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1. DMPP-4: Candidate sub-Neptune mass planets orbiting a naked-eye star

Author: Barnes, J. R., Standing, M. R., Haswell, C. A., Staab, D., Doherty, J. P. J., Waller-Bridge, M., Fossati, L., Soto, M., Anglada-Escudé, G., Llama, J., McCune, C., Lewis, F. W., Barnes, J. R., Standing, M. R., Haswell, C. A., Staab, D., Doherty, J. P. J., Waller-Bridge, M., Fossati, L., Soto, M., Anglada-Escudé, G., Llama, J., McCune, C., and Lewis, F. W.
Abstract: We present radial velocity measurements of the very bright ($V\sim5.7$) nearby F star, DMPP-4 (HD 184960). The anomalously low Ca II H&K emission suggests mass loss from planets orbiting a low activity host star. Periodic radial velocity variability with $\sim 10$ ms$^{-1}$ amplitude is found to persist over a $>4$ year timescale. Although the non-simultaneous photometric variability in four TESS sectors supports the view of an inactive star, we identify periodic photometric signals and also find spectroscopic evidence for stellar activity. We used a posterior sampling algorithm that includes the number of Keplerian signals, $N_\textrm{p}$, as a free parameter to test and compare (1) purely Keplerian models (2) a Keplerian model with linear activity correlation and (3) Keplerian models with Gaussian processes. A preferred model, with one Keplerian and quasi-periodic Gaussian process indicates a planet with a period of $P_\textrm{b} = 3.4982^{+0.0015}_{-0.0027}$ d and corresponding minimum mass of $m_\textrm{b}\,\textrm{sin}\,i = 12.2^{+1.8}_{-1.9}$ M$_\oplus$. Without further high time resolution observations over a longer timescale, we cannot definitively rule out the purely Keplerian model with 2 candidates planets with $P_\textrm{b} = 2.4570^{+0.0026}_{-0.0462}$ d, minimum mass $m_\textrm{b}\,\textrm{sin}\,i = 8.0^{+1.1}_{-1.5}$ M$_\oplus$ and $P_\textrm{c} = 5.4196^{+0.6766}_{-0.0030}$ d and corresponding minimum mass of $m_\textrm{b}\,\textrm{sin}\,i = 12.2^{+1.4}_{-1.6}$ M$_\oplus$. The candidate planets lie in the region below the lower-envelope of the Neptune Desert. Continued mass loss may originate from the highly irradiated planets or from an as yet undetected body in the system., Comment: 19 pages, 11 figures. Accepted for publication in MNRAS
Published: 2023
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2. Preclinical small molecule WEHI-7326 overcomes drug resistance and elicits response in patient-derived xenograft models of human treatment-refractory tumors

Author: Grohmann, C, Walker, F, Devlin, M, Luo, MX, Chüeh, AC, Doherty, J, Vaillant, F, Ho, GY, Wakefield, MJ, Weeden, CE, Kamili, A, Murray, J, Po’uha, ST, Weinstock, J, Kane, SR, Faux, MC, Broekhuizen, E, Zheng, Y, Shield-Artin, K, Kershaw, NJ, Tan, CW, Witchard, HM, Ebert, G, Charman, SA, Street, I, Kavallaris, M, Haber, M, Fletcher, JI, Asselin-Labat, ML, Scott, CL, Visvader, JE, Lindeman, GJ, Watson, KG, Burgess, AW, Lessene, G, Grohmann, C, Walker, F, Devlin, M, Luo, MX, Chüeh, AC, Doherty, J, Vaillant, F, Ho, GY, Wakefield, MJ, Weeden, CE, Kamili, A, Murray, J, Po’uha, ST, Weinstock, J, Kane, SR, Faux, MC, Broekhuizen, E, Zheng, Y, Shield-Artin, K, Kershaw, NJ, Tan, CW, Witchard, HM, Ebert, G, Charman, SA, Street, I, Kavallaris, M, Haber, M, Fletcher, JI, Asselin-Labat, ML, Scott, CL, Visvader, JE, Lindeman, GJ, Watson, KG, Burgess, AW, and Lessene, G
Abstract: Targeting cell division by chemotherapy is a highly effective strategy to treat a wide range of cancers. However, there are limitations of many standard-of-care chemotherapies: undesirable drug toxicity, side-effects, resistance and high cost. New small molecules which kill a wide range of cancer subtypes, with good therapeutic window in vivo, have the potential to complement the current arsenal of anti-cancer agents and deliver improved safety profiles for cancer patients. We describe results with a new anti-cancer small molecule, WEHI-7326, which causes cell cycle arrest in G2/M, cell death in vitro, and displays efficacious anti-tumor activity in vivo. WEHI-7326 induces cell death in a broad range of cancer cell lines, including taxane-resistant cells, and inhibits growth of human colon, brain, lung, prostate and breast tumors in mice xenografts. Importantly, the compound elicits tumor responses as a single agent in patient-derived xenografts of clinically aggressive, treatment-refractory neