidence for association with E2, resolving to three independent signals. Two additional independent signals were found on the X chromosome; FAMily with sequence similarity 9, member B (FAM9B), rs5934505 (P = 3.4 3 1028) and Xq27.3, rs5951794 (P = 3.1 3 10210). E1 signals were found in CYP19A1 (rs2899472, P = 5.5 3 10223), in Tripartite motif containing 4 (TRIM4; rs17277546, P = 5.8 3 10214), and CYP11B1/B2 (rs10093796, P = 1.2 3 1028). E2 signals in CYP19A1 and FAM9B were associated with bone mineral density (BMD). Mendelian randomization analysis suggested a causal effect of serum E2 on BMD in men. A 1 pg/mL genetically increased E2 was associated with a 0.048 standard deviation increase in lumbar spine BMD (P = 2.8 3 10212). In men and women combined, CYP19A1 alleles associated with higher E2 levels were associated with lower degrees of insulin resistance. Conclusions: Our findings confirm that CYP19A1 is an important genetic regulator of E2 and E1 levels and strengthen the causal importance of E2 for bone health in men. We also report two independent loci on the X-chromosome for E2, and one locus each in TRIM4 and CYP11B1/B2, for E1.},
author = {Eriksson, Anna L. and Perry, John R.B. and Coviello, Andrea D. and Delgado, Graciela E. and Ferrucci, Luigi and Hoffman, Andrew R. and Huhtaniemi, Ilpo T. and {Arfan Ikram}, M. and Karlsson, Magnus K. and Kleber, Marcus E. and Laughlin, Gail A. and Liu, Yongmei and Lorentzon, Mattias and Lunetta, Kathryn L. and Mellstr{\"{o}}m, Dan and Murabito, Joanne M. and Murray, Anna and Nethander, Maria and Nielson, Carrie M. and Prokopenko, Inga and Pye, Stephen R. and Raffel, Leslie J. and Rivadeneira, Fernando and Srikanth, Priya and Stolk, Lisette and Teumer, Alexander and Travison, Thomas G. and Uitterlinden, Andr{\'{e}} G. and Vaidya, Dhananjay and Vanderschueren, Dirk and Zmuda, Joseph M. and M{\"{a}}rz, Winfried and Orwoll, Eric S. and Ouyang, Pamela and Vandenput, Liesbeth and Wu, Frederick C.W. and {De Jong}, Frank H. and Bhasin, Shalender and Kiel, Douglas P. and Ohlsson, Claes},
doi = {10.1210/jc.2017-02060},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Eriksson et al. - 2018 - Genetic Determinants of Circulating Estrogen Levels and Evidence of a Causal Effect of Estradiol on Bone Densit.pdf:pdf},
issn = {19457197},
journal = {Journal of Clinical Endocrinology and Metabolism},
keywords = {Anna L Eriksson,Aromatase / genetics*,Bone Density / genetics*,Bone Density / physiology,Chromosomes,Claes Ohlsson,Cohort Studies,Estradiol / blood*,Estradiol / genetics,Estradiol / physiology,Estrone / blood,Estrone / genetics,Female,Gene Expression Regulation / physiology,Genome-Wide Association Study,Genotype,Gonadal Steroid Hormones / blood,Human,Humans,Insulin Resistance / genetics,Insulin Resistance / physiology,John R B Perry,Lumbar Vertebrae / physiology,MEDLINE,Male,Mendelian Randomization Analysis,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,PMC5868407,Polymorphism,PubMed Abstract,Research Support,Single Nucleotide,Testosterone / blood,X,doi:10.1210/jc.2017-02060,pmid:29325096},
month = {mar},
number = {3},
pages = {991--1004},
pmid = {29325096},
publisher = {Oxford University Press},
title = {{Genetic determinants of circulating estrogen levels and evidence of a causal effect of estradiol on bone density in men}},
url = {https://academic.oup.com/jcem/article/103/3/991/4794882 https://pubmed.ncbi.nlm.nih.gov/29325096/},
volume = {103},
year = {2018}
}
@article{Liu2013b,
abstract = {We performed a discovery genome-wide association study to identify genetic factors associated with variation in plasma estradiol (E2) concentrations using DNA from 772 postmenopausal women with estrogen receptor (ER)-positive breast cancer prior to the initiation of aromatase inhibitor therapy. Association analyses showed that the single nucleotide polymorphisms (SNP) (rs1864729) with the lowest P value (P = 3.49E-08), mapped to chromosome 8 near TSPYL5. We also identified 17 imputed SNPs in or near TSPYL5 with P values {\textless} 5E-08, one of which, rs2583506, created a functional estrogen response element. We then used a panel of lymphoblastoid cell lines (LCLs) stably transfected with ER$\alpha$ with known genome-wide SNP genotypes to demonstrate that TSPYL5 expression increased after E2 exposure of cells heterozygous for variant TSPYL5 SNP genotypes, but not in those homozygous for wild-type alleles. TSPYL5 knockdown decreased, and overexpression increased aromatase (CYP19A1) expression in MCF-7 cells, LCLs, and adipocytes through the skin/adipose (I.4) promoter. Chromatin immunoprecipitation assay showed that TSPYL5 bound to the CYP19A1 I.4 promoter. A putative TSPYL5 binding motif was identified in 43 genes, and TSPYL5 appeared to function as a transcription factor for most of those genes. In summary, genome-wide significant SNPs in TSPYL5 were associated with elevated plasma E2 in postmenopausal breast cancer patients. SNP rs2583506 created a functional estrogen response element, and LCLs with variant SNP genotypes displayed increased E2-dependent TSPYL5 expression. TSPYL5 induced CYP19A1 expression and that of many other genes. These studies have revealed a novel mechanism for regulating aromatase expression and plasma E2 concentrations in postmenopausal women with ER(+) breast cancer.},
author = {Liu, Mohan and Ingle, James N. and Fridley, Brooke L. and Buzdar, Aman U. and Robson, Mark E. and Kubo, Michiaki and Wang, Liewei and Batzler, Anthony and Jenkins, Gregory D. and Pietrzak, Tracy L. and Carlson, Erin E. and Goetz, Matthew P. and Northfelt, Donald W. and Perez, Edith A. and Williard, Clark V. and Schaid, Daniel J. and Nakamura, Yusuke and Weinshilboum, Richard M.},
doi = {10.1210/me.2012-1397},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Liu et al. - 2013 - TSPYL5 SNPs association with plasma estradiol concentrations and aromatase expression.pdf:pdf;:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Liu et al. - 2013 - TSPYl5 SNPs Association with plasma estradiol concentrations and aromatase expression(2).pdf:pdf},
issn = {1944-9917},
journal = {Molecular endocrinology (Baltimore, Md.)},
month = {apr},
number = {4},
pages = {657--70},
pmid = {23518928},
publisher = {The Endocrine Society},
title = {{TSPYL5 SNPs: association with plasma estradiol concentrations and aromatase expression.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/23518928 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3607698 /pmc/articles/PMC3607698/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3607698/},
volume = {27},
year = {2013}
}
@article{Riggs1998a,
abstract = {We propose here a new unitary model for the pathophysiology of involutional osteoporosis that identifies estrogen (E) deficiency as the cause of both the early, accelerated and the late, slow phases of bone loss in postmenopausal women and as a contributing cause of the continuous phase of bone loss in aging men. The accelerated phase in women is most apparent during the first decade after menopause, involves disproportionate loss of cancellous bone, and is mediated mainly by loss of the direct restraining effects of E on bone cell function. The ensuing slow phase continues throughout life in women, involves proportionate losses of cancellous and cortical bone, and is associated with progressive secondary hyperparathyroidism. This phase is mediated mainly by loss of E action on extraskeletal calcium homeostasis which results in net calcium wasting and increases in the level of dietary calcium intake required to maintain bone balance. Because elderly men have low circulating levels of both bioavailable E and bioavailable testosterone (T) and because recent data suggest that E is at least as important as T in determining bone mass in aging men, E deficiency may also contribute substantially to the continuous bone loss of aging men. In both genders, E deficiency increases bone resorption and may also impair a compensatory increase in bone formation. For the most part, this unitary model is well supported by observational and experimental data and provides plausible explanations to traditional objections to a unitary hypothesis.},
author = {Riggs, B. Lawrence and Khosla, Sundeep and Melton, L. Joseph},
doi = {10.1359/jbmr.1998.13.5.763},
issn = {08840431},
journal = {Journal of Bone and Mineral Research},
month = {may},
number = {5},
pages = {763--773},
publisher = {John Wiley {\&} Sons, Ltd},
title = {{A Unitary Model for Involutional Osteoporosis: Estrogen Deficiency Causes Both Type I and Type II Osteoporosis in Postmenopausal Women and Contributes to Bone Loss in Aging Men}},
url = {http://doi.wiley.com/10.1359/jbmr.1998.13.5.763},
volume = {13},
year = {1998}
}
@unpublished{Johansson2021,
address = {Uppsala},
author = {Johansson, {\AA}sa and Schmitz, Daniel and H{\"{o}}glund, Julia and Hadizadeh, Fatemeh and Karlsson, Torgny and Ek, Weronica E.},
institution = {Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University},
keywords = {Breast cancer,Endometrial cancer,Mendelian Randomization,Oestradiol,Ovarian cancer},
title = {{High oestradiol levels cause an increased risk for breast and endometrial cancer}},
year = {2021}
}
@article{Schmitz2021,
abstract = {Context. Estradiol is the primary female sex hormone and plays an important role for skeletal health in both sexes. Several enzymes are involved in estradiol metabolism but few genome-wide association studies (GWAS) have been performed to characterize the genetic contribution to variation in estrogen levels. Objective. Identify genetic loci affecting estradiol levels and estimate causal effect of estradiol on bone mineral density (BMD). Design. We performed GWAS for estradiol in males (N = 147,690) and females (N = 163,985) from UK Biobank (UKB). Estradiol was analyzed as a binary phenotype; above/below detection limit (175 pmol/L). We further estimated the causal effect of estradiol on BMD using Mendelian randomization. Results. We identified 14 independent loci associated (P{\&}lt;5x10-8) with estradiol levels in males, of which one (CYP3A7) was genome-wide and seven nominally (P{\&}lt;0.05) significant in females. In addition, one female specific locus was identified. Most loci contain functionally relevant genes that have not been discussed in relation to estradiol levels in previous GWAS. For example, SRD5A2, which encodes a steroid 5-alpha reductase that is involved in processing androgens, and UGT3A1 and UGT2B7 which encode enzymes likely to be involved in estradiol elimination. The allele that tags the O blood group, at the ABO locus, was associated with higher estradiol levels. We identified a causal effect of high estradiol levels on increased BMD in both males (P=1.58x10-11) and females (P=7.48x10-6). Conclusion. Our findings further support the importance of the body{\&}{\#}039;s own estrogen to maintain skeletal health in males and in females.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe research was funded by the Swedish Research Council ({\AA}.J), the cancer foundation ({\AA}.J), the brain foundation ({\AA}.J), the {\AA} Wiberg (W.E.E), M Borgstr{\"{o}}m (W.E.E), Hedstr{\"{o}}ms, K och O F (W.E.E), A and M Rudbergs (W.E.E) foundations.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:UKB has an ethics permit from the National Research Ethics Committee (REC reference 11 / NW / 0382). Ethical approval for the analyses performed in this study has also been approved by the Swedish Ethical Review Authority (Dnr: 2020-04415).All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesThe data used for this study is available for bona fide researchers from the UK Biobank Resource (http://www.ukbiobank.ac.uk/about-biobank-uk/), and can be accessed by an application to the UK Biobank. GEFOS data included in this study can be downloaded from http://www.gefos.org. https://doi.org/10.5281/zenodo.4575527},
author = {Schmitz, Daniel and Ek, Weronica E and Berggren, Elin and H{\"{o}}glund, Julia and Karlsson, Torgny and Johansson, {\AA}sa},
doi = {10.1210/clinem/dgab507},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Schmitz et al. - 2021 - Genome-wide Association Study of Estradiol Levels and the Causal Effect of Estradiol on Bone Mineral Density.pdf:pdf},
issn = {0021-972X},
journal = {The Journal of Clinical Endocrinology {\&} Metabolism},
month = {jul},
pages = {1--16},
publisher = {The Endocrine Society},
title = {{Genome-wide Association Study of Estradiol Levels and the Causal Effect of Estradiol on Bone Mineral Density}},
url = {https://academic.oup.com/jcem/advance-article/doi/10.1210/clinem/dgab507/6320117},
volume = {XX},
year = {2021}
}
@article{Vikan2010,
abstract = {Objective: To study the impact of endogenous sex hormone levels in community-dwelling men on later risk for type 2 diabetes. Design: Population-based prospective cohort study. Methods: For the analyses, 1454 men who participated in the fourth Troms{\o} study (1994-1995) were used. Cases of diabetes were retrieved and validated until 31.12.05 following a detailed protocol. The prospective association between sex hormones and diabetes was examined using Cox proportional hazard regression analysis, allowing for multivariate adjustments. Results: There was a significantly lowered multi-adjusted risk for later diabetes with higher normal total testosterone levels, both linearly per S.D. increase (hazard ratio (HR) 0.71, confidence interval (CI) 0.54-0.92) and in the higher quartiles of total testosterone than in the lowest quartiles (HR 0.53, CI 0.33-0.84). A reduced multi-adjusted risk for incident diabetes was also found for men with higher sex hormone-binding globulin (SHBG) levels, both linearly per S.D. increase (HR 0.55, CI 0.39-0.79) and when comparing the third (HR 0.38, CI 0.18-0.81) and the fourth quartile (HR 0.37, CI 0.17-0.82) to the lowest quartile. The associations with total testosterone and SHBG were no longer significant after inclusion of waist circumference to the multivariate models. Estradiol (E2) was positively associated with incident diabetes after multivariate adjustments including waist circumference when comparing the second (HR 0.49, CI 0.26-0.93) and the third (HR 0.51, CI 0.27-0.96) quartile to the highest quartile. Conclusion: Men with higher E2 levels had an increased risk of later diabetes independent of obesity, while men with lower total testosterone and SHBG had an increased risk of diabetes that appeared to be dependent on obesity. {\textcopyright} 2010 European Society of Endocrinology.},
author = {Vikan, Torkel and Schirmer, Henrik and Nj{\o}lstad, Inger and Svartberg, Johan},
doi = {10.1530/EJE-09-0943},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Vikan et al. - 2010 - Low testosterone and sex hormone-binding globulin levels and high estradiol levels are independent predictors of t.pdf:pdf},
issn = {08044643},
journal = {European Journal of Endocrinology},
month = {apr},
number = {4},
pages = {747--754},
title = {{Low testosterone and sex hormone-binding globulin levels and high estradiol levels are independent predictors of type 2 diabetes in men}},
volume = {162},
year = {2010}
}
@article{Ruth2020d,
abstract = {Testosterone supplementation is commonly used for its effects on sexual function, bone health and body composition, yet its effects on disease outcomes are unknown. To better understand this, we identified genetic determinants of testosterone levels and related sex hormone traits in 425,097 UK Biobank study participants. Using 2,571 genome-wide significant associations, we demonstrate that the genetic determinants of testosterone levels are substantially different between sexes and that genetically higher testosterone is harmful for metabolic diseases in women but beneficial in men. For example, a genetically determined 1 s.d. higher testosterone increases the risks of type 2 diabetes (odds ratio (OR) = 1.37 (95{\%} confidence interval (95{\%} CI): 1.22–1.53)) and polycystic ovary syndrome (OR = 1.51 (95{\%} CI: 1.33–1.72)) in women, but reduces type 2 diabetes risk in men (OR = 0.86 (95{\%} CI: 0.76–0.98)). We also show adverse effects of higher testosterone on breast and endometrial cancers in women and prostate cancer in men. Our findings provide insights into the disease impacts of testosterone and highlight the importance of sex-specific genetic analyses. Genetic analysis of data from over 400,000 participants in the UK Biobank Study shows that circulating testosterone levels have sex-specific implications for cardiometabolic diseases and cancer outcomes.},
author = {Ruth, Katherine S and Day, Felix R and Tyrrell, Jessica and Thompson, Deborah J and Wood, Andrew R and Mahajan, Anubha and Beaumont, Robin N and Wittemans, Laura and Martin, Susan and Busch, Alexander S. and Erzurumluoglu, A. Mesut and Hollis, Benjamin and O'Mara, Tracy A. and McCarthy, Mark I and Langenberg, Claudia and Easton, Douglas F and Wareham, Nicholas J and Burgess, Stephen and Murray, Anna and Ong, Ken K and Frayling, Timothy M and Perry, John R. B.},
doi = {10.1038/s41591-020-0751-5},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ruth et al. - 2020 - Using human genetics to understand the disease impacts of testosterone in men and women.pdf:pdf;:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ruth et al. - 2020 - Using human genetics to understand the disease impacts of testosterone in men and women.xlsx:xlsx},
issn = {1078-8956},
journal = {Nature Medicine},
keywords = {Diabetes,Endocrine cancer,Genetics research,Metabolic syndrome,Multihormonal system disorders},
month = {feb},
number = {2},
pages = {252--258},
publisher = {Nature Publishing Group},
title = {{Using human genetics to understand the disease impacts of testosterone in men and women}},
url = {http://www.nature.com/articles/s41591-020-0751-5},
volume = {26},
year = {2020}
}
@article{Nethander2018a,
abstract = {Context Observational studies indicate that serum estradiol (E2) is more strongly associated with bone mineral density (BMD) than serum testosterone (T) is, whereas both E2 and T associate with fracture risk in men. Objective To evaluate the possible causal effect of serum E2 and T on fracture risk in men. Design, Setting, and Participants A Mendelian randomization (MR) approach was undertaken using individual-level data on genotypes, BMD as estimated by quantitative ultrasound of the heel (eBMD), fractures (n = 17,650), and relevant covariates of 175,583 unrelated men of European origin from the UK Biobank. The genetic instruments for serum E2 and T were taken from the most recent large-scale genome-wide association study meta-analyses on these hormones in men. Results MR analyses demonstrated a causal effect of serum E2 on eBMD and fracture risk. A 1 SD (or 9.6 pg/mL) genetically instrumented decrease in serum E2 levels was associated with a 0.38 SD decrease in eBMD (P value: 9.7 × 10 -74) and an increased risk of any fracture (OR: 1.35; 95{\%} CI: 1.18, 1.55), nonvertebral major osteoporotic fractures (OR: 1.75; 95{\%} CI: 1.35, 2.27), and wrist fractures (OR: 2.27; 95{\%} CI: 1.62, 3.16). These causal effects of serum E2 levels on fracture risk were robust in sensitivity analyses and remained unchanged in stratified analyses for age, body mass index, eBMD, smoking status, and physical activity. MR analyses revealed no evidence of a causal effect of T levels on fracture risk. Conclusion Our findings provide evidence of a robust causal effect of serum E2, but not T, on fracture risk in men.},
author = {Nethander, Maria and Vandenput, Liesbeth and Eriksson, Anna L. and Windahl, Sara and Funck-Brentano, Thomas and Ohlsson, Claes},
doi = {10.1210/jc.2018-00934},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Nethander et al. - 2019 - Evidence of a Causal Effect of Estradiol on Fracture Risk in Men.pdf:pdf},
issn = {19457197},
journal = {Journal of Clinical Endocrinology and Metabolism},
month = {feb},
number = {2},
pages = {433--442},
pmid = {30215726},
title = {{Evidence of a Causal Effect of Estradiol on Fracture Risk in Men}},
url = {https://academic.oup.com/jcem/article/104/2/433/5094017},
volume = {104},
year = {2018}
}
@article{Cauley1999a,
abstract = {Background: The relation between endogenous steroid hormones and risk for breast cancer is uncertain. Measurement of sex hormone levels may identify women at high risk for breast cancer who should consider preventive therapies. Objective: To test the hypothesis that serum concentrations of estradiol and testosterone predict risk for breast cancer. Design: Prospective case-cohort study. Setting: Four clinical centers in the United States. Participants: 97 women with confirmed incident breast cancer and 244 randomly selected controls; all women were white, 65 years of age or older, and were not receiving estrogen. Measurements: Sex-steroid hormone concentrations were assayed by using serum that was collected at baseline and stored at -190 °C. Risk factors for breast cancer were ascertained by questionnaire. Incident cases of breast cancer were confirmed by review of medical records during an average period of 3.2 years. Results: The relative risk for breast cancer in women with the highest concentration of bioavailable estradiol (≥6.83 pmol/L or 1.9 pg/mL) was 3.6 (95{\%} CI, 1.3 to 10.0) compared with women with the lowest concentration. The risk for breast cancer in women with the highest concentration of free testosterone compared with those with the lowest concentration was 3.3 (CI, 1.1 to 10.3). The estimated incidence of breast cancer per 1000 person-years was 0.4 (CI, 0.0 to 1.3) in women with the lowest levels of bioavailable estradiol and free testosterone compared with 6.5 (CI, 2.7 to 10.3) in women with the highest concentrations of these hormones. Traditional risk factors for breast cancer were similar in case-patients and controls. Adjustments for these risk factors had little effect on the results. Conclusions: Estradiol and testosterone levels may play important roles in the development of breast cancer in older women. A single measurement of bioavailable estradiol and free testosterone may be used to estimate a woman's risk for breast cancer. Women identified as being at high risk for breast cancer as determined by these hormone levels may benefit from antiestrogen treatment for primary prevention.},
author = {Cauley, Jane A. and Lucas, Frances L. and Kuller, Lewis H. and Stone, Katie and Browner, Warren and Cummings, Steven R.},
doi = {10.7326/0003-4819-130-4_part_1-199902160-00004},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Cauley et al. - 1999 - Elevated serum estradiol and testosterone concentrations are associated with a high risk for breast cancer.pdf:pdf},
issn = {00034819},
journal = {Annals of Internal Medicine},
month = {feb},
number = {4 I},
pages = {270--277},
pmid = {10068384},
publisher = {American College of Physicians},
title = {{Elevated serum estradiol and testosterone concentrations are associated with a high risk for breast cancer}},
volume = {130},
year = {1999}
}
@article{Kierczak2021,
abstract = {Despite the success in identifying effects of common genetic variants, using genome-wide association studies (GWAS), much of the genetic contribution to complex traits remains unexplained. Here, we analysed high coverage whole-genome sequencing (WGS) data, to evaluate the contribution of rare genetic variants to 414 plasma proteins. The frequency distribution of genetic variants was skewed towards the rare spectrum, and damaging variants were more often rare. However, only 2.24{\%} of the heritability was estimated to be explained by rare variants. A gene-based approach, developed to also capture the effect of rare variants, identied associations for 249 of the proteins, which was 25{\%} more as compared to a GWAS. Out of those, 24 associations were driven by rare variants, clearly highlighting the capacity of aggregated tests and WGS data. We conclude that, while many rare variants have considerable phenotypic effects, their contribution to the missing heritability is limited by their low frequencies.},
author = {Kierczak, Marcin and Rafati, Nima and H{\"{o}}glund, Julia and Gourl{\'{e}}, Hadrien and Schmitz, Daniel and Ek, Weronica E. and Enroth, Stefan and Ekman, Diana and Nystedt, Bj{\"{o}}rn and Karlsson, Torgny and Johansson, {\AA}sa},
doi = {10.21203/RS.3.RS-625433/V1},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Kierczak et al. - 2021 - The contribution of rare whole genome sequencing variants to plasma protein levels and to the missing heritabil.pdf:pdf},
journal = {Nature Communications},
keywords = {GWAS,Hidden heritability,Missing heritability,Protein Biomarkers,Rare variants,SKAT},
month = {jun},
title = {{The contribution of rare whole genome sequencing variants to plasma protein levels and to the missing heritability}},
url = {https://www.researchsquare.com/article/rs-625433/v1},
volume = {In prepara},
year = {2021}
}
@article{Bates2013b,
abstract = {The female reproductive system contains two principal components: the uterus, which supports the developing fetus, and the ovaries, which produce the female gametes. This manuscript will review how the hypothalamus, pituitary, ovary and uterus are integrated into the female reproductive system. The endocrinology of pregnancy, as well as a cursory overview of reproductive pathology, will be presented in each section. In addition, the most common endocrinopathy in women, polycystic ovarian syndrome, as well as the early loss of reproductive function, premature ovarian failure, will receive special mention. {\textcopyright} 2013 John Wiley {\&} Sons A/S.},
author = {Bates, G. Wright and Bowling, Meaghan},
doi = {10.1111/j.1600-0757.2011.00409.x},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Bates, Bowling - 2013 - Physiology of the female reproductive axis.pdf:pdf},
issn = {09066713},
journal = {Periodontology 2000},
month = {feb},
number = {1},
pages = {89--102},
publisher = {John Wiley {\&} Sons, Ltd},
title = {{Physiology of the female reproductive axis}},
url = {http://doi.wiley.com/10.1111/j.1600-0757.2011.00409.x},
volume = {61},
year = {2013}
}
@article{Prescott2012f,
abstract = {Genome-wide association studies (GWAS) have successfully identified common genetic variants that contribute to breast cancer risk. Discovering additional variants has become difficult, as power to detect variants of weaker effect with present sample sizes is limited. An alternative approach is to look for variants associated with quantitative traits that in turn affect disease risk. As exposure to high circulating estradiol and testosterone, and low sex hormone-binding globulin (SHBG) levels is implicated in breast cancer etiology, we conducted GWAS analyses of plasma estradiol, testosterone, and SHBG to identify new susceptibility alleles. Cancer Genetic Markers of Susceptibility (CGEMS) data from the Nurses' Health Study (NHS), and Sisters in Breast Cancer Screening data were used to carry out primary meta-analyses among {\~{}}1600 postmenopausal women who were not taking postmenopausal hormones at blood draw. We observed a genome-wide significant association between SHBG levels and rs727428 (joint $\beta$ = -0.126; joint P = 2.09×10-16), downstream of the SHBG gene. No genome-wide significant associations were observed with estradiol or testosterone levels. Among variants that were suggestively associated with estradiol (P{\textless}10-5), several were located at the CYP19A1 gene locus. Overall results were similar in secondary meta-analyses that included {\~{}}900 NHS current postmenopausal hormone users. No variant associated with estradiol, testosterone, or SHBG at P{\textless}10-5 was associated with postmenopausal breast cancer risk among CGEMS participants. Our results suggest that the small magnitude of difference in hormone levels associated with common genetic variants is likely insufficient to detectably contribute to breast cancer risk.},
author = {Prescott, Jennifer and Thompson, Deborah J. and Kraft, Peter and Chanock, Stephen J. and Audley, Tina and Brown, Judith and Leyland, Jean and Folkerd, Elizabeth and Doody, Deborah and Hankinson, Susan E. and Hunter, David J. and Jacobs, Kevin B. and Dowsett, Mitch and Cox, David G. and Easton, Douglas F. and de Vivo, Immaculata},
doi = {10.1371/journal.pone.0037815},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Prescott et al. - 2012 - Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in po(4).pdf:pdf;:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Prescott et al. - 2012 - Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in po(5).pdf:pdf},
issn = {19326203},
journal = {PLoS ONE},
keywords = {Blood plasma,Breast Neoplasms / blood,Breast Neoplasms / genetics,Breast cancer,Cancer risk factors,Deborah J Thompson,Estradiol,Estradiol / blood*,Extramural,Female,Genome-Wide Association Study*,Genome-wide association studies,Humans,Immaculata De Vivo,Jennifer Prescott,MEDLINE,Metaanalysis,Middle Aged,N.I.H.,NCBI,NIH,NLM,National Center for Biotechnology Information,National Institutes of Health,National Library of Medicine,Non-U.S. Gov't,PMC3366971,Postmenopause / blood*,Postmenopause / genetics*,PubMed Abstract,Research Support,Sex Hormone-Binding Globulin / analysis*,Single nucleotide polymorphisms,Testosterone,Testosterone / blood*,doi:10.1371/journal.pone.0037815,pmid:22675492},
month = {jun},
number = {6},
pages = {37815},
pmid = {22675492},
publisher = {PLoS One},
title = {{Genome-wide association study of circulating estradiol, testosterone, and sex hormone-binding globulin in postmenopausal women}},
url = {https://pubmed.ncbi.nlm.nih.gov/22675492/ www.plosone.org},
volume = {7},
year = {2012}
}
@misc{Manolagas2013,
abstract = {Mouse models with cell-specific deletion of the estrogen receptor (ER) $\alpha$, the androgen receptor (AR) or the receptor activator of nuclear factor $\kappa$B ligand (RANKL), as well as cascade-selective estrogenic compounds have provided novel insights into the function and signalling of ER$\alpha$ and AR. The studies reveal that the effects of estrogens on trabecular versus cortical bone mass are mediated by direct effects on osteoclasts and osteoblasts, respectively. The protection of cortical bone mass by estrogens is mediated via ER$\alpha$, using a non-nucleus-initiated mechanism. By contrast, the AR of mature osteoblasts is indispensable for the maintenance of trabecular bone mass in male mammals, but not required for the anabolic effects of androgens on cortical bone. Most unexpectedly, and independently of estrogens, ER$\alpha$ in osteoblast progenitors stimulates Wnt signalling and periosteal bone accrual in response to mechanical strain. RANKL expression in B lymphocytes, but not T lymphocytes, contributes to the loss of trabecular bone caused by estrogen deficiency. In this Review, we summarize this evidence and discuss its implications for understanding the regulation of trabecular and cortical bone mass; the integration of hormonal and mechanical signals; the relative importance of estrogens versus androgens in the male skeleton; and, finally, the pathogenesis and treatment of osteoporosis. {\textcopyright} 2013 Macmillan Publishers Limited.},
author = {Manolagas, Stavros C. and O'Brien, Charles A. and Almeida, Maria},
booktitle = {Nature Reviews Endocrinology},
doi = {10.1038/nrendo.2013.179},
issn = {17595029},
pmid = {24042328},
title = {{The role of estrogen and androgen receptors in bone health and disease}},
year = {2013}
}
@book{Longo2012a,
author = {Longo, Dan L and Fauci, Anthony S and Kasper, Dennis L and Hauser, Stephen L and Jameson, J Larry and Loscalzo, Joseph},
publisher = {Mcgraw-hill New York},
title = {{Harrison's principles of internal medicine}},
volume = {2012},
year = {2012}
}
@article{Chen2013d,
abstract = {Background Sex hormones and gonadotropins exert a wide variety of effects in physiological and pathological processes. Accumulated evidence shows a strong heritable component of circulating concentrations of these hormones. Recently, several genome-wide association studies (GWASs) conducted in Caucasians have identified multiple loci that influence serum levels of sex hormones. However, the genetic determinants remain unknown in Chinese populations. In this study, we aimed to identify genetic variants associated with major sex hormones, gonadotropins, including testosterone, oestradiol, follicle-stimulating hormone (FSH), luteinising hormone (LH) and sex hormone binding globulin (SHBG) in a Chinese population. Methods A two-stage GWAS was conducted in a total of 3495 healthy Chinese men (1999 subjects in the GWAS discovery stage and 1496 in the confirmation stage). Results We identified a novel genetic region at 15q21.2 (rs2414095 in CYP19A1), which was significantly associated with oestradiol and FSH in the Chinese population at a genome-wide significant level (p=6.54×10-31 and 1.59×10-16, respectively). Another single nucleotide polymorphism in CYP19A1 gene was significantly associated with oestradiol level (rs2445762, p=7.75×10-28). In addition, we confirmed the previous GWAS-identified locus at 17p13.1 for testosterone (rs2075230, p=1.13×10-8) and SHBG level (rs2075230, p=4.75×10-19) in the Chinese population. Conclusions This study is the first GWAS investigation of genetic determinants of FSH and LH. The identification of novel susceptibility loci may provide more biological implications for the synthesis and metabolism of these hormones. More importantly, the confirmation of the genetic loci for testosterone and SHBG suggests common genetic components shared among different ethnicities.},
author = {Chen, Zhuo and Tao, Sha and Gao, Yong and Zhang, Ju and Hu, Yanling and Mo, Linjian and Kim, Seong-Tae and Yang, Xiaobo and Tan, Aihua and Zhang, Haiying and Qin, Xue and Li, Li and Wu, Yongming and Zhang, Shijun and Zheng, S. Lilly and Xu, Jianfeng and Mo, Zengnan and Sun, Jielin},
doi = {10.1136/jmedgenet-2013-101705},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Chen et al. - 2013 - Genome-wide association study of sex hormones, gonadotropins and sex hormone–binding protein in Chinese men.pdf:pdf},
issn = {0022-2593},
journal = {Journal of Medical Genetics},
month = {dec},
number = {12},
pages = {794--801},
publisher = {BMJ Publishing Group Ltd},
title = {{Genome-wide association study of sex hormones, gonadotropins and sex hormone–binding protein in Chinese men}},
url = {http://jmg.bmj.com/lookup/doi/10.1136/jmedgenet-2013-101705},
volume = {50},
year = {2013}
}
@article{Hess1997b,
abstract = {Oestrogen is considered to be the 'female' hormone, whereas testosterone is considered the 'male' hormone. However, both hormones are present in both sexes. Thus sexual distinctions are not qualitative differences, but rather result from quantitative divergence in hormone concentrations and differential expressions of steroid hormone receptors. In males, oestrogen is present in low concentrations in blood, but can be extraordinarily high in semen, and as high as 250 pg ml-1 in rete testis fluids, which is higher than serum oestradiol in the female. It is well known that male reproductive tissues express oestrogen receptors, but the role of oestrogen in male reproduction has remained unclear. Here we provide evidence of a physiological role for oestrogen in male reproductive organs. We show that oestrogen regulates the reabsorption of luminal fluid in the head of the epididymis. Disruption of this essential function causes sperm to enter the epididymis diluted, rather than concentrate, resulting in infertility. This finding raises further concern over the potential direct effects of environmental oestrogens on male reproduction and reported declines in human sperm counts.},
author = {Hess, Rex A. and Bunick, David and Lee, Ki-Ho and Bahr, Janice and Taylor, Julia A. and Korach, Kenneth S. and Lubahn, Dennis B.},
doi = {10.1038/37352},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Hess et al. - 1997 - A role for oestrogens in the male reproductive system.pdf:pdf},
issn = {0028-0836},
journal = {Nature},
keywords = {Humanities and Social Sciences,Science,multidisciplinary},
month = {dec},
number = {6659},
pages = {509--512},
publisher = {Nature Publishing Group},
title = {{A role for oestrogens in the male reproductive system}},
url = {http://www.nature.com/articles/37352},
volume = {390},
year = {1997}
}
@misc{Karlsson2019,
abstract = {Visceral adipose tissue (VAT)—fat stored around the internal organs—has been suggested as an independent risk factor for cardiovascular and metabolic disease1–3, as well as all-cause, cardiovascular-specific and cancer-specific mortality4,5. Yet, the contribution of genetics to VAT, as well as its disease-related effects, are largely unexplored due to the requirement for advanced imaging technologies to accurately measure VAT. Here, we develop sex-stratified, nonlinear prediction models (coefficient of determination = 0.76; typical 95{\%} confidence interval (CI) = 0.74–0.78) for VAT mass using the UK Biobafile:///Users/dansc755/Downloads/s41591-019-0563-7.pdfnk cohort. We performed a genome-wide association study for predicted VAT mass and identified 102 novel visceral adiposity loci. Predicted VAT mass was associated with increased risk of hypertension, heart attack/angina, type 2 diabetes and hyperlipidemia, and Mendelian randomization analysis showed visceral fat to be a causal risk factor for all four diseases. In particular, a large difference in causal effect between the sexes was found for type 2 diabetes, with an odds ratio of 7.34 (95{\%} CI = 4.48–12.0) in females and an odds ratio of 2.50 (95{\%} CI = 1.98–3.14) in males. Our findings bolster the role of visceral adiposity as a potentially independent risk factor, in particular for type 2 diabetes in Caucasian females. Independent validation in other cohorts is necessary to determine whether the findings can translate to other ethnicities, or outside the UK.},
annote = {Genome-wide association study in 11,097 men of European origin from nine epidemiological cohorts.},
author = {Karlsson, Torgny and Rask-Andersen, Mathias and Pan, Gang and H{\"{o}}glund, Julia and Wadelius, Claes and Ek, Weronica E. and Johansson, {\AA}sa},
booktitle = {Nature Medicine},
doi = {10.1038/s41591-019-0563-7},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Karlsson et al. - 2019 - Contribution of genetics to visceral adiposity and its relation to cardiovascular and metabolic disease.pdf:pdf},
issn = {1546170X},
keywords = {Diabetes,Epidemiology,Genome,Obesity,wide association studies},
month = {sep},
number = {9},
pages = {1390--1395},
pmid = {31501611},
publisher = {Nature Publishing Group},
title = {{Contribution of genetics to visceral adiposity and its relation to cardiovascular and metabolic disease}},
volume = {25},
year = {2019}
}
@misc{Thomas2013c,
abstract = {Many enzymes catalyse reactions that have an oestrogen as a substrate and/or a product. The reactions catalysed include aromatisation, oxidation, reduction, sulfonation, desulfonation, hydroxylation and methoxylation. The enzymes that catalyse these reactions must all recognise and bind oestrogen but, despite this, they have diverse structures. This review looks at each of these enzymes in turn, describing the structure and discussing the mechanism of the catalysed reaction. Since oestrogen has a role in many disease states inhibition of the enzymes of oestrogen metabolism may have an impact on the state or progression of the disease and inhibitors of these enzymes are briefly discussed. This article is part of a Special Issue entitled 'CSR 2013'. {\textcopyright} 2012 Elsevier Ltd. All rights reserved.},
author = {Thomas, Mark P. and Potter, Barry V.L.},
booktitle = {Journal of Steroid Biochemistry and Molecular Biology},
doi = {10.1016/j.jsbmb.2012.12.014},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Thomas, Potter - 2013 - The structural biology of oestrogen metabolism.pdf:pdf},
issn = {09600760},
keywords = {17$\beta$-Hydroxysteroid dehydrogenase,Aromatase,Oestrogen,Protein structure,Reaction mechanism,Sulfatase,Sulfotransferase},
pages = {27--49},
pmid = {23291110},
publisher = {Elsevier},
title = {{The structural biology of oestrogen metabolism}},
url = {/pmc/articles/PMC3866684/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866684/},
volume = {137},
year = {2013}
}
@article{Rosendaal2003b,
abstract = {Hundreds of millions of women worldwide use either oral contraceptives or postmenopausal hormone replacement. The use of oral contraceptives leads to an increased risk of venous thrombosis, of myocardial infarction, of stroke and of peripheral artery disease, the risks of which are highest during the first year of use. Women with coagulation abnormalities have a higher risk of venous thrombosis when they use oral contraceptives (or postmenopausal hormones) than women without these abnormalities. The risk of venous thrombosis is also higher for preparations containing desogestrel or gestodene (third-generation progestogens) than for those containing levonorgestrel (second-generation progestogens). A previous thrombosis as well as obesity also increase the risk of oral contraceptive-related thrombosis. Hormone replacement therapy increases the risk of venous thrombosis, and has no beneficial, and possibly even a detrimental, effect on the risk of arterial disease. The risk of arterial disease in oral contraceptive users and users of hormone replacement therapy is at most weakly affected by the presence of prothrombotic abnormalities. {\textcopyright} 2003 International Society on Thrombosis and Haemostasis.},
author = {Rosendaal, F. R. and {Van Hylckama Vlieg}, A. and Tanis, B. C. and Helmerhorst, F. M.},
doi = {10.1046/j.1538-7836.2003.00264.x},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Rosendaal et al. - 2003 - Estrogens, progestogens and thrombosis.pdf:pdf},
issn = {1538-7933},
journal = {Journal of Thrombosis and Haemostasis},
keywords = {Estrogens,Hormone replacement therapy,Myocardial infarction,Oral contraceptives,Progestogens,Stroke,Venous thrombosis},
month = {jul},
number = {7},
pages = {1371--1380},
publisher = {John Wiley {\&} Sons, Ltd},
title = {{Estrogens, progestogens and thrombosis}},
url = {http://doi.wiley.com/10.1046/j.1538-7836.2003.00264.x},
volume = {1},
year = {2003}
}
@article{Pott2019e,
abstract = {CONTEXT Steroid hormones are important regulators of physiological processes in humans and are under genetic control. A link to coronary artery disease (CAD) is supposed. OBJECTIVE Our main objective was to identify genetic loci influencing steroid hormone levels. As a secondary aim, we searched for causal effects of steroid hormones on CAD. DESIGN We conducted genome-wide meta-association studies for eight steroid hormones: cortisol, dehydroepiandrosterone sulfate (DHEAS), estradiol, and testosterone in two independent cohorts (LIFE-Adult, LIFE-Heart, maximum n = 7667), and progesterone, 17-hydroxyprogesterone, androstenedione, and aldosterone in LIFE-Heart only (maximum n = 2070). All genome-wide significant loci were tested for sex interactions. Furthermore, we tested whether previously reported CAD single-nucleotide polymorphisms were associated with our steroid hormone panel and investigated causal links between hormone levels and CAD status using Mendelian randomization (MR) approaches. RESULTS We discovered 15 novel associated loci for 17-hydroxyprogesterone, progesterone, DHEAS, cortisol, androstenedione, and estradiol. Five of these loci relate to genes directly involved in steroid metabolism, that is, CYP21A1, CYP11B1, CYP17A1, STS, and HSD17B12, almost completing the set of steroidogenic enzymes with genetic associations. Sexual dimorphisms were found for seven of the novel loci. Other loci correspond, for example, to the WNT4/$\beta$-catenin pathway. MR revealed that cortisol, androstenedione, 17-hydroxyprogesterone, and DHEA-S had causal effects on CAD. We also observed enrichment of cortisol and testosterone associations among known CAD hits. CONCLUSION Our study greatly improves insight into genetic regulation of steroid hormones and their dependency on sex. These results could serve as a basis for analyzing sexual dimorphism in other complex diseases.},
author = {Pott, Janne and Bae, Yoon Ju and Horn, Katrin and Teren, Andrej and K{\"{u}}hnapfel, Andreas and Kirsten, Holger and Ceglarek, Uta and Loeffler, Markus and Thiery, Joachim and Kratzsch, J{\"{u}}rgen and Scholz, Markus},
doi = {10.1210/jc.2019-00757},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Pott et al. - 2019 - Genetic Association Study of Eight Steroid Hormones and Implications for Sexual Dimorphism of Coronary Artery Di(2).pdf:pdf},
issn = {1945-7197},
journal = {The Journal of clinical endocrinology and metabolism},
month = {nov},
number = {11},
pages = {5008--5023},
pmid = {31169883},
publisher = {Oxford University Press},
title = {{Genetic Association Study of Eight Steroid Hormones and Implications for Sexual Dimorphism of Coronary Artery Disease.}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/31169883},
volume = {104},
year = {2019}
}
@incollection{Nakamoto2010a,
address = {Philadelphia},
author = {Nakamoto, Jon and Salameh, Wael Antoine and Carlton, Esther},
booktitle = {Endocrinology},
doi = {10.1016/B978-1-4160-5583-9.00155-6},
editor = {Jameson, J Larry and {De Groot}, Leslie J B T - Endocrinology (Sixth Edition)},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Nakamoto, Salameh, Carlton - 2010 - Endocrine Testing(2).pdf:pdf},
isbn = {978-1-4160-5583-9},
mendeley-groups = {Hormone GWAS/Estrogen,Half-Time Thesis},
pages = {2802--2834},
publisher = {Elsevier},
title = {{Endocrine Testing}},
url = {http://www.sciencedirect.com/science/article/pii/B9781416055839001556 https://linkinghub.elsevier.com/retrieve/pii/B9781416055839001556},
year = {2010}
}
@article{Ward2012,
abstract = {The resolution of genome-wide association studies (GWAS) is limited by the linkage disequilibrium (LD) structure of the population being studied. Selecting the most likely causal variants within an LD block is relatively straightforward within coding sequence, but is more difficult when all variants are intergenic. Predicting functional non-coding sequence has been recently facilitated by the availability of conservation and epigenomic information. We present HaploReg, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs. Sets of SNPs, such as those resulting from GWAS, are analyzed for an enrichment of cell type-specific enhancers. HaploReg will be useful to researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. The HaploReg database is available at http://compbio.mit.edu/HaploReg. {\textcopyright} The Author(s) 2011. Published by Oxford University Press.},
author = {Ward, Lucas D. and Kellis, Manolis},
doi = {10.1093/nar/gkr917},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ward, Kellis - 2012 - HaploReg A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of.pdf:pdf},
issn = {03051048},
journal = {Nucleic Acids Research},
keywords = {chromatin,enhancer of transcription,genome,genome-wide association study,linkage disequilibrium,mammals,open reading frames,phenotype,single nucleotide polymorphism},
mendeley-groups = {Tools,Hormone GWAS,Half-Time Thesis},
month = {jan},
number = {D1},
pages = {D930--D934},
pmid = {22064851},
publisher = {Oxford Academic},
title = {{HaploReg: A resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants}},
url = {http://compbio.mit.edu/HaploReg.},
volume = {40},
year = {2012}
}
@article{Carithers2015,
abstract = {Genome-wide association studies have identified thousands of loci for common diseases, but, for the majority of these, the mechanisms underlying disease susceptibility remain unknown. Most associated variants are not correlated with protein-coding changes, suggesting that polymorphisms in regulatory regions probably contribute to many disease phenotypes. Here we describe the Genotype-Tissue Expression (GTEx) project, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.},
author = {Carithers, Latarsha J. and Moore, Helen M.},
doi = {10.1089/bio.2015.29031.hmm},
isbn = {1546-1718 (Electronic) 1061-4036 (Linking)},
issn = {1947-5535},
journal = {Biopreservation and Biobanking},
mendeley-groups = {Half-Time Thesis},
number = {5},
pages = {307--308},
pmid = {23715323},
title = {{The Genotype-Tissue Expression (GTEx) Project}},
volume = {13},
year = {2015}
}
@article{Zhu2018,
abstract = {Health risk factors such as body mass index (BMI) and serum cholesterol are associated with many common diseases. It often remains unclear whether the risk factors are cause or consequence of disease, or whether the associations are the result of confounding. We develop and apply a method (called GSMR) that performs a multi-SNP Mendelian rando- mization analysis using summary-level data from genome-wide association studies to test the causal associations of BMI, waist-to-hip ratio, serum cholesterols, blood pressures, height, and years of schooling (EduYears) with common diseases (sample sizes of up to 405,072). We identify a number of causal associations including a protective effect of LDL-cholesterol against type-2 diabetes (T2D) that might explain the side effects of statins on T2D, a protective effect of EduYears against Alzheimer's disease, and bidirectional associations with opposite effects (e.g., higher BMI increases the risk of T2D but the effect of T2D on BMI is negative).},
author = {Zhu, Zhihong and Zheng, Zhili and Zhang, Futao and Wu, Yang and Trzaskowski, Maciej and Maier, Robert and Robinson, Matthew R. and McGrath, John J. and Visscher, Peter M. and Wray, Naomi R. and Yang, Jian},
doi = {10.1038/s41467-017-02317-2},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Zhu et al. - 2018 - Causal associations between risk factors and common diseases inferred from GWAS summary data.pdf:pdf},
isbn = {2041-1723 (Electronic) 2041-1723 (Linking)},
issn = {2041-1723},
journal = {Nature Communications},
mendeley-groups = {Hormone GWAS,Half-Time Thesis},
month = {dec},
number = {1},
pages = {224},
pmid = {29335400},
title = {{Causal associations between risk factors and common diseases inferred from GWAS summary data}},
url = {http://www.nature.com/articles/s41467-017-02317-2},
volume = {9},
year = {2018}
}
@article{Hemani2018,
abstract = {Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base (http://www.mrbase.org): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies.},
author = {Hemani, Gibran and Zheng, Jie and Elsworth, Benjamin and Wade, Kaitlin H. and Haberland, Valeriia and Baird, Denis and Laurin, Charles and Burgess, Stephen and Bowden, Jack and Langdon, Ryan and Tan, Vanessa Y. and Yarmolinsky, James and Shihab, Hashem A. and Timpson, Nicholas J. and Evans, David M. and Relton, Caroline and Martin, Richard M. and {Davey Smith}, George and Gaunt, Tom R. and Haycock, Philip C.},
doi = {10.7554/eLife.34408},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Hemani et al. - 2018 - The MR-base platform supports systematic causal inference across the human phenome.pdf:pdf},
issn = {2050084X},
journal = {eLife},
mendeley-groups = {Hormone GWAS,Half-Time Thesis},
month = {may},
pmid = {29846171},
publisher = {eLife Sciences Publications Ltd},
title = {{The MR-base platform supports systematic causal inference across the human phenome}},
volume = {7},
year = {2018}
}
@article{Estrada2012,
abstract = {Bone mineral density (BMD) is the most widely used predictor of fracture risk. We performed the largest meta-analysis to date on lumbar spine and femoral neck BMD, including 17 genome-wide association studies and 32,961 individuals of European and east Asian ancestry. We tested the top BMD-associated markers for replication in 50,933 independent subjects and for association with risk of low-trauma fracture in 31,016 individuals with a history of fracture (cases) and 102,444 controls. We identified 56 loci (32 new) associated with BMD at genome-wide significance (P {\textless} 5 × 10 -8). Several of these factors cluster within the RANK-RANKL-OPG, mesenchymal stem cell differentiation, endochondral ossification and Wnt signaling pathways. However, we also discovered loci that were localized to genes not known to have a role in bone biology. Fourteen BMD-associated loci were also associated with fracture risk (P {\textless} 5 × 10 -4, Bonferroni corrected), of which six reached P {\textless} 5 × 10 -8, including at 18p11.21 (FAM210A), 7q21.3 (SLC25A13), 11q13.2 (LRP5), 4q22.1 (MEPE), 2p16.2 (SPTBN1) and 10q21.1 (DKK1). These findings shed light on the genetic architecture and pathophysiological mechanisms underlying BMD variation and fracture susceptibility. {\textcopyright} 2012 Nature America, Inc. All rights reserved.},
author = {Estrada, Karol and Styrkarsdottir, Unnur and Evangelou, Evangelos and Hsu, Yi Hsiang and Duncan, Emma L and Ntzani, Evangelia E and Oei, Ling and Albagha, Omar M.E. and Amin, Najaf and Kemp, John P and Koller, Daniel L and Li, Guo and Liu, Ching Ti and Minster, Ryan L and Moayyeri, Alireza and Vandenput, Liesbeth and Willner, Dana and Xiao, Su Mei and Yerges-Armstrong, Laura M and Zheng, Hou Feng and Alonso, Nerea and Eriksson, Joel and Kammerer, Candace M and Kaptoge, Stephen K and Leo, Paul J and Thorleifsson, Gudmar and Wilson, Scott G. and Wilson, James F and Aalto, Ville and Alen, Markku and Aragaki, Aaron K and Aspelund, Thor and Center, Jacqueline R and Dailiana, Zoe and Duggan, David J and Garcia, Melissa and Garcia-Giralt, Nat{\`{a}}lia and Giroux, Sylvie and Hallmans, G{\"{o}}ran and Hocking, Lynne J and Husted, Lise Bjerre and Jameson, Karen A and Khusainova, Rita and Kim, Ghi Su and Kooperberg, Charles and Koromila, Theodora and Kruk, Marcin and Laaksonen, Marika and Lacroix, Andrea Z and Lee, Seung Hun and Leung, Ping C and Lewis, Joshua R and Masi, Laura and Mencej-Bedrac, Simona and Nguyen, Tuan V and Nogues, Xavier and Patel, Millan S and Prezelj, Janez and Rose, Lynda M and Scollen, Serena and Siggeirsdottir, Kristin and Smith, Albert V and Svensson, Olle and Trompet, Stella and Trummer, Olivia and {Van Schoor}, Natasja M. and Woo, Jean and Zhu, Kun and Balcells, Susana and Brandi, Maria Luisa and Buckley, Brendan M and Cheng, Sulin and Christiansen, Claus and Cooper, Cyrus and Dedoussis, George and Ford, Ian and Frost, Morten and Goltzman, David and Gonz{\'{a}}lez-Mac{\'{i}}as, Jes{\'{u}}s and K{\"{a}}h{\"{o}}nen, Mika and Karlsson, Magnus and Khusnutdinova, Elza and Koh, Jung Min and Kollia, Panagoula and Langdahl, Bente Lomholt and Leslie, William D and Lips, Paul and Ljunggren, {\O}sten and Lorenc, Roman S and Marc, Janja and Mellstr{\"{o}}m, Dan and Obermayer-Pietsch, Barbara and Olmos, Jos{\'{e}} M and Pettersson-Kymmer, Ulrika and Reid, David M. and Riancho, Jos{\'{e}} A and Ridker, Paul M and Rousseau, Fran{\c{c}}ois and Lagboom, P. Eline S. and Tang, Nelson L.S. and Urreizti, Roser and {Van Hul}, Wim and Viikari, Jorma and Zarrabeitia, Mar{\'{i}}a T and Aulchenko, Yurii S and Castano-Betancourt, Martha and Grundberg, Elin and Herrera, Lizbeth and Ingvarsson, Thorvaldur and Johannsdottir, Hrefna and Kwan, Tony and Li, Rui and Luben, Robert and Medina-G{\'{o}}mez, Carolina and {Th Palsson}, Stefan and Reppe, Sjur and Rotter, Jerome I and Sigurdsson, Gunnar and {Van Meurs}, Joyce B.J. and Verlaan, Dominique and Williams, Frances M.K. and Wood, Andrew R and Zhou, Yanhua and Gautvik, Kaare M and Pastinen, Tomi and Raychaudhuri, Soumya and Cauley, Jane A and Chasman, Daniel I and Clark, Graeme R and Cummings, Steven R and Danoy, Patrick and Dennison, Elaine M and Eastell, Richard and Eisman, John A and Gudnason, Vilmundur and Hofman, Albert and Jackson, Rebecca D and Jones, Graeme and Jukema, J Wouter and Khaw, Kay Tee and Lehtim{\"{a}}ki, Terho and Liu, Yongmei and Lorentzon, Mattias and Mccloskey, Eugene and Mitchell, Braxton D and Nandakumar, Kannabiran and Nicholson, Geoffrey C and Oostra, Ben A and Peacock, Munro and Pols, Huibert A.P. and Prince, Richard L and Raitakari, Olli and Reid, Ian R and Robbins, John and Sambrook, Philip N and Sham, Pak Chung and Shuldiner, Alan R and Tylavsky, Frances A and {Van Duijn}, Cornelia M. and Wareham, Nick J and Cupples, L Adrienne and Econs, Michael J and Evans, David M and Harris, Tamara B and Kung, Annie Wai Chee and Psaty, Bruce M and Reeve, Jonathan and Spector, Timothy D and Streeten, Elizabeth A and Zillikens, M Carola and Thorsteinsdottir, Unnur and Ohlsson, Claes and Karasik, David and Richards, J Brent and Brown, Matthew A and Stefansson, Kari and Uitterlinden, Andr{\'{e}} G and Ralston, Stuart H and Ioannidis, John P.A. and Kiel, Douglas P and Rivadeneira, Fernando},
doi = {10.1038/ng.2249},
issn = {10614036},
journal = {Nature Genetics},
mendeley-groups = {Half-Time Thesis,Hormone GWAS/Genetic Studies},
month = {apr},
number = {5},
pages = {491--501},
pmid = {22504420},
publisher = {Nat Genet},
title = {{Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture}},
volume = {44},
year = {2012}
}
@article{Ohmori1998,
abstract = {The catalytic properties of CYP3A7 in the metabolism of endogenous and exogenous substrates were compared with those of CYP3A4 and CYP3A5 using COS- 7 expressing enzymes. The highest activities of dehydroepiandrosterone (DHEA) and dehydroepiandrosterone 3-sulfate (DHEA-S) 16$\alpha$-hydroxylase were observed in COS-7 cells expressing CYP3A7. In contrast, the activity of testosterone 6$\beta$-hydroxylase of CYP3A7 expressed in COS-7 cells was much less than that of CYP3A4 expressed in COS-7 cells. The rate of carbamazepine 10,11-epoxidation was the greatest in COS-7 cells expressing CYP3A4, followed by CYP3A5 and CYP3A7. On the other hand, the formation of reductive metabolite of zonisamide was the highest in COS-7 cells expressing CYP3A4, followed by CYP3A7 and CYP3A5. Furthermore, the addition of triazolam resulted in a decrease in 6$\beta$-hydroxylation catalyzed by CYP3A7, but not by CYP3A4, whereas the pretreatment of microsomes with triacetyloleandomycin (TAO) resulted in a decrease in the reaction catalyzed by CYP3A4, but not by CYP3A7. Together with these results, it was suggested that CYP3A7 exerts differential catalytic properties not only in metabolism of endogenous substrates but also in drug metabolism compared to CYP3A4 and CYP3A5.},
author = {Ohmori, Shigeru and Nakasa, Hiromitsu and Asanome, Kazuki and Kurose, Yasusi and Ishii, Itsuko and Hosokawa, Masakiyo and Kitada, Mitsukazu},
doi = {10.1016/S0304-4165(97)00156-6},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ohmori et al. - 1998 - Differential catalytic properties in metabolism of endogenous and exogenous substrates among CYP3A enzymes expres.pdf:pdf},
issn = {03044165},
journal = {Biochimica et Biophysica Acta - General Subjects},
keywords = {(Human),COS-7 cell,CYP3A enzyme,CYP3A4,CYP3A5,CYP3A7,Carbamazepine,Expression,Steroid hydroxylation,Triazolam,Zonisamide},
mendeley-groups = {Hormone GWAS/Biochemical,Half-Time Thesis},
month = {may},
number = {3},
pages = {297--304},
pmid = {9555064},
publisher = {Elsevier},
title = {{Differential catalytic properties in metabolism of endogenous and exogenous substrates among CYP3A enzymes expressed in COS-7 cells}},
volume = {1380},
year = {1998}
}
@article{Simpson2001,
abstract = {There is a growing awareness that androgens and estrogens have general metabolic roles that are not directly involved in reproductive processes. These include actions on vascular function, lipid and carbohydrate metabolism, as well as bone mineralization and epiphyseal closure, in both sexes. In postmenopausal women, as in men, estrogen is no longer solely an endocrine factor, but instead is produced in a number of extragonadal sites and acts locally at these sites in a paracrine and intracrine fashion. These sites include breast, bone, vasculature, and brain. Within these sites, aromatase action can generate high levels of E2 locally without significantly affecting circulating levels. Circulating C19 steroid precursors are essential substrates for extragonadal estrogen synthesis. The levels of these androgenic precursors decline markedly with advancing age in women, possibly from the mid to late reproductive years. This may be a fundamental reason why women are at increased risk for bone mineral loss and fracture and possibly decline of cognitive function, compared with men. Aromatase expression in these various sites is under the control of tissue-specific promoters regulated by different cohorts of transcription factors. Thus, in principle, it should be possible to develop selective aromatase modulators that block aromatase expression, for example, in breast, but allow unimpaired estrogen synthesis in other tissues such as bone.},
author = {Simpson, Evan R. and Davis, Susan R.},
doi = {10.1210/endo.142.11.8547},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Simpson, Davis - 2001 - Minireview Aromatase and the Regulation of Estrogen Biosynthesis—Some New Perspectives.pdf:pdf},
issn = {0013-7227},
journal = {Endocrinology},
keywords = {estrogen biosynthesis},
mendeley-groups = {Hormone GWAS/Biochemical,Half-Time Thesis},
month = {nov},
number = {11},
pages = {4589--4594},
publisher = {Endocrine Society},
title = {{Minireview: Aromatase and the Regulation of Estrogen Biosynthesis—Some New Perspectives}},
url = {https://academic.oup.com/endo/article/142/11/4589/2988522},
volume = {142},
year = {2001}
}
@article{Ogasawara1996,
abstract = {Polymorphism of the ABO blood group gene was investigated in 262 healthy Japanese donors by a polymerase chain reactions-single-strand conformation polymorphism (PCR-SSCP) method, and 13 different alleles were identified. The number of alleles identified in each group was 4 for A1 (provisionally called ABO(*)A101, (*)A102, (*)A103 and (*)A104 according to the guidelines for human gene nomenclature), 4 for B (ABO(*)B101, (*)B102 and (*)B103), and 6 for O (ABO(*)O101, (*)O102, (*)O103, (*)O201, (*)O202 and (*)O203). Nucleotide sequences of the amplified fragments with different SSCP patterns were determined by direct sequencing. Phylogenetic network analysis revealed that these alleles could be classified into three major lineages, (*)A/(*)O1, (*)B and (*)O2. In Japanese, (*)A102 and (*)B101 were the predominant alleles with frequencies of 83{\%} and 97{\%} in each group, respectively, whereas in group O, two common alleles, (*)O101 (43{\%}) and (*)O201 (53{\%}), were observed. These results may be useful for the establishment of ABO genotyping, and these newly described ABO alleles would be advantageous indicators for population studies.},
author = {Ogasawara, Kenichi and Bannai, Makoto and Saitou, Naruya and Yabe, Ryuichi and Nakata, Kenichi and Takenaka, Michiko and Fujisawa, Kiyoshi and Uchikawa, Makoto and Ishikawa, Yoshihide and Juji, Takeo and Tokunaga, Katsushi},
doi = {10.1007/BF02346189},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ogasawara et al. - 1996 - Extensive polymorphism of ABO blood group gene Three major lineages of the alleles for the common ABO phenotyp.pdf:pdf},
issn = {03406717},
journal = {Human Genetics},
keywords = {Gene Function,Human Genetics,Metabolic Diseases,Molecular Medicine},
mendeley-groups = {Hormone GWAS/Biochemical,Half-Time Thesis},
number = {6},
pages = {777--783},
pmid = {8641696},
publisher = {Springer Verlag},
title = {{Extensive polymorphism of ABO blood group gene: Three major lineages of the alleles for the common ABO phenotypes}},
url = {https://link.springer.com/article/10.1007/BF02346189},
volume = {97},
year = {1996}
}
@inproceedings{Richardson2020,
abstract = {Objective:The aim of the study was to quantify baseline estradiol (E2) and estrone (E1) concentrations according to selected patient characteristics in a substudy nested within the MAP.3 chemoprevention trial.Methods:E2 and E1 levels were measured in 4,068 postmenopausal women using liquid chromatography-tandem mass spectrometry. Distributions were described by age, years since menopause, race, body mass index (BMI), smoking status, and use and duration of hormone therapy using the Kruskal-Wallis test. Multivariable linear regression was also used to identify characteristics associated with estrogen levels.Results:After truncation at the 97.5th percentile, the mean (SD)/median (IQR) values for E2 and E1 were 5.41 (4.67)/4.0 (2.4-6.7) pg/mL and 24.7 (14.1)/21 (15-31) pg/mL, respectively. E2 and E1 were strongly correlated (Pearson correlation [r] = 0.8, P {\textless} 0.01). The largest variation in E2 and E1 levels was by BMI; mean E2 and E1 levels were 3.5 and 19.1 pg/mL, respectively for women with BMI less than 25 and 7.5 and 30.6 pg/mL, respectively, for women with BMI greater than 30. E2 and E1 varied by age, BMI, smoking status, and prior hormone therapy in multivariable models (P {\textless} 0.01).Conclusions:There was large interindividual variability observed for E2 and E1 that varied significantly by participant characteristics, but with small absolute differences except in the case of BMI. Although the majority of participant characteristics were independently associated with E1 and E2, together, these factors only explained about 20{\%} of the variation in E1 and E2 levels.},
author = {Richardson, Harriet and Ho, Vikki and Pasquet, Romain and Singh, Ravinder J. and Goetz, Matthew P. and Tu, Dongsheng and Goss, Paul E. and Ingle, James N.},
booktitle = {Menopause},
doi = {10.1097/GME.0000000000001568},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Richardson et al. - 2020 - Baseline estrogen levels in postmenopausal women participating in the MAP.3 breast cancer chemoprevention tri.pdf:pdf},
issn = {15300374},
keywords = {Estradiol,Estrone,Postmenopausal women},
mendeley-groups = {Hormone GWAS/Estrogen,Hormone GWAS,Half-Time Thesis},
number = {6},
pages = {693--700},
pmid = {32433262},
publisher = {Lippincott Williams and Wilkins},
title = {{Baseline estrogen levels in postmenopausal women participating in the MAP.3 breast cancer chemoprevention trial}},
url = {/pmc/articles/PMC7469568/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7469568/},
volume = {27},
year = {2020}
}
@article{Kaaks2005,
abstract = {Considerable experimental and epidemiological evidence suggests that elevated endogenous sex steroids - notably androgens and oestrogens - promote breast tumour development. In spite of this evidence, postmenopausal androgen replacement therapy with dehydroepiandrosterone (DHEA) or testosterone has been advocated for the prevention of osteoporosis and improved sexual well-being. We have conducted a case-control study nested within the European Prospective Investigation into Cancer and Nutrition. Levels of DHEA sulphate (DHEAS), ($\Delta$4-androstenedione), testosterone, oestrone, oestradiol and sex-hormone binding globulin (SHBG) were measured in prediagnostic serum samples of 677 postmenopausal women who subsequently developed breast cancer and 1309 matched control subjects. Levels of free testosterone and free oestradiol were calculated from absolute concentrations of testosterone, oestradiol and SHBG. Logistic regression models were used to estimate relative risks of breast cancer by quintiles of hormone concentrations. For all sex steroids - the androgens as well as the oestrogens - elevated serum levels were positively associated with breast cancer risk, while SHBG levels were inversely related to risk. For the androgens, relative risk estimates (95{\%} confidence intervals) between the top and bottom quintiles of the exposure distribution were: DHEAS 1.69 (1.23-2.33), androstenedione 1.94 (1.40-2.69), testosterone 1.85 (1.33-2.57) and free testosterone 2.50 (1.76-3.55). For the oestrogens, relative risk estimates were: oestrone 2.07 (1.42-3.02), oestradiol 2.28 (1.61-3.23) and free oestradiol (odds ratios 2.13 (1.52-2.98)). Adjustments for body mass index or other potential confounding factors did not substantially alter any of these relative risk estimates. Our results have shown that, among postmenopausal women, not only elevated serum oestrogens but also serum androgens are associated with increased breast cancer risk. Since DHEAS and androstenedione are largely of adrenal origin in postmenopausal women, our results indicated that elevated adrenal androgen synthesis is a risk factor for breast cancer. The results from this study caution against the use of DHEA(S), or other androgens, for postmenopausal androgen replacement therapy. {\textcopyright} 2005 Society for Endocrinology Printed in Great Britain.},
author = {Kaaks, R and Rinaldi, S and Key, T J and Berrino, F and Peeters, P H M and Biessy, C and Dossus, L and Lukanova, A and Bingham, S and Khaw, K-T and Allen, N E and Bueno-de-Mesquita, H B and van Gils, C H and Grobbee, D and Boeing, H and Lahmann, P H and Nagel, G and Chang-Claude, J and Clavel-Chapelon, F and Fournier, A and Thiébaut, A and González, C A and Quirós, J R and Tormo, M-J and Ardanaz, E and Amiano, P and Krogh, V and Palli, D and Panico, S and Tumino, R and Vineis, P and Trichopoulou, A and Kalapothaki, V and Trichopoulos, D and Ferrari, P and Norat, T and Saracci, R and Riboli, E},
doi = {10.1677/ERC.1.01038},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Kaaks et al. - 2005 - Postmenopausal serum androgens, oestrogens and breast cancer risk the European prospective investigation into canc.pdf:pdf},
issn = {1351-0088},
journal = {Endocrine-Related Cancer},
mendeley-groups = {Half-Time Thesis},
month = {dec},
number = {4},
pages = {1071--1082},
publisher = {BioScientifica},
title = {{Postmenopausal serum androgens, oestrogens and breast cancer risk: the European prospective investigation into cancer and nutrition}},
url = {https://erc.bioscientifica.com/view/journals/erc/12/4/0121071.xml},
volume = {12},
year = {2005}
}
@article{Zhang2013,
abstract = {Plasma estrogen and androgen levels are positively associated with postmenopausal breast cancer risk, but how long a single blood measurement can predict risk and whether the associations vary by tumor hormone receptor status remain unclear. We conducted nested case–control analyses within the Nurses' Health Study. Blood samples were collected in 1989–1990 and again in 2000–2002. Among postmenopausal women not using postmenopausal hormones at blood collection, 707 cases were diagnosed through June 2010, with two matched controls per case. We used unconditional logistic regression analyses to estimate the relative risks controlling for other breast cancer risk factors. The intra-class correlation coefficients for two blood measurements collected 10 years apart ranged from 0.54 (dehydroepiandrosterone sulfate, DHEAS) to 0.74 (sex hormone-binding globulin, SHBG). Overall, women in the top (vs. bottom) 25 {\%} of levels of estradiol, free estradiol, testosterone, free testosterone, and DHEAS were at a 50–110 {\%} higher risk of breast cancer (p
                trend {\textless} 0.001). SHBG was inversely associated with risk (p
                trend = 0.004). RRs were similar when comparing cases diagnosed 1–10 versus 11–20 years (or 16–20 years) after blood collection (p
                interaction {\textgreater} 0.2). Except for DHEAS, the associations varied significantly by hormone receptor status (p
                heterogeneity ≤ 0.02). For example, the RRs (95 {\%} CIs) comparing the highest versus lowest quartile were 2.8 (2.0–4.0; p
                trend {\textless} 0.001) for ER +/PR + tumors versus 1.1 (0.6–2.1; p
                trend = 0.98) for ER−/PR− tumors for estradiol, and 1.8 (1.3–2.5; p
                trend {\textless} 0.001) versus 0.6 (0.3–1.2; p
                trend = 0.35) for testosterone. One measure of circulating sex hormones in postmenopausal women can predict risk of hormone receptor positive breast cancer for up to 16–20 years.},
author = {Zhang, Xuehong and Tworoger, Shelley S. and Eliassen, A. Heather and Hankinson, Susan E.},
doi = {10.1007/S10549-012-2391-Z},
issn = {1573-7217},
journal = {Breast Cancer Research and Treatment 2012 137:3},
keywords = {Oncology},
mendeley-groups = {Half-Time Thesis},
month = {jan},
number = {3},
pages = {883--892},
publisher = {Springer},
title = {{Postmenopausal plasma sex hormone levels and breast cancer risk over 20 years of follow-up}},
url = {https://link.springer.com/article/10.1007/s10549-012-2391-z},
volume = {137},
year = {2013}
}
@article{Kaaks2005a,
abstract = {Background: Contrasting etiologic hypotheses about the role of endogenous sex steroids in breast cancer development among premenopausal women implicate ovarian androgen excess and progesterone deficiency, estrogen excess, estrogen and progesterone excess, and both an excess or lack of adrenal androgens (dehydroepiandrosterone [DHEA] or its sulfate [DHEAS]) as risk factors. We conducted a case-control study nested within the European Prospective Investigation into Cancer and Nutrition cohort to examine associations among premenopausal serum concentrations of sex steroids and subsequent breast cancer risk. Methods: Levels of DHEAS, ($\Delta$4-)androstenedione, testosterone, and sex hormone binding globulin (SHBG) were measured in single prediagnostic serum samples from 370 premenopausal women who subsequently developed breast cancer (case patients) and from 726 matched cancer-free control subjects. Levels of progesterone, estrone, and estradiol were also measured for the 285 case patients and 555 matched control subjects who had provided information about the day of menstrual cycle at blood donation. Conditional logistic regression models were used to estimate relative risks of breast cancer by quartiles of hormone concentrations. All statistical tests were two-sided. Results: Increased risks of breast cancer were associated with elevated serum concentrations of testosterone (odds ratio [OR] for highest versus lowest quartile = 1.73, 95{\%} confidence interval [CI] = 1.16 to 2.57; Ptrend =.01), androstenedione (OR for highest versus lowest quartile = 1.56, 95{\%} CI = 1.05 to 2.32; Ptrend =.01), and DHEAS (OR for highest versus lowest quartile = 1.48, 95{\%} CI = 1.02 to 2.14; Ptrend =.10) but not SHBG. Elevated serum progesterone concentrations were associated with a statistically significant reduction in breast cancer risk (OR for highest versus lowest quartile = 0.61, 95{\%} CI = 0.38 to 0.98; Ptrend =.06). The absolute risk of breast cancer for women younger than 40 followed up for 10 years was estimated at 2.6{\%} for those in the highest quartile of serum testosterone versus 1.5{\%} for those in the lowest quartile; for the highest and lowest quartiles of progesterone, these estimates were 1.7{\%} and 2.6{\%}, respectively. Breast cancer risk was not statistically significantly associated with serum levels of the other hormones. Conclusions: Our results support the hypothesis that elevated blood concentrations of androgens are associated with an increased risk of breast cancer in premenopausal women. {\textcopyright} Oxford University Press 2005, all rights reserved.},
author = {Kaaks, Rudolf and Berrino, Franco and Key, Timothy and Rinaldi, Sabina and Dossus, Laure and Biessy, Carine and Secreto, Giorgio and Amiano, Pilar and Bingham, Sheila and Boeing, Heiner and de Mesquita, H. Bas Bueno and Chang-Claude, Jenny and Clavel-Chapelon, Fran{\c{c}}oise and Fournier, Agn{\`{e}}s and van Gils, Carla H. and Gonzalez, Carlos A. and Gurrea, Aurelio Barricarte and Critselis, Elena and Khaw, Kay Tee and Krogh, Vittorio and Lahmann, Petra H. and Nagel, Gabriele and Olsen, Anja and Onland-Moret, N. Charlotte and Overvad, Kim and Palli, Domenico and Panico, Salvatore and Peeters, Petra and Quir{\'{o}}s, J. Ram{\'{o}}n and Roddam, Andrew and Thiebaut, Anne and Tj{\o}nneland, Anne and Chirlaque, Ma Dolores and Trichopoulou, Antonia and Trichopoulos, Dimitrios and Tumino, Rosario and Vineis, Paolo and Norat, Teresa and Ferrari, Pietro and Slimani, Nadia and Riboli, Elio},
doi = {10.1093/JNCI/DJI132},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Kaaks et al. - 2005 - Serum Sex Steroids in Premenopausal Women and Breast Cancer Risk Within the European Prospective Investigation int.pdf:pdf},
issn = {0027-8874},
journal = {JNCI: Journal of the National Cancer Institute},
keywords = {adrenal glands,androgens,androstenedione,blood donors,breast cancer,breast cancer risk,cancer,dehydroepiandrosterone,estradiol,estrogen,estrone,hormones,menstrual cycle,nutrition in cancer,premenopause,progesterone,serum progesterone measurement,sex hormone-binding globulin,steroids,testosterone,testosterone measurement, serum},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {10},
pages = {755--765},
publisher = {Oxford Academic},
title = {{Serum Sex Steroids in Premenopausal Women and Breast Cancer Risk Within the European Prospective Investigation into Cancer and Nutrition (EPIC)}},
url = {https://academic.oup.com/jnci/article/97/10/755/2544018},
volume = {97},
year = {2005}
}
@article{Key2013,
abstract = {Background: Associations between circulating concentrations of oestrogens, progesterone, and androgens with breast cancer and related risk factors in premenopausal women are not well understood. We aimed to characterise these associations with a pooled analysis of data from seven studies. Methods: Individual participant data for prediagnostic sex hormone and sex hormone-binding globulin (SHBG) concentrations were contributed from seven prospective studies. We restricted analyses to women who were premenopausal and younger than 50 years at blood collection, and to women with breast cancer diagnosed before age 50 years. We estimated odds ratios (ORs) with 95{\%} CIs for breast cancer associated with hormone concentrations by conditional logistic regression in cases and controls matched for age, date of blood collection, and day of cycle, with stratification by study and further adjustment for cycle phase. We examined associations of hormones with risk factors for breast cancer in control women by comparing geometric mean hormone concentrations in categories of these risk factors, adjusted for study, age, phase of menstrual cycle, and body-mass index (BMI). All statistical tests were two-sided. Findings: We included data for up to 767 women with breast cancer and 1699 controls in the risk analyses. Breast cancer risk was associated with a doubling in concentrations of oestradiol (OR 1{\textperiodcentered}19, 95{\%} CI 1{\textperiodcentered}06-1{\textperiodcentered}35), calculated free oestradiol (1{\textperiodcentered}17, 1{\textperiodcentered}03-1{\textperiodcentered}33), oestrone (1{\textperiodcentered}27, 1{\textperiodcentered}05-1{\textperiodcentered}54), androstenedione (1{\textperiodcentered}30, 1{\textperiodcentered}10-1{\textperiodcentered}55), dehydroepiandrosterone sulphate (1{\textperiodcentered}17, 1{\textperiodcentered}04-1{\textperiodcentered}32), testosterone (1{\textperiodcentered}18, 1{\textperiodcentered}03-1{\textperiodcentered}35), and calculated free testosterone (1{\textperiodcentered}08, 0{\textperiodcentered}97-1{\textperiodcentered}21). Breast cancer risk was not associated with luteal phase progesterone (doubling in concentration OR 1{\textperiodcentered}00, 95{\%} CI 0{\textperiodcentered}92-1{\textperiodcentered}09), and adjustment for other factors had little effect on any of these ORs. Cross-sectional analyses in control women showed several associations of sex hormones with breast cancer risk factors. Interpretation: Circulating oestrogens and androgens are positively associated with the risk for breast cancer in premenopausal women. Funding: Cancer Research UK. {\textcopyright} 2013 Endogenous Hormones and Breast Cancer Collaborative Group. Open Access article distributed under the terms of CC BY.},
author = {Key, Timothy},
doi = {10.1016/S1470-2045(13)70301-2},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Key - 2013 - Sex hormones and risk of breast cancer in premenopausal women a collaborative reanalysis of individual participant data fro.pdf:pdf},
issn = {14702045},
journal = {The Lancet Oncology},
mendeley-groups = {Half-Time Thesis},
month = {sep},
number = {10},
pages = {1009--1019},
pmid = {23890780},
publisher = {Elsevier},
title = {{Sex hormones and risk of breast cancer in premenopausal women: A collaborative reanalysis of individual participant data from seven prospective studies}},
volume = {14},
year = {2013}
}
@article{Mungenast2014,
abstract = {Ovarian cancer is still the deadliest of all gynecologic malignancies in women worldwide. This is attributed to two main features of these tumors, namely, i) a diagnosis at an advanced tumor stage, and, ii) the rapid onset of resistance to standard chemotherapy after an initial successful therapy with platin- and taxol-derivatives. Therefore, novel targets for an early diagnosis and better treatment options for these tumors are urgently needed. Epidemiological data show that induction and biology of ovarian cancer is related to life-time estrogen exposure. Also experimental data reveal that ovarian cancer cells share a number of estrogen regulated pathways with other hormone-dependent cancers, e.g. breast and endometrial cancer. However, ovarian cancer is a heterogeneous disease and the subtypes are quite different with respect to mutations, origins, behaviours, markers and prognosis and respond differently to standard chemotherapy. Therefore, a characterization of ovarian cancer subtypes may lead to better treatment options for the various subtypes and in particular for the most frequently observed high-grade serous ovarian carcinoma. For this intention, further studies on estrogen-related pathways and estrogen formation in ovarian cancer cells are warranted. The review gives an overview on ovarian cancer subtypes and explains the role of estrogen in ovarian cancer. Furthermore, enzymes active to synthesize and metabolize estrogens are described and strategies to target these pathways are discussed.},
author = {Mungenast, Felicitas and Thalhammer, Theresia},
doi = {10.3389/FENDO.2014.00192},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Mungenast, Thalhammer - 2014 - Estrogen Biosynthesis and Action in Ovarian Cancer.pdf:pdf},
issn = {1664-2392},
journal = {Frontiers in Endocrinology},
keywords = {G-protein coupled estrogen receptor,Progesterone,estrogen receptor alpha/beta,estrogen sulfatase,estrogen sulfotransferase,estrogen synthesis,ovarian cancer},
mendeley-groups = {Half-Time Thesis},
number = {NOV},
pages = {192},
publisher = {Frontiers},
title = {{Estrogen Biosynthesis and Action in Ovarian Cancer}},
volume = {0},
year = {2014}
}
@article{Brinton2014,
abstract = {Endometrial cancer is clearly a hormonally responsive tumor, with a critical role played by estrogens unopposed by progestins. Numerous epidemiologic studies have shown substantial risk increases associated with use of unopposed estrogens, especially among thin women. This risk, however, can be reduced if progestins are added to the therapy. The manner in which progestins are prescribed is a critical determinant of risk. Most studies show that women who have ever used progestins continuously ({\textgreater}25 days/months) are at somewhat reduced risk relative to non-users (meta-analysis relative risk, RR, based on observational studies = 0.78, 95 confidence intervals, CI, 0.72-0.86). The reduced risk in greatest among heavy women. In contrast, women who have ever used progestins sequentially for {\textless}10 days each month are at increased risk, with meta-analysis results showing on overall RR of 1.76 (1.51-2.05); in contrast, progestins given for 10-24 days/month appear unrelated to risk (RR = 1.07, 0.92-1.24). These risks were based on varying patterns of usage, with little information available regarding how endometrial cancer risk is affected by duration of use, type and/or dose of estrogen or progestin, or mode of administration. Effects may also vary by clinical characteristics (e.g., differences for Type I vs. II tumors). Further resolution of many of these relationships may be dependent on pooling data from multiple studies to derive sufficient power for subgroups of users. With changing clinical practices, it will be important for future studies to monitor a wide range of exposures and to account for divergent effects of different usage patterns. This article is part of a Special Issue entitled 'Menopause'.},
author = {Brinton, Louise A. and Felix, Ashley S.},
doi = {10.1016/J.JSBMB.2013.05.001},
issn = {0960-0760},
journal = {The Journal of Steroid Biochemistry and Molecular Biology},
keywords = {Endometrial cancer,Epidemiology,Menopausal hormone therapy,Risk},
mendeley-groups = {Half-Time Thesis},
month = {jul},
pages = {83--89},
publisher = {Pergamon},
title = {{Menopausal hormone therapy and risk of endometrial cancer}},
volume = {142},
year = {2014}
}
@article{Karlsson2021,
abstract = {Oral contraceptive use has been suggested to influence the risk of breast, ovarian, and endometrial cancer. The purpose of this study is to clarify the time-dependent effects between long-term oral contraceptive use and cancer risk. We performed an observational study in 256,661 women from UK Biobank, born between 1939 and 1970. Information on cancer diagnoses were collected from self-reported data and from national registers until March 2019. Cumulative risk of cancer over the timespan of the study, as measured by the OR, and instantaneous risk, as measured by the HR, were assessed using Logistic and Cox regression analyses, respectively. The odds were lower among ever users, compared with never users, for ovarian cancer [OR ¼ 0.72; 95{\%} confidence interval (CI), 0.65–0.81] and endometrial cancer (OR ¼ 0.68; 95{\%} CI, 0.62–0.75), an association that was stronger with longer use (P {\textless} 0.001). Increased odds were seen for breast cancer in women when limiting the follow-up to 55 years of age (OR ¼ 1.10; 95{\%} CI, 1.03–1.17), but not for the full timespan. We only found a higher HR for breast cancer in former users immediately (≤2 years) after discontinued oral contraceptive use (HR ¼ 1.55; 95{\%} CI, 1.06–2.28), whereas the protective association for ovarian and endometrial cancer remained significant up to 35 years after last use of oral contraceptives. Given the body of evidence presented in our study, we argue that oral contraceptives can dramatically reduce women's risk of ovarian and endometrial cancer, whereas their effect on lifetime risk of breast cancer is limited. Significance: These results enable women and physicians to make more informed decisions considering oral contraceptive use, thus constituting an important step toward personalized medicine.},
author = {Karlsson, Torgny and Johansson, Therese and Hoglund, Julia and Ek, Weronica E and Johansson, {\AA}sa},
doi = {10.1158/0008-5472.CAN-20-2476},
issn = {15387445},
journal = {Cancer Research},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {4},
pages = {1153--1162},
title = {{Time-dependent effects of oral contraceptive use on breast, ovarian, and endometrial cancers}},
volume = {81},
year = {2021}
}
@article{Iversen2017,
abstract = {Background Oral contraceptives have been used by hundreds of millions of women around the world. Important questions remain regarding the very long-term cancer risks that are associated with oral contraception. Despite previous research, important questions remain about the safety of these contraceptives: (1) How long do endometrial, ovarian, and colorectal cancer benefits persist? (2) Does combined oral contraceptive use during the reproductive years produce new cancer risks later in life? (3) What is the overall balance of cancer among past users as they enter the later stages of their lives? Objectives The purpose of this study was to examine the very long-term cancer risks or benefits associated with the use of combined oral contraceptives, including the estimated overall life-time balance. Study Design The 46,022 women who were recruited to the UK Royal College of General Practitioners' Oral Contraception Study in 1968 and 1969 were observed for up to 44 years. Directly standardized rates of specific and any cancer were calculated for “ever” and “never” users of combined oral contraceptives; data were standardized for age, parity, social class, and smoking. Attributable risk and preventive fraction percentages were calculated. Poisson regression that adjusted for the same variables was used to estimate incidence rate ratios between ever and never users and to examine effects by time since last oral contraceptive use. Results There were 4661 ever users with at least 1 cancer during 884,895 woman-years of observation and 2341 never users with at least 1 cancer during 388,505 woman-years of observation. Ever use of oral contraceptives was associated with reduced colorectal (incidence rate ratio, 0.81; 99{\%} confidence interval, 0.66–0.99), endometrial (incidence rate ratio, 0.66; 99{\%} confidence interval, 0.48–0.89), ovarian (incidence rate ratio, 0.67; 99{\%} confidence interval, 0.50–0.89), and lymphatic and hematopoietic cancer (incidence rate ratio, 0.74; 99{\%} confidence interval, 0.58–0.94). An increased risk of lung cancer was seen only among ever users who smoked at recruitment. An increased risk of breast and cervical cancer that was seen in current and recent users appeared to be lost within approximately 5 years of stopping oral contraception, with no evidence of either cancer recurring at increased risk in ever users with time. There was no evidence of new cancer risks appearing later in life among women who had used oral contraceptives. Thus, the{\ldots}},
author = {Iversen, Lisa and Sivasubramaniam, Selvaraj and Lee, Amanda J and Fielding, Shona and Hannaford, Philip C},
doi = {10.1016/j.ajog.2017.02.002},
issn = {10976868},
journal = {American Journal of Obstetrics and Gynecology},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {6},
pages = {580.e1--580.e9},
title = {{Lifetime cancer risk and combined oral contraceptives: the Royal College of General Practitioners' Oral Contraception Study}},
volume = {216},
year = {2017}
}
@article{Thompson2016,
abstract = {Candidate gene studies have reported CYP19A1 variants to be associated with endometrial cancerandwith estradiol (E2) concentrations.We analyzed2937singlenucleotidepolymorphisms (SNPs) in 6608 endometrial cancer cases and 37 925 controls and report the first genome widesignificant association between endometrial cancer and a CYP19A1 SNP (rs727479 in intron 2, P=4.8×10-11). SNP rs727479 was also among those most strongly associated with circulating E2 concentrations in 2767 post-menopausal controls (P=7.4×10-8). The observed endometrial cancer odds ratio per rs727479 A-allele (1.15, CI=1.11-1.21) is compatible with that predicted by theobservedeffectonE2 concentrations (1.09, CI=1.03-1.21), consistentwith the hypothesis that endometrial cancer risk is driven by E2. From 28 candidate-causal SNPs, 12 co-located with three putative gene-regulatory elements and their risk alleles associated with higher CYP19A1 expression in bioinformatical analyses. For both phenotypes, the associationswith rs727479 were stronger amongwomen with a higher BMI (PinteractionZ0.034 and 0.066 respectively), suggesting a biologically plausible gene-environment interaction.},
author = {Thompson, Deborah J. and O'Mara, Tracy A. and Glubb, Dylan M. and Painter, Jodie N. and Cheng, Timothy and Folkerd, Elizabeth and Doody, Deborah and Dennis, Joe and Webb, Penelope M. and Gorman, Maggie and Martin, Lynn and Hodgson, Shirley and Michailidou, Kyriaki and Tyrer, Jonathan P. and Maranian, Mel J. and Hall, Per and Czene, Kamila and Darabi, Hatef and Li, Jingmei and Fasching, Peter A. and Hein, Alexander and Beckmann, Matthias W. and Ekici, Arif B. and D{\"{o}}rk, Thilo and Hillemanns, Peter and D{\"{u}}rst, Matthias and Runnebaum, Ingo and Zhao, Hui and Depreeuw, Jeroen and Schrauwen, Stefanie and Amant, Frederic and Goode, Ellen L. and Fridley, Brooke L. and Dowdy, Sean C. and Winham, Stacey J. and Salvesen, Helga B. and Trovik, Jone and Tormund, Njolstad S. and Werner, Henrica M.J. and Ashton, Katie and Proietto, Tony and Otton, Geoffrey and Carvajal-Carmona, Luis and Tham, Emma and Liu, Tao and Mints, Miriam and Scott, Rodney J. and McEvoy, Mark and Attia, John and Holliday, Elizabeth G. and Montgomery, Grant W. and Martin, Nicholas G. and Nyholt, Dale R. and Henders, Anjali K. and Hopper, John L. and Traficante, Nadia and Ruebner, Matthias and Swerdlow, Anthony J. and Burwinkel, Barbara and Brenner, Hermann and Meindl, Alfons and Brauch, Hiltrud and Lindblom, Annika and Lambrechts, Diether and Chang-Claude, Jenny and Couch, Fergus J. and Giles, Graham G. and Kristensen, Vessela N. and Cox, Angela and Bolla, Manjeet K. and Wang, Qin and Bojesen, Stig E. and Shah, Mitul and Luben, Robert and Khaw, Kay Tee and Pharoah, Paul D.P. and Dunning, Alison M. and Tomlinson, Ian and Dowsett, Mitch and Easton, Douglas F. and Spurdle, Amanda B.},
doi = {10.1530/ERC-15-0386},
issn = {14796821},
journal = {Endocrine-Related Cancer},
keywords = {CYP19A1,Endometrial cancer,Estradiol},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
month = {feb},
number = {2},
pages = {77--91},
pmid = {26574572},
title = {{CYP19A1 fine-mapping and Mendelian randomization: Estradiol is causal for endometrial cancer}},
url = {https://erc.bioscientifica.com/view/journals/erc/23/2/77.xml},
volume = {23},
year = {2016}
}
@article{Olena2017,
author = {Olena, Yavorska O and Burgess, Stephen},
journal = {International Journal of Epidemiology},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {6},
pages = {1734--1739},
title = {{MendelianRandomization: an R package for performing Mendelian randomization analyses using summarized data}},
volume = {46},
year = {2017}
}
@article{Michailidou2017,
abstract = {Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as BRCA1, and many common, mostly non-coding variants. However, much of the genetic contribution to breast cancer risk remains unknown. Here we report the results of a genome-wide association study of breast cancer in 122,977 cases and 105,974 controls of European ancestry and 14,068 cases and 13,104 controls of East Asian ancestry. We identified 65 new loci that are associated with overall breast cancer risk at P {\textless} 5 × 10-8. The majority of credible risk single-nucleotide polymorphisms in these loci fall in distal regulatory elements, and by integrating in silico data to predict target genes in breast cells at each locus, we demonstrate a strong overlap between candidate target genes and somatic driver genes in breast tumours. We also find that heritability of breast cancer due to all single-nucleotide polymorphisms in regulatory features was 2-5-fold enriched relative to the genome-wide average, with strong enrichment for particular transcription factor binding sites. These results provide further insight into genetic susceptibility to breast cancer and will improve the use of genetic risk scores for individualized screening and prevention.},
author = {Michailidou, Kyriaki and Lindstr{\"{o}}m, Sara and Dennis, Joe and Beesley, Jonathan and Hui, Shirley and Kar, Siddhartha and Lema{\c{c}}on, Audrey and Soucy, Penny and Glubb, Dylan and Rostamianfar, Asha and Bolla, Manjeet K and Wang, Qin and Tyrer, Jonathan and Dicks, Ed and Lee, Andrew and Wang, Zhaoming and Allen, Jamie and Keeman, Renske and Eilber, Ursula and French, Juliet D and Chen, Xiao Qing and Fachal, Laura and McCue, Karen and Reed, Amy E.Mc Cart and Ghoussaini, Maya and Carroll, Jason S and Jiang, Xia and Finucane, Hilary and Adams, Marcia and Adank, Muriel A and Ahsan, Habibul and Aittom{\"{a}}ki, Kristiina and Anton-Culver, Hoda and Antonenkova, Natalia N and Arndt, Volker and Aronson, Kristan J and Arun, Banu and Auer, Paul L and Bacot, Fran{\c{c}}ois and Barrdahl, Myrto and Baynes, Caroline and Beckmann, Matthias W and Behrens, Sabine and Benitez, Javier and Bermisheva, Marina and Bernstein, Leslie and Blomqvist, Carl and Bogdanova, V Natalia and Bojesen, Stig E and Bonanni, Bernardo and B{\o}rresen-Dale, Anne Lise and Brand, Judith S and Brauch, Hiltrud and Brennan, Paul and Brenner, Hermann and Brinton, Louise and Broberg, Per and Brock, Ian W and Broeks, Annegien and Brooks-Wilson, Angela and Brucker, Sara Y and Br{\"{u}}ning, Thomas and Burwinkel, Barbara and Butterbach, Katja and Cai, Qiuyin and Cai, Hui and Cald{\'{e}}s, Trinidad and Canzian, Federico and Carracedo, Angel and Carter, Brian D and Castelao, Jose E and Chan, Tsun L and Cheng, Ting Yuan David and Chia, Kee Seng and Choi, Ji Yeob and Christiansen, Hans and Clarke, Christine L and Coll{\'{e}}e, Margriet and Conroy, Don M and Cordina-Duverger, Emilie and Cornelissen, Sten and Cox, David G and Cox, Angela and Cross, Simon S and Cunningham, Julie M and Czene, Kamila and Daly, Mary B and Devilee, Peter and Doheny, Kimberly F and D{\"{o}}rk, Thilo and Dos-Santos-Silva, Isabel and Dumont, Martine and Durcan, Lorraine and Dwek, Miriam and Eccles, Diana M and Ekici, Arif B and Eliassen, A Heather and Ellberg, Carolina and Elvira, Mingajeva and Engel, Christoph and Eriksson, Mikael and Fasching, Peter A and Figueroa, Jonine and Flesch-Janys, Dieter and Fletcher, Olivia and Flyger, Henrik and Fritschi, Lin and Gaborieau, Valerie and Gabrielson, Marike and Gago-Dominguez, Manuela and Gao, Yu Tang and Gapstur, Susan M and Garc{\'{i}}a-S{\'{a}}enz, Jos{\'{e}} A and Gaudet, Mia M and Georgoulias, Vassilios and Giles, Graham G and Glendon, Gord and Goldberg, Mark S and Goldgar, David E and Gonz{\'{a}}lez-Neira, Anna and Aln{\ae}s, Grethe I.Grenaker and Grip, Mervi and Gronwald, Jacek and Grundy, Anne and Gu{\'{e}}nel, Pascal and Haeberle, Lothar and Hahnen, Eric and Haiman, Christopher A and H{\aa}kansson, Niclas and Hamann, Ute and Hamel, Nathalie and Hankinson, Susan and Harrington, Patricia and Hart, Steven N and Hartikainen, Jaana M and Hartman, Mikael and Hein, Alexander and Heyworth, Jane and Hicks, Belynda and Hillemanns, Peter and Ho, Dona N and Hollestelle, Antoinette and Hooning, Maartje J and Hoover, Robert N and Hopper, John L and Hou, Ming Feng and Hsiung, Chia Ni and Huang, Guanmengqian and Humphreys, Keith and Ishiguro, Junko and Ito, Hidemi and Iwasaki, Motoki and Iwata, Hiroji and Jakubowska, Anna and Janni, Wolfgang and John, Esther M and Johnson, Nichola and Jones, Kristine and Jones, Michael and Jukkola-Vuorinen, Arja and Kaaks, Rudolf and Kabisch, Maria and Kaczmarek, Katarzyna and Kang, Daehee and Kasuga, Yoshio and Kerin, Michael J and Khan, Sofia and Khusnutdinova, Elza and Kiiski, Johanna I and Kim, Sung Won and Knight, Julia A and Kosma, Veli Matti and Kristensen, Vessela N and Kr{\"{u}}ger, Ute and Kwong, Ava and Lambrechts, Diether and {Le Marchand}, Loic and Lee, Eunjung and Lee, Min Hyuk and Lee, Jong Won and Lee, Chuen Neng and Lejbkowicz, Flavio and Li, Jingmei and Lilyquist, Jenna and Lindblom, Annika and Lissowska, Jolanta and Lo, Wing Yee and Loibl, Sibylle and Long, Jirong and Lophatananon, Artitaya and Lubinski, Jan and Luccarini, Craig and Lux, Michael P and Ma, Edmond S K and MacInnis, Robert J and Maishman, Tom and Makalic, Enes and Malone, Kathleen E and Kostovska, Ivana Maleva and Mannermaa, Arto and Manoukian, Siranoush and Manson, Jo Ann E and Margolin, Sara and Mariapun, Shivaani and Martinez, Maria Elena and Matsuo, Keitaro and Mavroudis, Dimitrios and McKay, James and McLean, Catriona and Meijers-Heijboer, Hanne and Meindl, Alfons and Men{\'{e}}ndez, Primitiva and Menon, Usha and Meyer, Jeffery and Miao, Hui and Miller, Nicola and Taib, Nur Aishah Mohd and Muir, Kenneth and Mulligan, Anna Marie and Mulot, Claire and Neuhausen, Susan L and Nevanlinna, Heli and Neven, Patrick and Nielsen, Sune F and Noh, Dong Young and Nordestgaard, B{\o}rge G and Norman, Aaron and Olopade, Olufunmilayo I and Olson, Janet E and Olsson, H{\aa}kan and Olswold, Curtis and Orr, Nick and Pankratz, V Shane and Park, Sue K and Park-Simon, Tjoung Won and Lloyd, Rachel and Perez, Jose I A and Peterlongo, Paolo and Peto, Julian and Phillips, Kelly Anne and Pinchev, Mila and Plaseska-Karanfilska, Dijana and Prentice, Ross and Presneau, Nadege and Prokofyeva, Darya and Pugh, Elizabeth and Pylk{\"{a}}s, Katri and Rack, Brigitte and Radice, Paolo and Rahman, Nazneen and Rennert, Gadi and Rennert, Hedy S and Rhenius, Valerie and Romero, Atocha and Romm, Jane and Ruddy, Kathryn J and R{\"{u}}diger, Thomas and Rudolph, Anja and Ruebner, Matthias and Rutgers, Emiel J T and Saloustros, Emmanouil and Sandler, Dale P and Sangrajrang, Suleeporn and Sawyer, Elinor J and Schmidt, Daniel F and Schmutzler, Rita K and Schneeweiss, Andreas and Schoemaker, Minouk J and Schumacher, Fredrick and Sch{\"{u}}rmann, Peter and Scott, Rodney J and Scott, Christopher and Seal, Sheila and Seynaeve, Caroline and Shah, Mitul and Sharma, Priyanka and Shen, Chen Yang and Sheng, Grace and Sherman, Mark E and Shrubsole, Martha J and Shu, Xiao Ou and Smeets, Ann and Sohn, Christof and Southey, Melissa C and Spinelli, John J and Stegmaier, Christa and Stewart-Brown, Sarah and Stone, Jennifer and Stram, Daniel O and Surowy, Harald and Swerdlow, Anthony and Tamimi, Rulla and Taylor, Jack A and Tengstr{\"{o}}m, Maria and Teo, Soo H and Terry, Mary Beth and Tessier, Daniel C and Thanasitthichai, Somchai and Th{\"{o}}ne, Kathrin and Tollenaar, Rob A E M and Tomlinson, Ian and Tong, Ling and Torres, Diana and Truong, Th{\'{e}}r{\`{e}}se and Tseng, Chiu Chen and Tsugane, Shoichiro and Ulmer, Hans Ulrich and Ursin, Giske and Untch, Michael and Vachon, Celine and {Van Asperen}, Christi J and {Van Den Berg}, David and {Van Den Ouweland}, Ans M W and {Van Der Kolk}, Lizet and {Van Der Luijt}, Rob B and Vincent, Daniel and Vollenweider, Jason and Waisfisz, Quinten and Wang-Gohrke, Shan and Weinberg, Clarice R and Wendt, Camilla and Whittemore, Alice S and Wildiers, Hans and Willett, Walter and Winqvist, Robert and Wolk, Alicja and Wu, Anna H and Xia, Lucy and Yamaji, Taiki and Yang, Xiaohong R and Yip, Cheng Har and Yoo, Keun Young and Yu, Jyh Cherng and Zheng, Wei and Zheng, Ying and Zhu, Bin and Ziogas, Argyrios and Ziv, Elad and Lakhani, Sunil R and Antoniou, Antonis C and Droit, Arnaud and Andrulis, Irene L and Amos, Christopher I and Couch, Fergus J and Pharoah, Paul D P and Chang-Claude, Jenny and Hall, Per and Hunter, David J and Milne, Roger L and Garc{\'{i}}a-Closas, Montserrat and Schmidt, Marjanka K and Chanock, Stephen J and Dunning, Alison M and Edwards, Stacey L and Bader, Gary D and Chenevix-Trench, Georgia and Simard, Jacques and Kraft, Peter and Easton, Douglas F},
doi = {10.1038/nature24284},
issn = {14764687},
journal = {Nature},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
pages = {92--94},
title = {{Association analysis identifies 65 new breast cancer risk loci}},
volume = {551},
year = {2017}
}
@article{OMara2018,
abstract = {Endometrial cancer is the most commonly diagnosed cancer of the female reproductive tract in developed countries. Through genome-wide association studies (GWAS), we have previously identified eight risk loci for endometrial cancer. Here, we present an expanded meta-analysis of 12,906 endometrial cancer cases and 108,979 controls (including new genotype data for 5624 cases) and identify nine novel genome-wide significant loci, including a locus on 12q24.12 previously identified by meta-GWAS of endometrial and colorectal cancer. At five loci, expression quantitative trait locus (eQTL) analyses identify candidate causal genes; risk alleles at two of these loci associate with decreased expression of genes, which encode negative regulators of oncogenic signal transduction proteins (SH2B3 (12q24.12) and NF1 (17q11.2)). In summary, this study has doubled the number of known endometrial cancer risk loci and revealed candidate causal genes for future study.},
author = {O'Mara, Tracy A and Glubb, Dylan M and Amant, Frederic and Annibali, Daniela and Ashton, Katie and Attia, John and Auer, Paul L and Beckmann, Matthias W and Black, Amanda and Bolla, Manjeet K and Brauch, Hiltrud and Brenner, Hermann and Brinton, Louise and Buchanan, Daniel D and Burwinkel, Barbara and Chang-Claude, Jenny and Chanock, Stephen J and Chen, Chu and Chen, Maxine M and Cheng, Timothy H T and Clarke, Christine L and Clendenning, Mark and Cook, Linda S and Couch, Fergus J and Cox, Angela and Crous-Bous, Marta and Czene, Kamila and Day, Felix and Dennis, Joe and Depreeuw, Jeroen and Doherty, Jennifer Anne and D{\"{o}}rk, Thilo and Dowdy, Sean C and D{\"{u}}rst, Matthias and Ekici, Arif B and Fasching, Peter A and Fridley, Brooke L and Friedenreich, Christine M and Fritschi, Lin and Fung, Jenny and Garc{\'{i}}a-Closas, Montserrat and Gaudet, Mia M and Giles, Graham G and Goode, Ellen L and Gorman, Maggie and Haiman, Christopher A and Hall, Per and Hankison, Susan E and Healey, Catherine S and Hein, Alexander and Hillemanns, Peter and Hodgson, Shirley and Hoivik, Erling A and Holliday, Elizabeth G and Hopper, John L and Hunter, David J and Jones, Angela and Krakstad, Camilla and Kristensen, Vessela N and Lambrechts, Diether and Marchand, Le Loic and Liang, Xiaolin and Lindblom, Annika and Lissowska, Jolanta and Long, Jirong and Lu, Lingeng and Magliocco, Anthony M and Martin, Lynn and McEvoy, Mark and Meindl, Alfons and Michailidou, Kyriaki and Milne, Roger L and Mints, Miriam and Montgomery, Grant W and Nassir, Rami and Olsson, H{\aa}kan and Orlow, Irene and Otton, Geoffrey and Palles, Claire and Perry, John R B and Peto, Julian and Pooler, Loreall and Prescott, Jennifer and Proietto, Tony and Rebbeck, Timothy R and Risch, Harvey A and Rogers, Peter A W and R{\"{u}}bner, Matthias and Runnebaum, Ingo and Sacerdote, Carlotta and Sarto, Gloria E and Schumacher, Fredrick and Scott, Rodney J and Setiawan, V Wendy and Shah, Mitul and Sheng, Xin and Shu, Xiao Ou and Southey, Melissa C and Swerdlow, Anthony J and Tham, Emma and Trovik, Jone and Turman, Constance and Tyrer, Jonathan P and Vachon, Celine and {VanDen Berg}, David and Vanderstichele, Adriaan and Wang, Zhaoming and Webb, Penelope M and Wentzensen, Nicolas and Werner, Henrica M J and Winham, Stacey J and Wolk, Alicja and Xia, Lucy and Xiang, Yong Bing and Yang, Hannah P and Yu, Herbert and Zheng, Wei and Pharoah, Paul D P and Dunning, Alison M and Kraft, Peter and {De Vivo}, Immaculata and Tomlinson, Ian and Easton, Douglas F and Spurdle, Amanda B and Thompson, Deborah J},
doi = {10.1038/s41467-018-05427-7},
issn = {20411723},
journal = {Nature Communications},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {1},
title = {{Identification of nine new susceptibility loci for endometrial cancer}},
volume = {9},
year = {2018}
}
@article{Phelan2017,
abstract = {To identify common alleles associated with different histotypes of epithelial ovarian cancer (EOC), we pooled data from multiple genome-wide genotyping projects totaling 25,509 EOC cases and 40,941 controls. We identified nine new susceptibility loci for different EOC histotypes: six for serous EOC histotypes (3q28, 4q32.3, 8q21.11, 10q24.33, 18q11.2 and 22q12.1), two for mucinous EOC (3q22.3 and 9q31.1) and one for endometrioid EOC (5q12.3). We then performed meta-analysis on the results for high-grade serous ovarian cancer with the results from analysis of 31,448 BRCA1 and BRCA2 mutation carriers, including 3,887 mutation carriers with EOC. This identified three additional susceptibility loci at 2q13, 8q24.1 and 12q24.31. Integrated analyses of genes and regulatory biofeatures at each locus predicted candidate susceptibility genes, including OBFC1, a new candidate susceptibility gene for low-grade and borderline serous EOC.},
author = {Phelan, Catherine M and Kuchenbaecker, Karoline B and Tyrer, Jonathan P and Kar, Siddhartha P and Lawrenson, Kate and Winham, Stacey J and Dennis, Joe and Pirie, Ailith and Riggan, Marjorie J and Chornokur, Ganna and Earp, Madalene A and Lyra, Paulo C and Lee, Janet M and Coetzee, Simon and Beesley, Jonathan and McGuffog, Lesley and Soucy, Penny and Dicks, Ed and Lee, Andrew and Barrowdale, Daniel and Lecarpentier, Julie and Leslie, Goska and Aalfs, Cora M and Aben, Katja K H and Adams, Marcia and Adlard, Julian and Andrulis, Irene L and Anton-Culver, Hoda and Antonenkova, Natalia and Aravantinos, Gerasimos and Arnold, Norbert and Arun, Banu K and Arver, Brita and Azzollini, Jacopo and Balma{\~{n}}a, Judith and Banerjee, Susana N and Barjhoux, Laure and Barkardottir, Rosa B and Bean, Yukie and Beckmann, Matthias W and Beeghly-Fadiel, Alicia and Benitez, Javier and Bermisheva, Marina and Bernardini, Marcus Q and Birrer, Michael J and Bjorge, Line and Black, Amanda and Blankstein, Kenneth and Blok, Marinus J and Bodelon, Clara and Bogdanova, Natalia and Bojesen, Anders and Bonanni, Bernardo and Borg, {\AA}ke and Bradbury, Angela R and Brenton, James D and Brewer, Carole and Brinton, Louise and Broberg, Per and Brooks-Wilson, Angela and Bruinsma, Fiona and Brunet, Joan and Buecher, Bruno and Butzow, Ralf and Buys, Saundra S and Caldes, Trinidad and Caligo, Maria A and Campbell, Ian and Cannioto, Rikki and Carney, Michael E and Cescon, Terence and Chan, Salina B and Chang-Claude, Jenny and Chanock, Stephen and Chen, Xiao Qing and Chiew, Yoke Eng and Chiquette, Jocelyne and Chung, Wendy K and Claes, Kathleen B M and Conner, Thomas and Cook, Linda S and Cook, Jackie and Cramer, Daniel W and Cunningham, Julie M and D'Aloisio, Aimee A and Daly, Mary B and Damiola, Francesca and Damirovna, Sakaeva Dina and Dansonka-Mieszkowska, Agnieszka and Dao, Fanny and Davidson, Rosemarie and DeFazio, Anna and Delnatte, Capucine and Doheny, Kimberly F and Diez, Orland and Ding, Yuan Chun and Doherty, Jennifer Anne and Domchek, Susan M and Dorfling, Cecilia M and D{\"{o}}rk, Thilo and Dossus, Laure and Duran, Mercedes and D{\"{u}}rst, Matthias and Dworniczak, Bernd and Eccles, Diana and Edwards, Todd and Eeles, Ros and Eilber, Ursula and Ejlertsen, Bent and Ekici, Arif B and Ellis, Steve and Elvira, Mingajeva and Eng, Kevin H and Engel, Christoph and Evans, D Gareth and Fasching, Peter A and Ferguson, Sarah and Ferrer, Sandra Fert and Flanagan, James M and Fogarty, Zachary C and Fortner, Ren{\'{e}}e T and Fostira, Florentia and Foulkes, William D and Fountzilas, George and Fridley, Brooke L and Friebel, Tara M and Friedman, Eitan and Frost, Debra and Ganz, Patricia A and Garber, Judy and Garc{\'{i}}a, Mar{\'{i}}a J and Garcia-Barberan, Vanesa and Gehrig, Andrea and Gentry-Maharaj, Aleksandra and Gerdes, Anne Marie and Giles, Graham G and Glasspool, Rosalind and Glendon, Gord and Godwin, Andrew K and Goldgar, David E and Goranova, Teodora and Gore, Martin and Greene, Mark H and Gronwald, Jacek and Gruber, Stephen and Hahnen, Eric and Haiman, Christopher A and H{\aa}kansson, Niclas and Hamann, Ute and Hansen, Thomas V O and Harrington, Patricia A and Harris, Holly R and Hauke, Jan and Hein, Alexander and Henderson, Alex and Hildebrandt, Michelle A T and Hillemanns, Peter and Hodgson, Shirley and H{\o}gdall, Claus K and H{\o}gdall, Estrid and Hogervorst, Frans B L and Holland, Helene and Hooning, Maartje J and Hosking, Karen and Huang, Ruea Yea and Hulick, Peter J and Hung, Jillian and Hunter, David J and Huntsman, David G and Huzarski, Tomasz and Imyanitov, Evgeny N and Isaacs, Claudine and Iversen, Edwin S and Izatt, Louise and Izquierdo, Angel and Jakubowska, Anna and James, Paul and Janavicius, Ramunas and Jernetz, Mats and Jensen, Allan and Jensen, Uffe Birk and John, Esther M and Johnatty, Sharon and Jones, Michael E and Kannisto, P{\"{a}}ivi and Karlan, Beth Y and Karnezis, Anthony and Kast, Karin and Kennedy, Catherine J and Khusnutdinova, Elza and Kiemeney, Lambertus A and Kiiski, Johanna I and Kim, Sung Won and Kjaer, Susanne K and K{\"{o}}bel, Martin and Kopperud, Reidun K and Kruse, Torben A and Kupryjanczyk, Jolanta and Kwong, Ava and Laitman, Yael and Lambrechts, Diether and Larra{\~{n}}aga, Nerea and Larson, Melissa C and Lazaro, Conxi and Le, Nhu D and {Le Marchand}, Loic and Lee, Jong Won and Lele, Shashikant B and Leminen, Arto and Leroux, Dominique and Lester, Jenny and Lesueur, Fabienne and Levine, Douglas A and Liang, Dong and Liebrich, Clemens and Lilyquist, Jenna and Lipworth, Loren and Lissowska, Jolanta and Lu, Karen H and Lubi{\'{n}}ski, Jan and Luccarini, Craig and Lundvall, Lene and Mai, Phuong L and Mendoza-Fandi{\~{n}}o, Gustavo and Manoukian, Siranoush and Massuger, Leon F A G and May, Taymaa and Mazoyer, Sylvie and McAlpine, Jessica N and McGuire, Valerie and McLaughlin, John R and McNeish, Iain and Meijers-Heijboer, Hanne and Meindl, Alfons and Menon, Usha and Mensenkamp, Arjen R and Merritt, Melissa A and Milne, Roger L and Mitchell, Gillian and Modugno, Francesmary and Moes-Sosnowska, Joanna and Moffitt, Melissa and Montagna, Marco and Moysich, Kirsten B and Mulligan, Anna Marie and Musinsky, Jacob and Nathanson, Katherine L and Nedergaard, Lotte and Ness, Roberta B and Neuhausen, Susan L and Nevanlinna, Heli and Niederacher, Dieter and Nussbaum, Robert L and Odunsi, Kunle and Olah, Edith and Olopade, Olufunmilayo I and Olsson, H{\aa}kan and Olswold, Curtis and O'Malley, David M and Ong, Kai Ren and Onland-Moret, N Charlotte and Orr, Nicholas and Orsulic, Sandra and Osorio, Ana and Palli, Domenico and Papi, Laura and Park-Simon, Tjoung Won and Paul, James and Pearce, Celeste L and Pedersen, Inge S{\o}kilde and Peeters, Petra H M and Peissel, Bernard and Peixoto, Ana and Pejovic, Tanja and Pelttari, Liisa M and Permuth, Jennifer B and Peterlongo, Paolo and Pezzani, Lidia and Pfeiler, Georg and Phillips, Kelly Anne and Piedmonte, Marion and Pike, Malcolm C and Piskorz, Anna M and Poblete, Samantha R and Pocza, Timea and Poole, Elizabeth M and Poppe, Bruce and Porteous, Mary E and Prieur, Fabienne and Prokofyeva, Darya and Pugh, Elizabeth and Pujana, Miquel Angel and Pujol, Pascal and Radice, Paolo and Rantala, Johanna and Rappaport-Fuerhauser, Christine and Rennert, Gad and Rhiem, Kerstin and Rice, Patricia and Richardson, Andrea and Robson, Mark and Rodriguez, Gustavo C and Rodr{\'{i}}guez-Antona, Cristina and Romm, Jane and Rookus, Matti A and Rossing, Mary Anne and Rothstein, Joseph H and Rudolph, Anja and Runnebaum, Ingo B and Salvesen, Helga B and Sandler, Dale P and Schoemaker, Minouk J and Senter, Leigha and Setiawan, V Wendy and Severi, Gianluca and Sharma, Priyanka and Shelford, Tameka and Siddiqui, Nadeem and Side, Lucy E and Sieh, Weiva and Singer, Christian F and Sobol, Hagay and Song, Honglin and Southey, Melissa C and Spurdle, Amanda B and Stadler, Zsofia and Steinemann, Doris and Stoppa-Lyonnet, Dominique and Sucheston-Campbell, Lara E and Sukiennicki, Grzegorz and Sutphen, Rebecca and Sutter, Christian and Swerdlow, Anthony J and Szabo, Csilla I and Szafron, Lukasz and Tan, Yen Y and Taylor, Jack A and Tea, Muy Kheng and Teixeira, Manuel R and Teo, Soo Hwang and Terry, Kathryn L and Thompson, Pamela J and Thomsen, Liv Cecilie Vestrheim and Thull, Darcy L and Tihomirova, Laima and Tinker, V Anna and Tischkowitz, Marc and Tognazzo, Silvia and Toland, Amanda Ewart and Tone, Alicia and Trabert, Britton and Travis, Ruth C and Trichopoulou, Antonia and Tung, Nadine and Tworoger, Shelley S and {Van Altena}, Anne M and {Van Den Berg}, David and {Van Der Hout}, Annemarie H and {Van Der Luijt}, Rob B and {Van Heetvelde}, Mattias and {Van Nieuwenhuysen}, Els and {Van Rensburg}, Elizabeth J and Vanderstichele, Adriaan and Varon-Mateeva, Raymonda and Vega, Ana and Edwards, Digna Velez and Vergote, Ignace and Vierkant, Robert A and Vijai, Joseph and Vratimos, Athanassios and Walker, Lisa and Walsh, Christine and Wand, Dorothea and Wang-Gohrke, Shan and Wappenschmidt, Barbara and Webb, Penelope M and Weinberg, Clarice R and Weitzel, Jeffrey N and Wentzensen, Nicolas and Whittemore, Alice S and Wijnen, Juul T and Wilkens, Lynne R and Wolk, Alicja and Woo, Michelle and Wu, Xifeng and Wu, Anna H and Yang, Hannah and Yannoukakos, Drakoulis and Ziogas, Argyrios and Zorn, Kristin K and Narod, Steven A and Easton, Douglas F and Amos, Christopher I and Schildkraut, Joellen M and Ramus, Susan J and Ottini, Laura and Goodman, Marc T and Park, Sue K and Kelemen, Linda E and Risch, Harvey A and Thomassen, Mads and Offit, Kenneth and Simard, Jacques and Schmutzler, Rita Katharina and Hazelett, Dennis and Monteiro, Alvaro N and Couch, Fergus J and Berchuck, Andrew and Chenevix-Trench, Georgia and Goode, Ellen L and Sellers, Thomas A and Gayther, Simon A and Antoniou, Antonis C and Pharoah, Paul D P},
doi = {10.1038/ng.3826},
issn = {15461718},
journal = {Nature Genetics},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {5},
pages = {680--691},
title = {{Identification of 12 new susceptibility loci for different histotypes of epithelial ovarian cancer}},
volume = {49},
year = {2017}
}
@article{Chen2014,
abstract = {Age atmenopause marks the end of a woman's reproductive life and its timing associates with risks for cancer, cardiovascular and bone disorders.GWAS and candidate gene studies conducted in women of European ancestry have identified 27 loci associated with age at men opause. The relevance of these loci to women of African ancestry has not been previously studied. We therefore sought to uncover additional menopause loci and investigate the relevance of European menopause loci by performing a GWAS meta-analysis in 6510 women with Africanancestry derivedfrom 11studies across the USA.We did not identify any additional loci significantly associated with age at men opause in African Americans.We replicated the associations between six lociandage at men opause (P-value {\textless} 0.05): AMHR2, RHBLD2, PRIM1, HK3/UMC1, BRSK1/TMEM150B and MCM8. In addition, associations of 14 loci are directionally consistent with previous reports. We provide evidence that genetic variants influencing reproductive traits identified in European populations are also important in women of African ancestry residing in USA. {\textcopyright} The Author 2014. Published by Oxford University Press. All rights reserved.},
author = {Chen, Christina T L and Liu, Ching Ti and Chen, Gary K and Andrews, Jeanette S and Arnold, Alice M and Dreyfus, Jill and Franceschini, Nora and Garcia, Melissa E and Kerr, Kathleen F and Li, Guo and Lohman, Kurt K and Musani, Solomon K and Nalls, Michael A and Raffel, Leslie J and Smith, Jennifer and Ambrosone, Christine B and Bandera, V Elisa and Bernstein, Leslie and Britton, Angela and Brzyski, Robert G and Cappola, Anne and Carlson, Christopher S and Couper, David and Deming, Sandra L and Goodarzi, Mark O and Heiss, Gerardo and John, Esther M and Lu, Xiaoning and Marchand, Le Loic and Marciante, Kristin and Mcknight, Barbara and Millikan, Robert and Nock, Nora L and Olshan, Andrew F and Press, Michael F and Vaiyda, Dhananjay and Woods, Nancy F and Taylor, Herman A and Zhao, Wei and Zheng, Wei and Evans, Michele K and Harris, Tamara B and Henderson, Brian E and Kardia, Sharon L R and Kooperberg, Charles and Liu, Yongmei and Mosley, Thomas H and Psaty, Bruce and Wellons, Melissa and Windham, Beverly G and Zonderman, Alan B and Cupples, L Adrienne and Demerath, Ellen W and Haiman, Christopher and Murabito, Joanne M and Rajkovic, Aleksandar},
doi = {10.1093/hmg/ddu041},
issn = {14602083},
journal = {Human Molecular Genetics},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {12},
pages = {3327--3342},
title = {{Meta-analysis of loci associated with age at natural menopause in African-American women}},
volume = {23},
year = {2014}
}
@article{Stolk2012,
abstract = {To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P {\textless} 5 - 10 g8). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-I °B signaling and mitochondrial dysfunction as biological processes related to timing of menopause. {\textcopyright} 2012 Nature America, Inc. All rights reserved.},
author = {Stolk, Lisette and Perry, John R B and Chasman, Daniel I and He, Chunyan and Mangino, Massimo and Sulem, Patrick and Barbalic, Maja and Broer, Linda and Byrne, Enda M and Ernst, Florian and Esko, Tmu and Franceschini, Nora and Gudbjartsson, Daniel F and Hottenga, Jouke Jan and Kraft, Peter and McArdle, Patrick F and Porcu, Eleonora and Shin, So Youn and Smith, V Albert and {Van Wingerden}, Sophie and Zhai, Guangju and Zhuang, V Wei and Albrecht, Eva and Alizadeh, Behrooz Z and Aspelund, Thor and Bandinelli, Stefania and Lauc, Lovorka Barac and Beckmann, Jacques S and Boban, Mladen and Boerwinkle, Eric and Broekmans, Frank J and Burri, Andrea and Campbell, Harry and Chanock, Stephen J and Chen, Constance and Cornelis, Marilyn C and Corre, Tanguy and Coviello, Andrea D and D'Adamo, Pio and Davies, Gail and {De Faire}, Ulf and {De Geus}, Eco J C and Deary, Ian J and Dedoussis, George V Z and Deloukas, Panagiotis and Ebrahim, Shah and Eiriksdottir, Gudny and Emilsson, Valur and Eriksson, Johan G and Fauser, Bart C J M and Ferreli, Liana and Ferrucci, Luigi and Fischer, Krista and Folsom, Aaron R and Garcia, Melissa E and Gasparini, Paolo and Gieger, Christian and Glazer, Nicole and Grobbee, Diederick E and Hall, Per and Haller, Toomas and Hankinson, Susan E and Hass, Merli and Hayward, Caroline and Heath, Andrew C and Hofman, Albert and Ingelsson, Erik and Janssens, A Cecile J W and Johnson, Andrew D and Karasik, David and Kardia, Sharon L R and Keyzer, Jules and Kiel, Douglas P and Kolcic, Ivana and Kutalik, Zoltn and Lahti, Jari and Lai, Sandra and Laisk, Triin and Laven, Joop S E and Lawlor, Debbie A and Liu, Jianjun and Lopez, Lorna M and Louwers, V Yvonne and Magnusson, Patrik K E and Marongiu, Mara and Martin, Nicholas G and Klaric, Irena Martinovic and Masciullo, Corrado and McKnight, Barbara and Medland, Sarah E and Melzer, David and Mooser, Vincent and Navarro, Pau and Newman, Anne B and Nyholt, Dale R and Onland-Moret, N Charlotte and Palotie, Aarno and Par{\'{e}}, Guillaume and Parker, Alex N and Pedersen, Nancy L and Peeters, Petra H M and Pistis, Giorgio and Plump, Andrew S and Polasek, Ozren and Pop, Victor J M and Psaty, Bruce M and {R Currency Signikk{\"{o}}nen}, Katri and Rehnberg, Emil and Rotter, Jerome I and Rudan, Igor and Sala, Cinzia and Salumets, Andres and Scuteri, Angelo and Singleton, Andrew and Smith, Jennifer A and Snieder, Harold and Soranzo, Nicole and Stacey, Simon N and Starr, John M and Stathopoulou, Maria G and Stirrups, Kathleen and Stolk, Ronald P and Styrkarsdottir, Unnur and Sun, V Yan and Tenesa, Albert and Thorand, Barbara and Toniolo, Daniela and Tryggvadottir, Laufey and Tsui, Kim and Ulivi, Sheila and {Van Dam}, Rob M and {Van Der Schouw}, Yvonne T and {Van Gils}, Carla H and {Van Nierop}, Peter and Vink, Jacqueline M and Visscher, Peter M and Voorhuis, Marlies and Waeber, G{\'{e}}rard and Wallaschofski, Henri and Wichmann, H Erich and Widen, Elisabeth and {Wijnands-Van Gent}, Colette J M and Willemsen, Gonneke and Wilson, James F and Wolffenbuttel, Bruce H R and Wright, Alan F and Yerges-Armstrong, Laura M and Zemunik, Tatijana and Zgaga, Lina and Zillikens, M Carola and Zygmunt, Marek and Arnold, Alice M and Boomsma, Dorret I and Buring, Julie E and Crisponi, Laura and Demerath, Ellen W and Gudnason, Vilmundur and Harris, Tamara B and Hu, Frank B and Hunter, David J and Launer, Lenore J and Metspalu, Andres and Montgomery, Grant W and Oostra, Ben A and Ridker, Paul M and Sanna, Serena and Schlessinger, David and Spector, Tim D and Stefansson, Kari and Streeten, Elizabeth A and Thorsteinsdottir, Unnur and Uda, Manuela and Uitterlinden, Andr{\'{e}} G and {Van Duijn}, Cornelia M and V{\"{o}}lzke, Henry and Murray, Anna and Murabito, Joanne M and Visser, Jenny A and Lunetta, Kathryn L},
doi = {10.1038/ng.1051},
issn = {10614036},
journal = {Nature Genetics},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {3},
pages = {260--268},
title = {{Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways}},
volume = {44},
year = {2012}
}
@article{Miyashita2020,
abstract = {The master regulator of neuroendocrine differentiation, achaete-scute complex homolog 1 (ASCL1) defines a subgroup of lung adenocarcinoma. However, the mechanistic role of ASCL1 in lung tumorigenesis and its relation to the immune microenvironment is principally unknown. Here, the immune landscape of ASCL1-positive lung adenocarcinomas was characterized by immunohistochemistry. Furthermore, ASCL1 was transduced in mouse lung adenocarcinoma cell lines and comparative RNA-sequencing and secretome analyses were performed. The effects of ASCL1 on tumorigenesis were explored in an orthotopic syngeneic transplantation model. ASCL1-positive lung adenocarcinomas revealed lower infiltration of CD8+, CD4+, CD20+, and FOXP3+ lymphocytes and CD163+ macrophages indicating an immune desert phenotype. Ectopic ASCL1 upregulated cyclin transcript levels, stimulated cell proliferation, and enhanced tumor growth in mice. ASCL1 suppressed secretion of chemokines, including CCL20, CXCL2, CXCL10, and CXCL16, indicating effects on immune cell trafficking. In accordance with lower lymphocytes infiltration, ASCL1-positive lung adenocarcinomas demonstrated lower abundance of CXCR3-and CCR6-expressing cells. In conclusion, ASCL1 mediates its tumor-promoting effect not only through cell-autonomous signaling but also by modulating chemokine production and immune responses. These findings suggest that ASCL1-positive tumors represent a clinically relevant lung cancer entity.},
author = {Miyashita, Naoya and Horie, Masafumi and Mikami, Yu and Urushiyama, Hirokazu and Fukuda, Kensuke and Miyakawa, Kazuko and Matsuzaki, Hirotaka and Makita, Kosuke and Morishita, Yasuyuki and Harada, Hiroaki and Backman, Max and Lindskog, Cecilia and Brunnstr{\"{o}}m, Hans and Micke, Patrick and Nagase, Takahide and Saito, Akira},
doi = {10.1016/j.canlet.2020.06.002},
issn = {18727980},
journal = {Cancer Letters},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
pages = {121--132},
title = {{ASCL1 promotes tumor progression through cell-autonomous signaling and immune modulation in a subset of lung adenocarcinoma}},
volume = {489},
year = {2020}
}
@article{Moore2017,
abstract = {Objective This study evaluated single nucleotide polymorphisms (SNPs) associated with progression free (PFS) and overall survival (OS) in patients with advanced stage serous EOC. Methods Patients enrolled in GOG-172 and 182 who provided specimens for translational research and consent were included. Germline DNA was evaluated with the Illumina's HumanOMNI1-Quad beadchips and scanned using Illumina's iScan optical imaging system. SNPs with allele frequency {\textgreater} 0.05 and genotyping rate {\textgreater} 0.98 were included. Analysis of SNPs for PFS and OS was done using Cox regression. Statistical significance was determined using Bonferroni corrected p-values with genomic control adjustment. Results The initial GWAS analysis included 1,124,677 markers in 396 patients. To obtain the final data set, quality control checks were performed and limited to serous tumors and self-identified Caucasian race. In total 636,555 SNPs and 289 patients passed all the filters. The pre-specified statistical level of significance was 7.855e− 08. No SNPs met this criteria for PFS or OS, however, two SNPs were close to significance (rs10899426 p-2.144e−08) (rs6256 p-9.774e− 07) for PFS and 2 different SNPs were identified (rs295315 p-7.536e−07; rs17693104 p-7.734e−07) which were close to significance for OS. Conclusions Using the pre-specified level of significance of 1 × 10− 08, we did not identify any SNPs of statistical significance for OS or PFS, however several were close. The SNP's identified in this GWAS study will require validation and these preliminary findings may lead to identification of novel pathways and biomarkers.},
author = {Moore, Kathleen N and Tritchler, David and Kaufman, Kenneth M and Lankes, Heather and Quinn, Michael C J and {Van Le}, Linda and Berchuck, Andrew and Backes, Floor J and Tewari, Krishnansu S and Lee, Roger B and Kesterson, Joshua P and Wenham, Robert M and Armstrong, Deborah K and Krivak, Thomas C and Bookman, Michael A and Birrer, Michael J},
doi = {10.1016/j.ygyno.2017.08.024},
issn = {10956859},
journal = {Gynecologic Oncology},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {2},
pages = {396--401},
title = {{Genome-wide association study evaluating single-nucleotide polymorphisms and outcomes in patients with advanced stage serous ovarian or primary peritoneal cancer: An NRG Oncology/Gynecologic Oncology Group study}},
volume = {147},
year = {2017}
}
@article{Pickrell2016,
abstract = {We performed a scan for genetic variants associated with multiple phenotypes by comparing large genome-wide association studies (GWAS) of 42 traits or diseases. We identified 341 loci (at a false discovery rate of 10{\%}) associated with multiple traits. Several loci are associated with multiple phenotypes; for example, a nonsynonymous variant in the zinc transporter SLC39A8 influences seven of the traits, including risk of schizophrenia (rs13107325: log-transformed odds ratio (log OR) = 0.15, P = 2 × 10 {\^{a}} '12) and Parkinson disease (log OR = {\^{a}} '0.15, P = 1.6 × 10 {\^{a}} '7), among others. Second, we used these loci to identify traits that have multiple genetic causes in common. For example, variants associated with increased risk of schizophrenia also tended to be associated with increased risk of inflammatory bowel disease. Finally, we developed a method to identify pairs of traits that show evidence of a causal relationship. For example, we show evidence that increased body mass index causally increases triglyceride levels.},
author = {Pickrell, Joseph K and Berisa, Tomaz and Liu, Jimmy Z and S{\'{e}}gurel, Laure and Tung, Joyce Y and Hinds, David A},
doi = {10.1038/ng.3570},
issn = {15461718},
journal = {Nature Genetics},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {7},
pages = {709--717},
title = {{Detection and interpretation of shared genetic influences on 42 human traits}},
volume = {48},
year = {2016}
}
@article{Trabert2016,
abstract = {Background: Hormonal and reproductive factors contribute to the development of ovarian cancer, but few studies have examined associations between circulating estrogens and estrogen metabolites and ovarian cancer risk. We evaluated whether serum estrogens and estrogen metabolite levels are associated with ovarian cancer risk among postmenopausal women in a nested case-control study in the Women's Health Initiative (WHI) Observational Study (OS). Methods: We selected all 169 eligible epithelial ovarian cancer cases and 412 matched controls from women enrolled in WHI-OS who were not using menopausal hormones at baseline. Baseline levels of 15 estrogens and estrogen metabolites were measured via liquid chromatography/tandem mass spectrometry. Associations with ovarian cancer risk overall and stratified by histologic subtype (serous/nonserous) were analyzed using logistic regression. The mean time from serum collection to cancer diagnosis was 6.9 years. Results: Overall, we observed modest ovarian cancer risk associations among women with higher levels of estrone [OR (95{\%} confidence interval) quintile (Q)5 vs. Q1: 1.54 (0.82-2.90), Ptrend = 0.05], as well as 2-and 4-methoxyestrone metabolites [2.03 (1.06-3.88), Ptrend = 0.02; 1.86 (0.98-3.56), Ptrend = 0.01, respectively]. Associations of estrogens and estrogen metabolites varied substantially by histologic subtype. Associations with serous tumors were universally null, while estrone [2.65 (1.09-6.45), Ptrend = 0.01, Pheterogeneity = 0.04], unconjugated estradiol [2.72 (1.04-7.14), Ptrend = 0.03, Pheterogeneity = 0.02] and many of the 2-, 4-, and 16-pathway metabolites were positively associated with nonserous tumors. Conclusions: Our study provides novel molecular data showing an association of the parent estrogens and several estrogen metabolites with nonserous ovarian cancers. Impact: These findings further support the heterogeneous etiology of ovarian cancer.},
author = {Trabert, Britton and Brinton, Louise A and Anderson, Garnet L and Pfeiffer, Ruth M and Falk, Roni T and Strickler, Howard D and Sliesoraitis, Sarunas and Kuller, Lewis H and Gass, Margery L and Fuhrman, Barbara J and Xu, Xia and Wentzensen, Nicolas},
doi = {10.1158/1055-9965.EPI-15-1272-T},
issn = {10559965},
journal = {Cancer Epidemiology Biomarkers and Prevention},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
pages = {648--656},
title = {{Circulating estrogens and postmenopausal ovarian cancer risk in the women's health initiative observational study}},
volume = {4},
year = {2016}
}
@article{Key2011,
author = {Key, T J and Appleby, P N and Hines, L M and Al., Et},
journal = {Br J Cancer},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {5},
pages = {709--722},
title = {{Circulating sex hormones and breast cancer risk factors in postmenopausal women: reanalysis of 13 studies}},
volume = {105},
year = {2011}
}
@article{Rodriguez2019,
author = {Rodriguez, Adriana C and Blanchard, Zannel and Maurer, Kathryn A and Gertz, Jason},
journal = {Hormonal cancer},
mendeley-groups = {Estradiol Cancer MR,Half-Time Thesis},
number = {2-3},
pages = {51--63},
title = {{Estrogen Signaling in Endometrial Cancer: a Key Oncogenic Pathway with Several Open Questions}},
volume = {10},
year = {2019}
}
@article{Sudmant2015,
abstract = {Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.},
author = {Sudmant, Peter H. and Rausch, Tobias and Gardner, Eugene J. and Handsaker, Robert E. and Abyzov, Alexej and Huddleston, John and Zhang, Yan and Ye, Kai and Jun, Goo and Fritz, Markus His Yang and Konkel, Miriam K. and Malhotra, Ankit and St{\"{u}}tz, Adrian M. and Shi, Xinghua and Casale, Francesco Paolo and Chen, Jieming and Hormozdiari, Fereydoun and Dayama, Gargi and Chen, Ken and Malig, Maika and Chaisson, Mark J.P. and Walter, Klaudia and Meiers, Sascha and Kashin, Seva and Garrison, Erik and Auton, Adam and Lam, Hugo Y.K. and Mu, Xinmeng Jasmine and Alkan, Can and Antaki, Danny and Bae, Taejeong and Cerveira, Eliza and Chines, Peter and Chong, Zechen and Clarke, Laura and Dal, Elif and Ding, Li and Emery, Sarah and Fan, Xian and Gujral, Madhusudan and Kahveci, Fatma and Kidd, Jeffrey M. and Kong, Yu and Lameijer, Eric Wubbo and McCarthy, Shane and Flicek, Paul and Gibbs, Richard A. and Marth, Gabor and Mason, Christopher E. and Menelaou, Androniki and Muzny, Donna M. and Nelson, Bradley J. and Noor, Amina and Parrish, Nicholas F. and Pendleton, Matthew and Quitadamo, Andrew and Raeder, Benjamin and Schadt, Eric E. and Romanovitch, Mallory and Schlattl, Andreas and Sebra, Robert and Shabalin, Andrey A. and Untergasser, Andreas and Walker, Jerilyn A. and Wang, Min and Yu, Fuli and Zhang, Chengsheng and Zhang, Jing and Zheng-Bradley, Xiangqun and Zhou, Wanding and Zichner, Thomas and Sebat, Jonathan and Batzer, Mark A. and McCarroll, Steven A. and Mills, Ryan E. and Gerstein, Mark B. and Bashir, Ali and Stegle, Oliver and Devine, Scott E. and Lee, Charles and Eichler, Evan E. and Korbel, Jan O.},
doi = {10.1038/nature15394},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Sudmant et al. - 2015 - An integrated map of structural variation in 2,504 human genomes.pdf:pdf},
issn = {14764687},
journal = {Nature},
keywords = {Genomics,Structural variation},
mendeley-groups = {Half-Time Thesis},
month = {sep},
number = {7571},
pages = {75--81},
pmid = {26432246},
publisher = {Nature Publishing Group},
title = {{An integrated map of structural variation in 2,504 human genomes}},
url = {https://www.nature.com/articles/nature15394},
volume = {526},
year = {2015}
}
@article{Buniello2019,
abstract = {The GWAS Catalog delivers a high-quality curated collection of all published genome-wide association studies enabling investigations to identify causal variants, understand disease mechanisms, and establish targets for novel therapies. The scope of the Catalog has also expanded to targeted and exome arrays with 1000 new associations added for these technologies. As of September 2018, the Catalog contains 5687 GWAS comprising 71673 variant-trait associations from 3567 publications. New content includes 284 full P-value summary statistics datasets for genome-wide and new targeted array studies, representing 6 × 10 9 individual variant-trait statistics. In the last 12 months, the Catalog's user interface was accessed by 1/490000 unique users who viewed {\textgreater}1 million pages. We have improved data access with the release of a new RESTful API to support high-throughput programmatic access, an improved web interface and a new summary statistics database. Summary statistics provision is supported by a new format proposed as a community standard for summary statistics data representation. This format was derived from our experience in standardizing heterogeneous submissions, mapping formats and in harmonizing content. Availability: https://www.ebi.ac.uk/gwas/.},
author = {Buniello, Annalisa and MacArthur, Jacqueline A L and Cerezo, Maria and Harris, Laura W and Hayhurst, James and Malangone, Cinzia and McMahon, Aoife and Morales, Joannella and Mountjoy, Edward and Sollis, Elliot and Suveges, Daniel and Vrousgou, Olga and Whetzel, Patricia L and Amode, Ridwan and Guillen, Jose A and Riat, Harpreet S and Trevanion, Stephen J and Hall, Peggy and Junkins, Heather and Flicek, Paul and Burdett, Tony and Hindorff, Lucia A and Cunningham, Fiona and Parkinson, Helen},
doi = {10.1093/NAR/GKY1120},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Buniello et al. - 2019 - The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics.pdf:pdf},
issn = {0305-1048},
journal = {Nucleic Acids Research},
keywords = {community,datasets,genome,genome-wide association study},
mendeley-groups = {Half-Time Thesis},
month = {jan},
number = {D1},
pages = {D1005--D1012},
publisher = {Oxford Academic},
title = {{The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019}},
url = {https://academic.oup.com/nar/article/47/D1/D1005/5184712},
volume = {47},
year = {2019}
}
@article{Auton2015a,
abstract = {The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes {\textgreater}99{\%} of SNP variants with a frequency of {\textgreater}1{\%} for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.},
author = {Auton, Adam and Abecasis, Gon{\c{c}}alo R. and Altshuler, David M. and Durbin, Richard M. and Bentley, David R. and Chakravarti, Aravinda and Clark, Andrew G. and Donnelly, Peter and Eichler, Evan E. and Flicek, Paul and Gabriel, Stacey B. and Gibbs, Richard A. and Green, Eric D. and Hurles, Matthew E. and Knoppers, Bartha M. and Korbel, Jan O. and Lander, Eric S. and Lee, Charles and Lehrach, Hans and Mardis, Elaine R. and Marth, Gabor T. and McVean, Gil A. and Nickerson, Deborah A. and Schmidt, Jeanette P. and Sherry, Stephen T. and Wang, Jun and Wilson, Richard K. and Boerwinkle, Eric and Doddapaneni, Harsha and Han, Yi and Korchina, Viktoriya and Kovar, Christie and Lee, Sandra and Muzny, Donna and Reid, Jeffrey G. and Zhu, Yiming and Chang, Yuqi and Feng, Qiang and Fang, Xiaodong and Guo, Xiaosen and Jian, Min and Jiang, Hui and Jin, Xin and Lan, Tianming and Li, Guoqing and Li, Jingxiang and Li, Yingrui and Liu, Shengmao and Liu, Xiao and Lu, Yao and Ma, Xuedi and Tang, Meifang and Wang, Bo and Wang, Guangbiao and Wu, Honglong and Wu, Renhua and Xu, Xun and Yin, Ye and Zhang, Dandan and Zhang, Wenwei and Zhao, Jiao and Zhao, Meiru and Zheng, Xiaole and Gupta, Namrata and Gharani, Neda and Toji, Lorraine H. and Gerry, Norman P. and Resch, Alissa M. and Barker, Jonathan and Clarke, Laura and Gil, Laurent and Hunt, Sarah E. and Kelman, Gavin and Kulesha, Eugene and Leinonen, Rasko and McLaren, William M. and Radhakrishnan, Rajesh and Roa, Asier and Smirnov, Dmitriy and Smith, Richard E. and Streeter, Ian and Thormann, Anja and Toneva, Iliana and Vaughan, Brendan and Zheng-Bradley, Xiangqun and Grocock, Russell and Humphray, Sean and James, Terena and Kingsbury, Zoya and Sudbrak, Ralf and Albrecht, Marcus W. and Amstislavskiy, Vyacheslav S. and Borodina, Tatiana A. and Lienhard, Matthias and Mertes, Florian and Sultan, Marc and Timmermann, Bernd and Yaspo, Marie Laure and Fulton, Lucinda and Ananiev, Victor and Belaia, Zinaida and Beloslyudtsev, Dimitriy and Bouk, Nathan and Chen, Chao and Church, Deanna and Cohen, Robert and Cook, Charles and Garner, John and Hefferon, Timothy and Kimelman, Mikhail and Liu, Chunlei and Lopez, John and Meric, Peter and O'Sullivan, Chris and Ostapchuk, Yuri and Phan, Lon and Ponomarov, Sergiy and Schneider, Valerie and Shekhtman, Eugene and Sirotkin, Karl and Slotta, Douglas and Zhang, Hua and Balasubramaniam, Senduran and Burton, John and Danecek, Petr and Keane, Thomas M. and Kolb-Kokocinski, Anja and McCarthy, Shane and Stalker, James and Quail, Michael and Davies, Christopher J. and Gollub, Jeremy and Webster, Teresa and Wong, Brant and Zhan, Yiping and Campbell, Christopher L. and Kong, Yu and Marcketta, Anthony and Yu, Fuli and Antunes, Lilian and Bainbridge, Matthew and Sabo, Aniko and Huang, Zhuoyi and Coin, Lachlan J.M. and Fang, Lin and Li, Qibin and Li, Zhenyu and Lin, Haoxiang and Liu, Binghang and Luo, Ruibang and Shao, Haojing and Xie, Yinlong and Ye, Chen and Yu, Chang and Zhang, Fan and Zheng, Hancheng and Zhu, Hongmei and Alkan, Can and Dal, Elif and Kahveci, Fatma and Garrison, Erik P. and Kural, Deniz and Lee, Wan Ping and Leong, Wen Fung and Stromberg, Michael and Ward, Alistair N. and Wu, Jiantao and Zhang, Mengyao and Daly, Mark J. and DePristo, Mark A. and Handsaker, Robert E. and Banks, Eric and Bhatia, Gaurav and {Del Angel}, Guillermo and Genovese, Giulio and Li, Heng and Kashin, Seva and McCarroll, Steven A. and Nemesh, James C. and Poplin, Ryan E. and Yoon, Seungtai C. and Lihm, Jayon and Makarov, Vladimir and Gottipati, Srikanth and Keinan, Alon and Rodriguez-Flores, Juan L. and Rausch, Tobias and Fritz, Markus H. and St{\"{u}}tz, Adrian M. and Beal, Kathryn and Datta, Avik and Herrero, Javier and Ritchie, Graham R.S. and Zerbino, Daniel and Sabeti, Pardis C. and Shlyakhter, Ilya and Schaffner, Stephen F. and Vitti, Joseph and Cooper, David N. and Ball, Edward V. and Stenson, Peter D. and Barnes, Bret and Bauer, Markus and Cheetham, R. Keira and Cox, Anthony and Eberle, Michael and Kahn, Scott and Murray, Lisa and Peden, John and Shaw, Richard and Kenny, Eimear E. and Batzer, Mark A. and Konkel, Miriam K. and Walker, Jerilyn A. and MacArthur, Daniel G. and Lek, Monkol and Herwig, Ralf and Ding, Li and Koboldt, Daniel C. and Larson, David and Ye, Kai and Gravel, Simon and Swaroop, Anand and Chew, Emily and Lappalainen, Tuuli and Erlich, Yaniv and Gymrek, Melissa and Willems, Thomas Frederick and Simpson, Jared T. and Shriver, Mark D. and Rosenfeld, Jeffrey A. and Bustamante, Carlos D. and Montgomery, Stephen B. and {De La Vega}, Francisco M. and Byrnes, Jake K. and Carroll, Andrew W. and DeGorter, Marianne K. and Lacroute, Phil and Maples, Brian K. and Martin, Alicia R. and Moreno-Estrada, Andres and Shringarpure, Suyash S. and Zakharia, Fouad and Halperin, Eran and Baran, Yael and Cerveira, Eliza and Hwang, Jaeho and Malhotra, Ankit and Plewczynski, Dariusz and Radew, Kamen and Romanovitch, Mallory and Zhang, Chengsheng and Hyland, Fiona C.L. and Craig, David W. and Christoforides, Alexis and Homer, Nils and Izatt, Tyler and Kurdoglu, Ahmet A. and Sinari, Shripad A. and Squire, Kevin and Xiao, Chunlin and Sebat, Jonathan and Antaki, Danny and Gujral, Madhusudan and Noor, Amina and Ye, Kenny and Burchard, Esteban G. and Hernandez, Ryan D. and Gignoux, Christopher R. and Haussler, David and Katzman, Sol J. and Kent, W. James and Howie, Bryan and Ruiz-Linares, Andres and Dermitzakis, Emmanouil T. and Devine, Scott E. and Kang, Hyun Min and Kidd, Jeffrey M. and Blackwell, Tom and Caron, Sean and Chen, Wei and Emery, Sarah and Fritsche, Lars and Fuchsberger, Christian and Jun, Goo and Li, Bingshan and Lyons, Robert and Scheller, Chris and Sidore, Carlo and Song, Shiya and Sliwerska, Elzbieta and Taliun, Daniel and Tan, Adrian and Welch, Ryan and Wing, Mary Kate and Zhan, Xiaowei and Awadalla, Philip and Hodgkinson, Alan and Li, Yun and Shi, Xinghua and Quitadamo, Andrew and Lunter, Gerton and Marchini, Jonathan L. and Myers, Simon and Churchhouse, Claire and Delaneau, Olivier and Gupta-Hinch, Anjali and Kretzschmar, Warren and Iqbal, Zamin and Mathieson, Iain and Menelaou, Androniki and Rimmer, Andy and Xifara, Dionysia K. and Oleksyk, Taras K. and Fu, Yunxin and Liu, Xiaoming and Xiong, Momiao and Jorde, Lynn and Witherspoon, David and Xing, Jinchuan and Browning, Brian L. and Browning, Sharon R. and Hormozdiari, Fereydoun and Sudmant, Peter H. and Khurana, Ekta and Tyler-Smith, Chris and Albers, Cornelis A. and Ayub, Qasim and Chen, Yuan and Colonna, Vincenza and Jostins, Luke and Walter, Klaudia and Xue, Yali and Gerstein, Mark B. and Abyzov, Alexej and Balasubramanian, Suganthi and Chen, Jieming and Clarke, Declan and Fu, Yao and Harmanci, Arif O. and Jin, Mike and Lee, Donghoon and Liu, Jeremy and Mu, Xinmeng Jasmine and Zhang, Jing and Zhang, Yan and Hartl, Chris and Shakir, Khalid and Degenhardt, Jeremiah and Meiers, Sascha and Raeder, Benjamin and Casale, Francesco Paolo and Stegle, Oliver and Lameijer, Eric Wubbo and Hall, Ira and Bafna, Vineet and Michaelson, Jacob and Gardner, Eugene J. and Mills, Ryan E. and Dayama, Gargi and Chen, Ken and Fan, Xian and Chong, Zechen and Chen, Tenghui and Chaisson, Mark J. and Huddleston, John and Malig, Maika and Nelson, Bradley J. and Parrish, Nicholas F. and Blackburne, Ben and Lindsay, Sarah J. and Ning, Zemin and Zhang, Yujun and Lam, Hugo and Sisu, Cristina and Challis, Danny and Evani, Uday S. and Lu, James and Nagaswamy, Uma and Yu, Jin and Li, Wangshen and Habegger, Lukas and Yu, Haiyuan and Cunningham, Fiona and Dunham, Ian and Lage, Kasper and Jespersen, Jakob Berg and Horn, Heiko and Kim, Donghoon and Desalle, Rob and Narechania, Apurva and Sayres, Melissa A.Wilson and Mendez, Fernando L. and Poznik, G. David and Underhill, Peter A. and Mittelman, David and Banerjee, Ruby and Cerezo, Maria and Fitzgerald, Thomas W. and Louzada, Sandra and Massaia, Andrea and Yang, Fengtang and Kalra, Divya and Hale, Walker and Dan, Xu and Barnes, Kathleen C. and Beiswanger, Christine and Cai, Hongyu and Cao, Hongzhi and Henn, Brenna and Jones, Danielle and Kaye, Jane S. and Kent, Alastair and Kerasidou, Angeliki and Mathias, Rasika and Ossorio, Pilar N. and Parker, Michael and Rotimi, Charles N. and Royal, Charmaine D. and Sandoval, Karla and Su, Yeyang and Tian, Zhongming and Tishkoff, Sarah and Via, Marc and Wang, Yuhong and Yang, Huanming and Yang, Ling and Zhu, Jiayong and Bodmer, Walter and Bedoya, Gabriel and Cai, Zhiming and Gao, Yang and Chu, Jiayou and Peltonen, Leena and Garcia-Montero, Andres and Orfao, Alberto and Dutil, Julie and Martinez-Cruzado, Juan C. and Mathias, Rasika A. and Hennis, Anselm and Watson, Harold and McKenzie, Colin and Qadri, Firdausi and LaRocque, Regina and Deng, Xiaoyan and Asogun, Danny and Folarin, Onikepe and Happi, Christian and Omoniwa, Omonwunmi and Stremlau, Matt and Tariyal, Ridhi and Jallow, Muminatou and Joof, Fatoumatta Sisay and Corrah, Tumani and Rockett, Kirk and Kwiatkowski, Dominic and Kooner, Jaspal and Hien, Tran Tinh and Dunstan, Sarah J. and ThuyHang, Nguyen and Fonnie, Richard and Garry, Robert and Kanneh, Lansana and Moses, Lina and Schieffelin, John and Grant, Donald S. and Gallo, Carla and Poletti, Giovanni and Saleheen, Danish and Rasheed, Asif and Brooks, Lisa D. and Felsenfeld, Adam L. and McEwen, Jean E. and Vaydylevich, Yekaterina and Duncanson, Audrey and Dunn, Michael and Schloss, Jeffery A.},
doi = {10.1038/nature15393},
issn = {14764687},
journal = {Nature},
keywords = {*Internationality,Datasets as Topic,Demography,Disease Susceptibility,Exome/genetics,Genetic Variation/*genetics,Genetics, Medical,Genetics, Population/*standards,Genome, Human/*genetics,Genome-Wide Association Study,Genomics/*standards,Genotype,Haplotypes/genetics,High-Throughput Nucleotide Sequencing,Humans,INDEL Mutation/genetics,Physical Chromosome Mapping,Polymorphism, Single Nucleotide/genetics,Quantitative Trait Loci/genetics,Rare Diseases/genetics,Reference Standards,Sequence Analysis, DNA},
language = {eng},
mendeley-groups = {CNV-Project/Zhiweis references,Half-Time Thesis},
month = {oct},
number = {7571},
pages = {68--74},
pmid = {26432245},
title = {{A global reference for human genetic variation}},
url = {https://pubmed.ncbi.nlm.nih.gov/26432245 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4750478/},
volume = {526},
year = {2015}
}
@article{Ameur2017,
abstract = {Here we describe the SweGen data set, a comprehensive map of genetic variation in the Swedish population. These data represent a basic resource for clinical genetics laboratories as well as for sequencing-based association studies by providing information on genetic variant frequencies in a cohort that is well matched to national patient cohorts. To select samples for this study, we first examined the genetic structure of the Swedish population using high-density SNP-array data from a nation-wide cohort of over 10 000 Swedish-born individuals included in the Swedish Twin Registry. A total of 1000 individuals, reflecting a cross-section of the population and capturing the main genetic structure, were selected for whole-genome sequencing. Analysis pipelines were developed for automated alignment, variant calling and quality control of the sequencing data. This resulted in a genome-wide collection of aggregated variant frequencies in the Swedish population that we have made available to the scientific community through the website 
                  https://swefreq.nbis.se
                  
                . A total of 29.2 million single-nucleotide variants and 3.8 million indels were detected in the 1000 samples, with 9.9 million of these variants not present in current databases. Each sample contributed with an average of 7199 individual-specific variants. In addition, an average of 8645 larger structural variants (SVs) were detected per individual, and we demonstrate that the population frequencies of these SVs can be used for efficient filtering analyses. Finally, our results show that the genetic diversity within Sweden is substantial compared with the diversity among continental European populations, underscoring the relevance of establishing a local reference data set.},
author = {Ameur, Adam and Dahlberg, Johan and Olason, Pall and Vezzi, Francesco and Karlsson, Robert and Martin, Marcel and Viklund, Johan and K{\"{a}}h{\"{a}}ri, Andreas Kusalananda and Lundin, P{\"{a}}r and Che, Huiwen and Thutkawkorapin, Jessada and Eisfeldt, Jesper and Lampa, Samuel and Dahlberg, Mats and Hagberg, Jonas and Jareborg, Niclas and Liljedahl, Ulrika and Jonasson, Inger and Johansson, {\AA}sa and Feuk, Lars and Lundeberg, Joakim and Syv{\"{a}}nen, Ann-Christine and Lundin, Sverker and Nilsson, Daniel and Nystedt, Bj{\"{o}}rn and Magnusson, Patrik KE and Gyllensten, Ulf},
doi = {10.1038/ejhg.2017.130},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Ameur et al. - 2017 - SweGen a whole-genome data resource of genetic variability in a cross-section of the Swedish population.pdf:pdf},
issn = {1476-5438},
journal = {European Journal of Human Genetics 2017 25:11},
keywords = {Genetic databases,Genetics research,Next,Rare variants,Structural variation,generation sequencing},
mendeley-groups = {Half-Time Thesis},
month = {aug},
number = {11},
pages = {1253--1260},
publisher = {Nature Publishing Group},
title = {{SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population}},
url = {https://www.nature.com/articles/ejhg2017130},
volume = {25},
year = {2017}
}
@article{Abyzov2011b,
abstract = {Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed a method, CNVnator, for CNV discovery and genotyping from read-depth (RD) analysis of personal genome sequencing. Our method is based on combining the established mean-shift approach with additional refinements (multiple-bandwidth partitioning and GC correction) to broaden the range of discovered CNVs. We calibrated CNVnator using the extensive validation performed by the 1000 Genomes Project. Because of this, we could use CNVnator for CNV discovery and genotyping in a population and characterization of atypical CNVs, such as de novo and multi-allelic events. Overall, for CNVs accessible by RD, CNVnator has high sensitivity (86{\%}-96{\%}), low false-discovery rate (3{\%}-20{\%}), high genotyping accuracy (93{\%}-95{\%}), and high resolution in breakpoint discovery ({\textless}200 bp in 90{\%} of cases with high sequencing coverage). Furthermore, CNVnator is complementary in a straightforward way to split-read and read-pair approaches: It misses CNVs created by retrotransposable elements, but more than half of the validated CNVs that it identifies are not detected by split-read or read-pair. By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, we estimated that at least 11{\%} of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier. Moreover, among these events, we observed cases with allele distribution strongly deviating from Hardy-Weinberg equilibrium, possibly implying selection on certain complex loci. Finally, by combining discovery and genotyping, we identified six potential de novo CNVs in two family trios. {\textcopyright} 2011 by Cold Spring Harbor Laboratory Press.},
author = {Abyzov, Alexej and Urban, Alexander E. and Snyder, Michael and Gerstein, Mark},
doi = {10.1101/gr.114876.110},
edition = {2011/02/07},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Abyzov et al. - 2011 - CNVnator An approach to discover, genotype, and characterize typical and atypical CNVs from family and population.pdf:pdf},
issn = {10889051},
journal = {Genome Research},
keywords = {*Algorithms,*Software,Base Composition,DNA Copy Number Variations/*genetics,DNA/*methods,Ethnic Groups/genetics,Genome,Genotype,Human/*genetics,Humans,Metagenomics/*methods,Sensitivity and Specificity,Sequence Analysis},
language = {eng},
mendeley-groups = {CNV-Project/Zhiweis references,CNV-Project/CNV Calling,Half-Time Thesis},
month = {jun},
number = {6},
pages = {974--984},
pmid = {21324876},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing}},
url = {https://pubmed.ncbi.nlm.nih.gov/21324876 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3106330/ http://www.genome.org/cgi/doi/10.1101/gr.114876.110.},
volume = {21},
year = {2011}
}
@article{Belmont2005,
abstract = {Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million single nucleotide polymorphisms (SNPs) for which accurate and complete genotypes have been obtained in 269 DNA samples from four populations, including ten 500-kilobase regions in which essentially all information about common DNA variation has been extracted. These data document the generality of recombination hotspots, a block-like structure of linkage disequilibrium and low haplotype diversity, leading to substantial correlations of SNPs with many of their neighbours. We show how the HapMap resource can guide the design and analysis of genetic association studies, shed light on structural variation and recombination, and identify loci that may have been subject to natural selection during human evolution.},
author = {Belmont, John W. and Boudreau, Andrew and Leal, Suzanne M. and Hardenbol, Paul and Pasternak, Shiran and Wheeler, David A. and Willis, Thomas D. and Yu, Fuli and Yang, Huanming and Gao, Yang and Hu, Haoran and Hu, Weitao and Li, Chaohua and Lin, Wei and Liu, Siqi and Pan, Hao and Tang, Xiaoli and Wang, Jian and Wang, Wei and Yu, Jun and Zhang, Bo and Zhang, Qingrun and Zhao, Hongbin and Zhou, Jun and Barry, Rachel and Blumenstiel, Brendan and Camargo, Amy and Defelice, Matthew and Faggart, Maura and Goyette, Mary and Gupta, Supriya and Moore, Jamie and Nguyen, Huy and Parkin, Melissa and Roy, Jessica and Stahl, Erich and Winchester, Ellen and Altshuler, David and Shen, Yan and Yao, Zhijian and Huang, Wei and Chu, Xun and He, Yungang and Jin, Li and Liu, Yangfan and Shen, Yayun and Sun, Weiwei and Wang, Haifeng and Wang, Yi and Wang, Ying and Xiong, Xiaoyan and Xu, Liang and Waye, Mary M.Y. and Tsui, Stephen K.W. and Xue, Hong and Wong, J. Tze Fei and Galver, Launa M. and Fan, Jian Bing and Murray, Sarah S. and Oliphant, Arnold R. and Chee, Mark S. and Montpetit, Alexandre and Chagnon, Fanny and Ferretti, Vincent and Leboeuf, Martin and Olivier, Jean Fran{\c{c}}ois and Phillips, Michael S. and Roumy, St{\'{e}}phanie and Sall{\'{e}}e, Cl{\'{e}}mentine and Verner, Andrei and Hudson, Thomas J. and Frazer, Kelly A. and Ballinger, Dennis G. and Cox, David R. and Hinds, David A. and Stuve, Laura L. and Kwok, Pui Yan and Cai, Dongmei and Koboldt, Daniel C. and Miller, Raymond D. and Pawlikowska, Ludmila and Taillon-Miller, Patricia and Xiao, Ming and Tsui, Lap Chee and Mak, William and Sham, Pak C. and Song, You Qiang and Tam, Paul K.H. and Nakamura, Yusuke and Kawaguchi, Takahisa and Kitamoto, Takuya and Morizono, Takashi and Nagashima, Atsushi and Ohnishi, Yozo and Sekine, Akihiro and Tanaka, Toshihiro and Deloukas, Panos and Bird, Christine P. and Delgado, Marcos and Dermitzakis, Emmanouil T. and Gwilliam, Rhian and Hunt, Sarah and Morrison, Jonathan and Powell, Don and Stranger, Barbara E. and Whittaker, Pamela and Bentley, David R. and {De Bakker}, Paul I.W. and Barrett, Jeff and Fry, Ben and Maller, Julian and McCarroll, Steve and Patterson, Nick and Pe'er, Itsik and Purcell, Shaun and Richter, Daniel J. and Sabeti, Pardis and Saxena, Richa and Schaffner, Stephen F. and Varilly, Patrick and Stein, Lincoln D. and Krishnan, Lalitha and Smith, Albert Vernon and Thorisson, Gudmundur A. and Chakravarti, Aravinda and Chen, Peter E. and Cutler, David J. and Kashuk, Carl S. and Lin, Shin and Abecasis, Gon{\c{c}}alo R. and Guan, Weihua and Munro, Heather M. and Qin, Zhaohui Steve and Thomas, Daryl J. and McVean, Gilean and Bottolo, Leonardo and Eyheramendy, Susana and Freeman, Colin and Marchini, Jonathan and Myers, Simon and Spencer, Chris and Stephens, Matthew and Donnelly, Peter and Cardon, Lon R. and Clarke, Geraldine and Evans, David M. and Morris, Andrew P. and Weir, Bruce S. and Tsunoda, Tatsuhiko and Mullikin, James C. and Sherry, Stephen T. and Feolo, Michael and Zhang, Houcan and Zeng, Changqing and Zhao, Hui and Matsuda, Ichiro and Fukushima, Yoshimitsu and Macer, Darryl R. and Suda, Eiko and Rotimi, Charles N. and Adebamowo, Clement A. and Ajayi, Ike and Aniagwu, Toyin and Marshall, Patricia A. and Nkwodimmah, Chibuzor and Royal, Charmaine D.M. and Leppert, Mark F. and Dixon, Missy and Peiffer, Andy and Qiu, Renzong and Kent, Alastair and Kato, Kazuto and Niikawa, Norio and Adewole, Isaac F. and Knoppers, Bartha M. and Foster, Morris W. and Clayton, Ellen Wright and Watkin, Jessica and Gibbs, Richard A. and Muzny, Donna and Nazareth, Lynne and Sodergren, Erica and Weinstock, George M. and Yakub, Imtiaz and Gabriel, Stacey B. and Onofrio, Robert C. and Ziaugra, Liuda and Birren, Bruce W. and Daly, Mark J. and Wilson, Richard K. and Fulton, Lucinda L. and Rogers, Jane and Burton, John and Carter, Nigel P. and Clee, Christopher M. and Griffiths, Mark and Jones, Matthew C. and McLay, Kirsten and Plumb, Robert W. and Ross, Mark T. and Sims, Sarah K. and Willey, David L. and Chen, Zhu and Han, Hua and Kang, Le and Godbout, Martin and Wallenburg, John C. and L'Archev{\^{e}}que, Paul and Bellemare, Guy and Saeki, Koji and Wang, Hongguang and An, Daochang and Fu, Hongbo and Li, Qing and Wang, Zhen and Wang, Renwu and Holden, Arthur L. and Brooks, Lisa D. and McEwen, Jean E. and Bird, Christianne R. and Guyer, Mark S. and Nailer, Patrick J. and Wang, Vivian Ota and Peterson, Jane L. and Shi, Michael and Spiegel, Jack and Sung, Lawrence M. and Witonsky, Jonathan and Zacharia, Lynn F. and Collins, Francis S. and Kennedy, Karen and Jamieson, Ruth and Stewart, John},
doi = {10.1038/nature04226},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Belmont et al. - 2005 - A haplotype map of the human genome.pdf:pdf},
issn = {1476-4687},
journal = {Nature 2005 437:7063},
keywords = {Humanities and Social Sciences,Science,multidisciplinary},
mendeley-groups = {Half-Time Thesis},
month = {oct},
number = {7063},
pages = {1299--1320},
publisher = {Nature Publishing Group},
title = {{A haplotype map of the human genome}},
url = {https://www.nature.com/articles/nature04226},
volume = {437},
year = {2005}
}
@article{J2015,
abstract = {Background: The number of Mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. This is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. However, some genetic variants may not be valid instrumental variables, in particular due to them having more than one proximal phenotypic correlate (pleiotropy). Methods: We view Mendelian randomization with multiple instruments as a meta-analysis, and show that bias caused by pleiotropy can be regarded as analogous to small study bias. Causal estimates using each instrument can be displayed visually by a funnel plot to assess potential asymmetry. Egger regression, a tool to detect small study bias in meta-analysis, can be adapted to test for bias from pleiotropy, and the slope coefficient from Egger regression provides an estimate of the causal effect. Under the assumption that the association of each genetic variant with the exposure is independent of the pleiotropic effect of the variant (not via the exposure), Egger's test gives a valid test of the null causal hypothesis and a consistent causal effect estimate even when all the genetic variants are invalid instrumental variables. Results: We illustrate the use of this approach by re-analysing two published Mendelian randomization studies of the causal effect of height on lung function, and the causal effect of blood pressure on coronary artery disease risk. The conservative nature of this approach is illustrated with these examples. Conclusions: An adaption of Egger regression (which we call MR-Egger) can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations. The approach provides a sensitivity analysis for the robustness of the findings from a Mendelian randomization investigation.},
author = {Bowden, Jack and Smith, George Davey and Burgess, Stephen},
doi = {10.1093/ije/dyv080},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/J, G, S - 2015 - Mendelian randomization with invalid instruments effect estimation and bias detection through Egger regression.pdf:pdf},
issn = {14643685},
journal = {International Journal of Epidemiology},
keywords = {Invalid instruments,MR-Egger test,Mendelian randomization,Meta-analysis,Pleiotropy,Small study bias},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {2},
pages = {512--525},
pmid = {26050253},
publisher = {Int J Epidemiol},
title = {{Mendelian randomization with invalid instruments: Effect estimation and bias detection through Egger regression}},
url = {https://pubmed.ncbi.nlm.nih.gov/26050253/},
volume = {44},
year = {2015}
}
@article{Burgess2019,
abstract = {This paper provides guidelines for performing Mendelian randomization investigations. It is aimed at practitioners seeking to undertake analyses and write up their findings, and at journal editors and reviewers seeking to assess Mendelian randomization manuscripts. The guidelines are divided into nine sections: motivation and scope, data sources, choice of genetic variants, variant harmonization, primary analysis, supplementary and sensitivity analyses (one section on robust statistical methods and one on other approaches), data presentation, and interpretation. These guidelines will be updated based on feedback from the community and advances in the field. Updates will be made periodically as needed, and at least every 18 months.},
author = {Burgess, Stephen and Smith, George Davey and Davies, Neil M. and Dudbridge, Frank and Gill, Dipender and Glymour, M. Maria and Hartwig, Fernando P. and Holmes, Michael V. and Minelli, Cosetta and Relton, Caroline L. and Theodoratou, Evropi},
doi = {10.12688/WELLCOMEOPENRES.15555.2},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Burgess et al. - 2019 - Guidelines for performing Mendelian randomization investigations.pdf:pdf},
journal = {Wellcome Open Research},
keywords = {Causal inference,Genetic epidemiology,Guidelines,Mendelian randomization},
mendeley-groups = {Half-Time Thesis},
pmid = {32760811},
publisher = {The Wellcome Trust},
title = {{Guidelines for performing Mendelian randomization investigations}},
url = {/pmc/articles/PMC7384151/ /pmc/articles/PMC7384151/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7384151/},
volume = {4},
year = {2019}
}
@article{Burgess2013,
abstract = {Genome-wide association studies, which typically report regression coefficients summarizing the associations of many genetic variants with various traits, are potentially a powerful source of data for Mendelian randomization investigations. We demonstrate how such coefficients from multiple variants can be combined in a Mendelian randomization analysis to estimate the causal effect of a risk factor on an outcome. The bias and efficiency of estimates based on summarized data are compared to those based on individual-level data in simulation studies. We investigate the impact of gene-gene interactions, linkage disequilibrium, and 'weak instruments' on these estimates. Both an inverse-variance weighted average of variant-specific associations and a likelihood-based approach for summarized data give similar estimates and precision to the two-stage least squares method for individual-level data, even when there are gene-gene interactions. However, these summarized data methods overstate precision when variants are in linkage disequilibrium. If the P-value in a linear regression of the risk factor for each variant is less than 1×10-5, then weak instrument bias will be small. We use these methods to estimate the causal association of low-density lipoprotein cholesterol (LDL-C) on coronary artery disease using published data on five genetic variants. A 30{\%} reduction in LDL-C is estimated to reduce coronary artery disease risk by 67{\%} (95{\%} CI: 54{\%} to 76{\%}). We conclude that Mendelian randomization investigations using summarized data from uncorrelated variants are similarly efficient to those using individual-level data, although the necessary assumptions cannot be so fully assessed. {\textcopyright} 2013 WILEY PERIODICALS, INC.},
author = {Burgess, Stephen and Butterworth, Adam and Thompson, Simon G},
doi = {10.1002/GEPI.21758},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Burgess, Butterworth, Thompson - 2013 - Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data.pdf:pdf},
journal = {Genetic Epidemiology},
keywords = {Causal inference,Genome-wide association study,Instrumental variables,Mendelian randomization,Weak instruments},
mendeley-groups = {Half-Time Thesis},
month = {nov},
number = {7},
pages = {658},
pmid = {24114802},
publisher = {Wiley-Blackwell},
title = {{Mendelian Randomization Analysis With Multiple Genetic Variants Using Summarized Data}},
url = {/pmc/articles/PMC4377079/ /pmc/articles/PMC4377079/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377079/},
volume = {37},
year = {2013}
}
@article{Bowden2016,
abstract = {Developments in genome-wide association studies and the increasing availability of summary genetic association data have made application of Mendelian randomization relatively straightforward. However, obtaining reliable results from a Mendelian randomization investigation remains problematic, as the conventional inverse-variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. We present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. This estimator is consistent even when up to 50{\%} of the information comes from invalid instrumental variables. In a simulation analysis, it is shown to have better finite-sample Type 1 error rates than the inverse-variance weighted method, and is complementary to the recently proposed MR-Egger (Mendelian randomization-Egger) regression method. In analyses of the causal effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol on coronary artery disease risk, the inverse-variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and MR-Egger regression methods suggest a null effect of high-density lipoprotein cholesterol that corresponds with the experimental evidence. Both median-based and MR-Egger regression methods should be considered as sensitivity analyses for Mendelian randomization investigations with multiple genetic variants.},
author = {Bowden, Jack and Smith, George Davey and Haycock, Philip C. and Burgess, Stephen},
doi = {10.1002/GEPI.21965},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Bowden et al. - 2016 - Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator.pdf:pdf},
journal = {Genetic Epidemiology},
keywords = {Egger regression,Instrumental variables,Mendelian randomization,Pleiotropy,Robust statistics},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {4},
pages = {304},
pmid = {27061298},
publisher = {Wiley-Blackwell},
title = {{Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator}},
url = {/pmc/articles/PMC4849733/ /pmc/articles/PMC4849733/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4849733/},
volume = {40},
year = {2016}
}
@article{Bowden2015,
abstract = {Background: The number of Mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. This is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. However, some genetic variants may not be valid instrumental variables, in particular due to them having more than one proximal phenotypic correlate (pleiotropy). Methods: We view Mendelian randomization with multiple instruments as a meta-analysis, and show that bias caused by pleiotropy can be regarded as analogous to small study bias. Causal estimates using each instrument can be displayed visually by a funnel plot to assess potential asymmetry. Egger regression, a tool to detect small study bias in meta-analysis, can be adapted to test for bias from pleiotropy, and the slope coefficient from Egger regression provides an estimate of the causal effect. Under the assumption that the association of each genetic variant with the exposure is independent of the pleiotropic effect of the variant (not via the exposure), Egger's test gives a valid test of the null causal hypothesis and a consistent causal effect estimate even when all the genetic variants are invalid instrumental variables. Results: We illustrate the use of this approach by re-analysing two published Mendelian randomization studies of the causal effect of height on lung function, and the causal effect of blood pressure on coronary artery disease risk. The conservative nature of this approach is illustrated with these examples. Conclusions: An adaption of Egger regression (which we call MR-Egger) can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations. The approach provides a sensitivity analysis for the robustness of the findings from a Mendelian randomization investigation.},
author = {Bowden, Jack and Smith, George Davey and Burgess, Stephen},
doi = {10.1093/IJE/DYV080},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Bowden, Smith, Burgess - 2015 - Mendelian randomization with invalid instruments effect estimation and bias detection through Egger regr.pdf:pdf},
journal = {International Journal of Epidemiology},
keywords = {Invalid instruments,MR-Egger test,Mendelian randomization,Meta-analysis,Pleiotropy,Small study bias},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {2},
pages = {512},
pmid = {26050253},
publisher = {Oxford University Press},
title = {{Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression}},
url = {/pmc/articles/PMC4469799/ /pmc/articles/PMC4469799/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4469799/},
volume = {44},
year = {2015}
}
@article{Bowden2017,
abstract = {We note that in some cases, bias from violations of the InSIDE assumption can be solved by finding a specific sub-sample for which the first stage effect does not exist (the effect of the instrument on the exposure is zero). In such a subsample, the direct effect of an SNP can be estimated and used to correct the causal effect estimate. A recent study in this journal shows that this strategy is able to produce unbiased estimates. 10},
author = {Bowden, Jack},
doi = {10.1093/ije/dyx192},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Bowden - 2017 - Misconceptions on the use of MR-Egger regression and the evaluation of the InSIDE assumption.pdf:pdf},
issn = {14643685},
journal = {International Journal of Epidemiology},
mendeley-groups = {Hormone GWAS,Half-Time Thesis},
month = {dec},
number = {6},
pages = {2097--2099},
pmid = {29025021},
publisher = {Oxford University Press},
title = {{Misconceptions on the use of MR-Egger regression and the evaluation of the InSIDE assumption}},
url = {https://academic.oup.com/ije/article/46/6/2097/4157383},
volume = {46},
year = {2017}
}
@article{Quenez2020,
abstract = {The detection of copy-number variations (CNVs) from NGS data is underexploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and whole-exome sequencing (WES) data, and compared CNV calls to quantitative multiplex PCR of short fluorescent fragments (QMSPF) or array comparative genomic hybridization (aCGH) results. From GP data of 3776 samples, we reached an overall positive predictive value (PPV) of 87.8{\%}. This dataset included a complete comprehensive QMPSF comparison of four genes (60 exons) on which we obtained 100{\%} sensitivity and specificity. From WES data, we first compared 137 samples with aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25{\%} sensitivity. The overall PPV was 86.4{\%} following the targeted confirmation of candidate CNVs from 1056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs with a resolution of single exons, allowing the detection of CNVs that were missed by aCGH. Overall, switching to an NGS-only approach should be cost-effective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at: 
                https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centered-workflow
                
              .},
author = {Quenez, Olivier and Cassinari, Kevin and Coutant, Sophie and Lecoquierre, Fran{\c{c}}ois and {Le Guennec}, Kilan and Rousseau, St{\'{e}}phane and Richard, Anne-Claire and Vasseur, St{\'{e}}phanie and Bouvignies, Emilie and Bou, Jacqueline and Lienard, Gwendoline and Manase, Sandrine and Fourneaux, Steeve and Drouot, Nathalie and Nguyen-Viet, Virginie and Vezain, Myriam and Chambon, Pascal and Joly-Helas, G{\'{e}}raldine and {Le Meur}, Nathalie and Castelain, Mathieu and Boland, Anne and Deleuze, Jean-Fran{\c{c}}ois and Tournier, Isabelle and Charbonnier, Fran{\c{c}}oise and Kasper, Edwige and Bougeard, Ga{\"{e}}lle and Frebourg, Thierry and Saugier-Veber, Pascale and Baert-Desurmont, St{\'{e}}phanie and Campion, Dominique and Rovelet-Lecrux, Anne and Nicolas, Ga{\"{e}}l},
doi = {10.1038/s41431-020-0672-2},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Quenez et al. - 2020 - Detection of copy-number variations from NGS data using read depth information a diagnostic performance evaluatio.pdf:pdf},
issn = {1476-5438},
journal = {European Journal of Human Genetics 2020 29:1},
keywords = {DNA sequencing,Data processing,Genetics research},
mendeley-groups = {Half-Time Thesis},
month = {jun},
number = {1},
pages = {99--109},
publisher = {Nature Publishing Group},
title = {{Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation}},
url = {https://www.nature.com/articles/s41431-020-0672-2},
volume = {29},
year = {2020}
}
@article{MacDonald1993,
abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}The Huntington's disease (HD) gene has been mapped in 4p16.3 but has eluded identification. We have used haplotype analysis of linkage disequilibrium to spotlight a small segment of 4p16.3 as the likely location of the defect. A new gene, 1715, isolated using cloned trapped exons from the target area contains a polymorphic trinucleotide repeat that is expanded and unstable on {\textless}i{\textgreater}HD{\textless}/i{\textgreater} chromosomes. A (CAG){\textless}sub{\textgreater}n{\textless}/sub{\textgreater} repeat longer than the normal range was observed on HD chromosomes from all 75 disease families examined, comprising a variety of ethnic backgrounds and 4p 16.3 haplotypes. The (CAG){\textless}sub{\textgreater}n{\textless}/sub{\textgreater} repeat appears to be located within the coding sequence of a predicted ≈348 kd protein that is widely expressed but unrelated to any known gene. Thus, the {\textless}i{\textgreater}HD{\textless}/i{\textgreater} mutation involves an unstable DNA segment, similar to those described in fragile X syndrome, spino-bulbar muscular atrophy, and myotonic dystrophy, acting in the context of a novel 4p16.3 gene to produce a dominant phenotype.{\textless}/p{\textgreater}},
author = {MacDonald, Marcy E. and Ambrose, Christine M. and Duyao, Mabel P. and Myers, Richard H. and Lin, Carol and Srinidhi, Lakshmi and Barnes, Glenn and Taylor, Sherryl A. and James, Marianne and Groot, Nicolet and MacFarlane, Heather and Jenkins, Barbara and Anderson, Mary Anne and Wexler, Nancy S. and Gusella, James F. and Bates, Gillian P. and Baxendale, Sarah and Hummerich, Holger and Kirby, Susan and North, Mike and Youngman, Sandra and Mott, Richard and Zehetner, Gunther and Sedlacek, Zdenek and Poustka, Annemarie and Frischauf, Anna-Maria and Lehrach, Hans and Buckler, Alan J. and Church, Deanna and Doucette-Stamm, Lynn and O'Donovan, Michael C. and Riba-Ramirez, Laura and Shah, Manish and Stanton, Vincent P. and Strobel, Scott A. and Draths, Karen M. and Wales, Jennifer L. and Dervan, Peter and Housman, David E. and Altherr, Michael and Shiang, Rita and Thompson, Leslie and Fielder, Thomas and Wasmuth, John J. and Tagle, Danilo and Valdes, John and Elmer, Lawrence and Allard, Marc and Castilla, Lucio and Swaroop, Manju and Blanchard, Kris and Collins, Francis S. and Snell, Russell and Holloway, Tracey and Gillespie, Kathleen and Datson, Nicole and Shaw, Duncan and Harper, Peter S.},
doi = {10.1016/0092-8674(93)90585-E},
issn = {0092-8674},
journal = {Cell},
mendeley-groups = {Half-Time Thesis},
month = {mar},
number = {6},
pages = {971--983},
pmid = {8458085},
publisher = {Elsevier},
title = {{A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes}},
url = {http://www.cell.com/article/009286749390585E/fulltext http://www.cell.com/article/009286749390585E/abstract https://www.cell.com/cell/abstract/0092-8674(93)90585-E},
volume = {72},
year = {1993}
}
@article{Verkerk1991,
abstract = {{\textless}h2{\textgreater}Abstract{\textless}/h2{\textgreater}{\textless}p{\textgreater}Fragile X syndrome Is the most frequent form of inherited mental retardation and Is associated with a fragile site at Xg27.3. We identified human YAC clones that span fragile X site-induced translocation breakpoints coincident with the fragile X site. A gene ({\textless}i{\textgreater}FMR-1{\textless}/i{\textgreater}) was identified within 8 four cosmid contig of YAC DNA that expresses a 4.8 kb message in human brain. Within a 7.4 kb EcoFII genomic fragment, containing {\textless}i{\textgreater}FMR-1{\textless}/i{\textgreater} exonic sequences distal to a CpG island previously shown to be hypermethylated in fragile X patients, is a fragile X site-induced breakpoint cluster region that exhibits length variation in fragile X chromosomes. This fragment contains a lengthy CGG repeat that is 250 by distal of the CpG island and maps within a {\textless}i{\textgreater}FMR-1{\textless}/i{\textgreater} axon. Localization of the brain-expressed {\textless}i{\textgreater}FMR-1{\textless}/i{\textgreater} gene to this EcoRl fragment suggests the involvement of this gene in the phenotypic expression of the fragile X syndrome.{\textless}/p{\textgreater}},
author = {Verkerk, Annemiske J.M.H. and Pieretti, Maura and Sutcliffe, James S. and Fu, Ying-Hui and Kuhl, Derek P.A. and Pizzuti, Antonio and Reiner, Orly and Richards, Stephen and Victoria, Maureen F. and Zhang, Fuping and Eussen, Bert E. and van Ommen, Gert-Jan B. and Blonden, Lau A.J. and Riggins, Gregory J. and Chastain, Jane L. and Kunst, Catherine B. and Galjaard, Hans and Caskey, C. Thomas and Nelson, David L. and Oostra, Ben A. and Warren, Stephen T.},
doi = {10.1016/0092-8674(91)90397-H},
issn = {0092-8674},
journal = {Cell},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {5},
pages = {905--914},
pmid = {1710175},
publisher = {Elsevier},
title = {{Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome}},
url = {http://www.cell.com/article/009286749190397H/fulltext http://www.cell.com/article/009286749190397H/abstract https://www.cell.com/cell/abstract/0092-8674(91)90397-H},
volume = {65},
year = {1991}
}
@article{Travison2014,
abstract = {Objective Circulating testosterone, oestradiol and oestrone concentrations vary considerably between men. Although a substantial proportion of this variation may be attributed to morbidity and behavioural factors, these cannot account for its entirety, suggesting genetic inheritance as a potential additional determinant. The analysis described here was intended to estimate the heritability of male circulating total testosterone (TT), calculated free testosterone (cFT), oestrone (E1), oestradiol (E2) and sex hormone binding globulin (SHBG), along with the genetic correlation between these factors. Design Cross-sectional, observational analysis of data from male members of the Offspring and Generation 3 cohorts of the Framingham Heart Study. Data were collected in the years 1998-2005. Participants A total of 3367 community-dwelling men contributed to the analysis, including 1066 father/son and 1284 brother pairs among other family relationships. Measurements Levels of serum sex steroids (TT, E1 and E2) were measured by liquid chromatography-tandem mass spectrometry, SHBG by immunofluorometric assay and cFT by mass action equation. Heritability was obtained using variance components analysis with adjustment for covariates including age, diabetes mellitus, body mass index and smoking status. Results Age-adjusted heritability estimates were 0{\textperiodcentered}19, 0{\textperiodcentered}40, 0{\textperiodcentered}40, 0{\textperiodcentered}30 and 0{\textperiodcentered}41 for cFT, TT, E1, E2 and SHBG, respectively. Adjustment for covariates did not substantially attenuate these estimates; SHBG-adjusted TT results were similar to those obtained for cFT. Genetic correlation coefficients ($\rho$G) indicated substantial genetic association between TT and cFT ($\rho$G = 0{\textperiodcentered}68), between TT and SHBG (pG = 0{\textperiodcentered}87), between E1 and E2 ($\rho$G = 0{\textperiodcentered}46) and between TT and E2 ($\rho$G = 0{\textperiodcentered}48). Conclusion Circulating testosterone, oestradiol and oestrone concentrations exhibit substantial heritability in adult men. Significant genetic association between testosterone and oestrogen levels suggests shared genetic pathways. {\textcopyright} 2013 John Wiley {\&} Sons Ltd.},
author = {Travison, TG and Zhuang, WV and Lunetta, KL and Karasik, D and Bhasin, S and Kiel, DP and Coviello, AD and Murabito, JM},
doi = {10.1111/CEN.12260},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Travison et al. - 2014 - The Heritability of Circulating Testosterone, Estradiol, Estrone, and SHBG Concentrations in Men The Framingham.pdf:pdf},
journal = {Clinical endocrinology},
keywords = {Estradiol,Estrone,Heritability,Key Terms Testosterone,Sex Hormone-Binding Globulin},
mendeley-groups = {Half-Time Thesis},
month = {feb},
number = {2},
pages = {277--282},
pmid = {23746309},
publisher = {NIH Public Access},
title = {{The Heritability of Circulating Testosterone, Estradiol, Estrone, and SHBG Concentrations in Men: The Framingham Heart Study}},
url = {/pmc/articles/PMC3825765/ /pmc/articles/PMC3825765/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3825765/},
volume = {80},
year = {2014}
}
@article{DeCoster2021,
abstract = {Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale. Long-read sequencing at the population scale presents specific challenges but is becoming increasingly accessible. In this Review, Sedlazeck and colleagues discuss the major platforms and analytical tools, considerations in project design and challenges in scaling long-read sequencing to populations.},
author = {{De Coster}, Wouter and Weissensteiner, Matthias H. and Sedlazeck, Fritz J.},
doi = {10.1038/s41576-021-00367-3},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/De Coster, Weissensteiner, Sedlazeck - 2021 - Towards population-scale long-read sequencing.pdf:pdf},
issn = {1471-0064},
journal = {Nature Reviews Genetics 2021 22:9},
keywords = {Genome informatics,Population genetics,Sequencing},
mendeley-groups = {Half-Time Thesis},
month = {may},
number = {9},
pages = {572--587},
publisher = {Nature Publishing Group},
title = {{Towards population-scale long-read sequencing}},
url = {https://www.nature.com/articles/s41576-021-00367-3},
volume = {22},
year = {2021}
}
@article{Porubsky2021,
abstract = {Human genomes are typically assembled as consensus sequences that lack information on parental haplotypes. Here we describe a reference-free workflow for diploid de novo genome assembly that combines the chromosome-wide phasing and scaffolding capabilities of single-cell strand sequencing1,2 with continuous long-read or high-fidelity3 sequencing data. Employing this strategy, we produced a completely phased de novo genome assembly for each haplotype of an individual of Puerto Rican descent (HG00733) in the absence of parental data. The assemblies are accurate (quality value {\textgreater} 40) and highly contiguous (contig N50 {\textgreater} 23 Mbp) with low switch error rates (0.17{\%}), providing fully phased single-nucleotide variants, indels and structural variants. A comparison of Oxford Nanopore Technologies and Pacific Biosciences phased assemblies identified 154 regions that are preferential sites of contig breaks, irrespective of sequencing technology or phasing algorithms.},
author = {Porubsky, David and Ebert, Peter and Audano, Peter A. and Vollger, Mitchell R. and Harvey, William T. and Marijon, Pierre and Ebler, Jana and Munson, Katherine M. and Sorensen, Melanie and Sulovari, Arvis and Haukness, Marina and Ghareghani, Maryam and Consortium, Human Genome Structural Variation and Lansdorp, Peter M. and Paten, Benedict and Devine, Scott E. and Sanders, Ashley D. and Lee, Charles and Chaisson, Mark J. P. and Korbel, Jan O. and Eichler, Evan E. and Marschall, Tobias},
doi = {10.1038/S41587-020-0719-5},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Porubsky et al. - 2021 - Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.pdf:pdf},
journal = {Nature Biotechnology},
mendeley-groups = {Half-Time Thesis},
number = {3},
pages = {302},
pmid = {33288906},
publisher = {Nature Publishing Group},
title = {{Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads}},
url = {/pmc/articles/PMC7954704/ /pmc/articles/PMC7954704/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954704/},
volume = {39},
year = {2021}
}
@article{Logsdon2021,
abstract = {The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric $\alpha$-satellite array, a 644-kb copy number polymorphism in the $\beta$-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric $\alpha$-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order $\alpha$-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order $\alpha$-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric $\alpha$-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence. The complete assembly of human chromosome 8 resolves previous gaps and reveals hidden complex forms of genetic variation, enabling functional and evolutionary characterization of primate centromeres.},
author = {Logsdon, Glennis A. and Vollger, Mitchell R. and Hsieh, PingHsun and Mao, Yafei and Liskovykh, Mikhail A. and Koren, Sergey and Nurk, Sergey and Mercuri, Ludovica and Dishuck, Philip C. and Rhie, Arang and de Lima, Leonardo G. and Dvorkina, Tatiana and Porubsky, David and Harvey, William T. and Mikheenko, Alla and Bzikadze, Andrey V. and Kremitzki, Milinn and Graves-Lindsay, Tina A. and Jain, Chirag and Hoekzema, Kendra and Murali, Shwetha C. and Munson, Katherine M. and Baker, Carl and Sorensen, Melanie and Lewis, Alexandra M. and Surti, Urvashi and Gerton, Jennifer L. and Larionov, Vladimir and Ventura, Mario and Miga, Karen H. and Phillippy, Adam M. and Eichler, Evan E.},
doi = {10.1038/s41586-021-03420-7},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Logsdon et al. - 2021 - The structure, function and evolution of a complete human chromosome 8.pdf:pdf},
issn = {1476-4687},
journal = {Nature 2021 593:7857},
keywords = {Centromeres,Evolutionary genetics,Genome evolution,Genomics},
mendeley-groups = {Half-Time Thesis},
month = {apr},
number = {7857},
pages = {101--107},
publisher = {Nature Publishing Group},
title = {{The structure, function and evolution of a complete human chromosome 8}},
url = {https://www.nature.com/articles/s41586-021-03420-7},
volume = {593},
year = {2021}
}
@article{Lander2001,
abstract = {The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.},
author = {Lander, Eric S. and Linton, Lauren M. and Birren, Bruce and Nusbaum, Chad and Zody, Michael C. and Baldwin, Jennifer and Devon, Keri and Dewar, Ken and Doyle, Michael and Fitzhugh, William and Funke, Roel and Gage, Diane and Harris, Katrina and Heaford, Andrew and Howland, John and Kann, Lisa and Lehoczky, Jessica and Levine, Rosie and McEwan, Paul and McKernan, Kevin and Meldrim, James and Mesirov, Jill P. and Miranda, Cher and Morris, William and Naylor, Jerome and Raymond, Christina and Rosetti, Mark and Santos, Ralph and Sheridan, Andrew and Sougnez, Carrie and Stange-Thomann, Nicole and Stojanovic, Nikola and Subramanian, Aravind and Wyman, Dudley and Rogers, Jane and Sulston, John and Ainscough, Rachael and Beck, Stephan and Bentley, David and Burton, John and Clee, Christopher and Carter, Nigel and Coulson, Alan and Deadman, Rebecca and Deloukas, Panos and Dunham, Andrew and Dunham, Ian and Durbin, Richard and French, Lisa and Grafham, Darren and Gregory, Simon and Hubbard, Tim and Humphray, Sean and Hunt, Adrienne and Jones, Matthew and Lloyd, Christine and McMurray, Amanda and Matthews, Lucy and Mercer, Simon and Milne, Sarah and Mullikin, James C. and Mungall, Andrew and Plumb, Robert and Ross, Mark and Shownkeen, Ratna and Sims, Sarah and Waterston, Robert H. and Wilson, Richard K. and Hillier, Ladeana W. and McPherson, John D. and Marra, Marco A. and Mardis, Elaine R. and Fulton, Lucinda A. and Chinwalla, Asif T. and Pepin, Kymberlie H. and Gish, Warren R. and Chissoe, Stephanie L. and Wendl, Michael C. and Delehaunty, Kim D. and Miner, Tracie L. and Delehaunty, Andrew and Kramer, Jason B. and Cook, Lisa L. and Fulton, Robert S. and Johnson, Douglas L. and Minx, Patrick J. and Clifton, Sandra W. and Hawkins, Trevor and Branscomb, Elbert and Predki, Paul and Richardson, Paul and Wenning, Sarah and Slezak, Tom and Doggett, Norman and Cheng, Jan Fang and Olsen, Anne and Lucas, Susan and Elkin, Christopher and Uberbacher, Edward and Frazier, Marvin and Gibbs, Richard A. and Muzny, Donna M. and Scherer, Steven E. and Bouck, John B. and Sodergren, Erica J. and Worley, Kim C. and Rives, Catherine M. and Gorrell, James H. and Metzker, Michael L. and Naylor, Susan L. and Kucherlapati, Raju S. and Nelson, David L. and Weinstock, George M. and Sakaki, Yoshiyuki and Fujiyama, Asao and Hattori, Masahira and Yada, Tetsushi and Toyoda, Atsushi and Itoh, Takehiko and Kawagoe, Chiharu and Watanabe, Hidemi and Totoki, Yasushi and Taylor, Todd and Weissenbach, Jean and Heilig, Roland and Saurin, William and Artiguenave, Francois and Brottier, Philippe and Bruls, Thomas and Pelletier, Eric and Robert, Catherine and Wincker, Patrick and Rosenthal, Andr{\'{e}} and Platzer, Matthias and Nyakatura, Gerald and Taudien, Stefan and Rump, Andreas and Smith, Douglas R. and Doucette-Stamm, Lynn and Rubenfield, Marc and Weinstock, Keith and Hong, Mei Lee and Dubois, Joann and Yang, Huanming and Yu, Jun and Wang, Jian and Huang, Guyang and Gu, Jun and Hood, Leroy and Rowen, Lee and Madan, Anup and Qin, Shizen and Davis, Ronald W. and Federspiel, Nancy A. and Abola, A. Pia and Proctor, Michael J. and Roe, Bruce A. and Chen, Feng and Pan, Huaqin and Ramser, Juliane and Lehrach, Hans and Reinhardt, Richard and McCombie, W. Richard and {De La Bastide}, Melissa and Dedhia, Neilay and Bl{\"{o}}cker, Helmut and Hornischer, Klaus and Nordsiek, Gabriele and Agarwala, Richa and Aravind, L. and Bailey, Jeffrey A. and Bateman, Alex and Batzoglou, Serafim and Birney, Ewan and Bork, Peer and Brown, Daniel G. and Burge, Christopher B. and Cerutti, Lorenzo and Chen, Hsiu Chuan and Church, Deanna and Clamp, Michele and Copley, Richard R. and Doerks, Tobias and Eddy, Sean R. and Eichler, Evan E. and Furey, Terrence S. and Galagan, James and Gilbert, James G.R. and Harmon, Cyrus and Hayashizaki, Yoshihide and Haussler, David and Hermjakob, Henning and Hokamp, Karsten and Jang, Wonhee and Johnson, L. Steven and Jones, Thomas A. and Kasif, Simon and Kaspryzk, Arek and Kennedy, Scot and Kent, W. James and Kitts, Paul and Koonin, Eugene V. and Korf, Ian and Kulp, David and Lancet, Doron and Lowe, Todd M. and McLysaght, Aoife and Mikkelsen, Tarjei and Moran, John V. and Mulder, Nicola and Pollara, Victor J. and Ponting, Chris P. and Schuler, Greg and Schultz, J{\"{o}}rg and Slater, Guy and Smit, Arian F.A. and Stupka, Elia and Szustakowki, Joseph and Thierry-Mieg, Danielle and Thierry-Mieg, Jean and Wagner, Lukas and Wallis, John and Wheeler, Raymond and Williams, Alan and Wolf, Yuri I. and Wolfe, Kenneth H. and Yang, Shiaw Pyng and Yeh, Ru Fang and Collins, Francis and Guyer, Mark S. and Peterson, Jane and Felsenfeld, Adam and Wetterstrand, Kris A. and Myers, Richard M. and Schmutz, Jeremy and Dickson, Mark and Grimwood, Jane and Cox, David R. and Olson, Maynard V. and Kaul, Rajinder and Raymond, Christopher and Shimizu, Nobuyoshi and Kawasaki, Kazuhiko and Minoshima, Shinsei and Evans, Glen A. and Athanasiou, Maria and Schultz, Roger and Patrinos, Aristides and Morgan, Michael J.},
doi = {10.1038/35057062},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Lander et al. - 2001 - Initial sequencing and analysis of the human genome.pdf:pdf},
issn = {1476-4687},
journal = {Nature 2001 409:6822},
keywords = {Humanities and Social Sciences,Science,multidisciplinary},
mendeley-groups = {Half-Time Thesis},
month = {feb},
number = {6822},
pages = {860--921},
publisher = {Nature Publishing Group},
title = {{Initial sequencing and analysis of the human genome}},
url = {https://www.nature.com/articles/35057062},
volume = {409},
year = {2001}
}
@article{Aird2011,
abstract = {Despite the ever-increasing output of Illumina sequencing data, loci with extreme base compositions are often under-represented or absent. To evaluate sources of base-composition bias, we traced genomic sequences ranging from 6{\%} to 90{\%} GC through the process by quantitative PCR. We identified PCR during library preparation as a principal source of bias and optimized the conditions. Our improved protocol significantly reduces amplification bias and minimizes the previously severe effects of PCR instrument and temperature ramp rate.},
author = {Aird, Daniel and Ross, Michael G and Chen, Wei-Sheng and Danielsson, Maxwell and Fennell, Timothy and Russ, Carsten and Jaffe, David B and Nusbaum, Chad and Gnirke, Andreas},
doi = {10.1186/GB-2011-12-2-R18},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Aird et al. - 2011 - Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.pdf:pdf},
issn = {1474-760X},
journal = {Genome Biology 2011 12:2},
keywords = {Animal Genetics and Genomics,Bioinformatics,Evolutionary Biology,Human Genetics,Microbial Genetics and Genomics,Plant Genetics and Genomics},
mendeley-groups = {Half-Time Thesis},
month = {feb},
number = {2},
pages = {1--14},
publisher = {BioMed Central},
title = {{Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries}},
url = {https://genomebiology.biomedcentral.com/articles/10.1186/gb-2011-12-2-r18},
volume = {12},
year = {2011}
}
@article{Payne2019,
abstract = {Motivation: The Oxford Nanopore Technologies (ONT) MinION is used for sequencing a wide variety of sample types with diverse methods of sample extraction. Nanopore sequencers output FAST5 files containing signal data subsequently base called to FASTQ format. Optionally, ONT devices can collect data from all sequencing channels simultaneously in a bulk FAST5 file enabling inspection of signal in any channel at any point. We sought to visualize this signal to inspect challenging or difficult to sequence samples. Results: The BulkVis tool can load a bulk FAST5 file and overlays MinKNOW (the software that controls ONT sequencers) classifications on the signal trace and can show mappings to a reference. Users can navigate to a channel and time or, given a FASTQ header from a read, jump to its specific position. BulkVis can export regions as Nanopore base caller compatible reads. Using BulkVis, we find long reads can be incorrectly divided by MinKNOW resulting in single DNA molecules being split into two or more reads. The longest seen to date is 2 272 580 bases in length and reported in eleven consecutive reads. We provide helper scripts that identify and reconstruct split reads given a sequencing summary file and alignment to a reference. We note that incorrect read splitting appears to vary according to input sample type and is more common in'ultra-long' read preparations.},
author = {Payne, Alexander and Holmes, Nadine and Rakyan, Vardhman and Loose, Matthew},
doi = {10.1093/BIOINFORMATICS/BTY841},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Payne et al. - 2019 - BulkVis a graphical viewer for Oxford nanopore bulk FAST5 files.pdf:pdf},
journal = {Bioinformatics},
mendeley-groups = {Half-Time Thesis},
month = {jul},
number = {13},
pages = {2193},
pmid = {30462145},
publisher = {Oxford University Press},
title = {{BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files}},
url = {/pmc/articles/PMC6596899/ /pmc/articles/PMC6596899/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6596899/},
volume = {35},
year = {2019}
}
@article{Wenger2019,
abstract = {The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8{\%}) long high-fidelity (HiFi) reads with an average length of 13.5 kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91{\%} for single-nucleotide variants (SNVs), 95.98{\%} for insertions and deletions {\textless}50 bp (indels) and 95.99{\%} for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the ‘genome in a bottle' (GIAB) benchmark set. Nearly all (99.64{\%}) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of {\textgreater}15 megabases (Mb) and concordance of 99.997{\%}, substantially outperforming assembly with less-accurate long reads.},
author = {Wenger, Aaron M. and Peluso, Paul and Rowell, William J. and Chang, Pi-Chuan and Hall, Richard J. and Concepcion, Gregory T. and Ebler, Jana and Fungtammasan, Arkarachai and Kolesnikov, Alexey and Olson, Nathan D. and T{\"{o}}pfer, Armin and Alonge, Michael and Mahmoud, Medhat and Qian, Yufeng and Chin, Chen-Shan and Phillippy, Adam M. and Schatz, Michael C. and Myers, Gene and DePristo, Mark A. and Ruan, Jue and Marschall, Tobias and Sedlazeck, Fritz J. and Zook, Justin M. and Li, Heng and Koren, Sergey and Carroll, Andrew and Rank, David R. and Hunkapiller, Michael W.},
doi = {10.1038/S41587-019-0217-9},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Wenger et al. - 2019 - Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.pdf:pdf},
journal = {Nature biotechnology},
mendeley-groups = {Half-Time Thesis},
month = {oct},
number = {10},
pages = {1155},
pmid = {31406327},
publisher = {NIH Public Access},
title = {{Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome}},
url = {/pmc/articles/PMC6776680/ /pmc/articles/PMC6776680/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776680/},
volume = {37},
year = {2019}
}
@article{Hoijer2018,
abstract = {Amplification of DNA is required as a mandatory step during library preparation in most targeted sequencing protocols. This can be a critical limitation when targeting regions that are highly repetitive or with extreme guanine–cytosine (GC) content, including repeat expansions associated with human disease. Here, we used an amplification-free protocol for targeted enrichment utilizing the CRISPR/Cas9 system (No-Amp Targeted sequencing) in combination with single molecule, real-time (SMRT) sequencing for studying repeat elements in the huntingtin (HTT) gene, where an expanded CAG repeat is causative for Huntington disease. We also developed a robust data analysis pipeline for repeat element analysis that is independent of alignment of reads to a reference genome. The method was applied to 11 diagnostic blood samples, and for all 22 alleles the resulting CAG repeat count agreed with previous results based on fragment analysis. The amplification-free protocol also allowed for studying somatic variability of repeat elements in our samples, without the interference of PCR stutter. In summary, with No-Amp Targeted sequencing in combination with our analysis pipeline, we could accurately study repeat elements that are difficult to investigate using PCR-based methods.},
author = {H{\"{o}}ijer, Ida and Tsai, Yu-Chih and Clark, Tyson A. and Kotturi, Paul and Dahl, Niklas and Stattin, Eva-Lena and Bondeson, Marie-Louise and Feuk, Lars and Gyllensten, Ulf and Ameur, Adam},
doi = {10.1002/HUMU.23580},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/H{\"{o}}ijer et al. - 2018 - Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing.pdf:pdf},
issn = {1098-1004},
journal = {Human Mutation},
keywords = {Amp Targeted sequencing,HTT,Huntington disease,No,SMRT sequencing,amplification,free sequencing,repeat expansion,somatic mosaicism,targeted enrichment,targeted sequencing},
mendeley-groups = {Half-Time Thesis},
month = {sep},
number = {9},
pages = {1262--1272},
publisher = {John Wiley {\&} Sons, Ltd},
title = {{Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing}},
url = {https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23580 https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23580 https://onlinelibrary.wiley.com/doi/10.1002/humu.23580},
volume = {39},
year = {2018}
}
@article{Rang2018,
abstract = {Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this new way of sequencing and has used it successfully for a variety of research applications. A major limitation of nanopore sequencing is its high error rate, which despite recent improvements to the nanopore chemistry and computational tools still ranges between 5{\%} and 15{\%}. Here, we review computational approaches determining the nanopore sequencing error rate. Furthermore, we outline strategies for translation of raw sequencing data into base calls for detection of base modifications and for obtaining consensus sequences.},
author = {Rang, Franka J. and Kloosterman, Wigard P. and de Ridder, Jeroen},
doi = {10.1186/S13059-018-1462-9},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Rang, Kloosterman, Ridder - 2018 - From squiggle to basepair computational approaches for improving nanopore sequencing read accuracy.pdf:pdf},
journal = {Genome Biology},
mendeley-groups = {Half-Time Thesis},
month = {jul},
number = {1},
pmid = {30005597},
publisher = {BioMed Central},
title = {{From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy}},
url = {/pmc/articles/PMC6045860/ /pmc/articles/PMC6045860/?report=abstract https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6045860/},
volume = {19},
year = {2018}
}
@article{Chen2016a,
abstract = {We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios.},
author = {Chen, Xiaoyu and Schulz-Trieglaff, Ole and Shaw, Richard and Barnes, Bret and Schlesinger, Felix and K{\"{a}}llberg, Morten and Cox, Anthony J. and Kruglyak, Semyon and Saunders, Christopher T.},
doi = {10.1093/bioinformatics/btv710},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Chen et al. - 2016 - Manta rapid detection of structural variants and indels for germline and cancer sequencing applications.pdf:pdf},
issn = {14602059},
journal = {Bioinformatics},
mendeley-groups = {CNV-Project/Zhiweis references,CNV-Project/CNV Calling,Half-Time Thesis},
month = {apr},
number = {8},
pages = {1220--1222},
pmid = {26647377},
publisher = {Oxford University Press (OUP)},
title = {{Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications}},
url = {http://dx.doi.org/10.1093/bioinformatics/btv710 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btv710},
volume = {32},
year = {2016}
}
@article{Heller2019a,
abstract = {Motivation: Structural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single-molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long-read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities. Results: We present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long-read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from Pacific Biosciences and Nanopore sequencing machines.},
author = {Heller, David and Vingron, Martin},
doi = {10.1093/bioinformatics/btz041},
editor = {Birol, Inanc},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Heller, Vingron - 2019 - SVIM structural variant identification using mapped long reads.pdf:pdf},
issn = {14602059},
journal = {Bioinformatics},
mendeley-groups = {CNV-Project/CNV Calling,Half-Time Thesis},
month = {sep},
number = {17},
pages = {2907--2915},
pmid = {30668829},
publisher = {Oxford University Press},
title = {{SVIM: Structural variant identification using mapped long reads}},
url = {https://academic.oup.com/bioinformatics/article/35/17/2907/5298305},
volume = {35},
year = {2019}
}
@article{Sedlazeck2018a,
abstract = {Structural variations are the greatest source of genetic variation, but they remain poorly understood because of technological limitations. Single-molecule long-read sequencing has the potential to dramatically advance the field, although high error rates are a challenge with existing methods. Addressing this need, we introduce open-source methods for long-read alignment (NGMLR; https://github.com/philres/ngmlr) and structural variant identification (Sniffles; https://github.com/fritzsedlazeck/Sniffles) that provide unprecedented sensitivity and precision for variant detection, even in repeat-rich regions and for complex nested events that can have substantial effects on human health. In several long-read datasets, including healthy and cancerous human genomes, we discovered thousands of novel variants and categorized systematic errors in short-read approaches. NGMLR and Sniffles can automatically filter false events and operate on low-coverage data, thereby reducing the high costs that have hindered the application of long reads in clinical and research settings.},
annote = {Simulation},
author = {Sedlazeck, Fritz J. and Rescheneder, Philipp and Smolka, Moritz and Fang, Han and Nattestad, Maria and {Von Haeseler}, Arndt and Schatz, Michael C.},
doi = {10.1038/s41592-018-0001-7},
file = {:Users/dansc755/Library/Application Support/Mendeley Desktop/Downloaded/Sedlazeck et al. - 2018 - Accurate detection of complex structural variations using single-molecule sequencing.pdf:pdf},
issn = {15487105},
journal = {Nature Methods},
keywords = {Genome informatics,Software,Structural variation},
mendeley-groups = {CNV-Project/CNV Calling,Half-Time Thesis},
month = {jun},
number = {6},
pages = {461--468},
pmid = {29713083},
publisher = {Nature Publishing Group},
title = {{Accurate detection of complex structural variations using single-molecule sequencing}},
url = {https://doi.org/10.1038/s41592-018-0001-7},
volume = {15},
year = {2018}
}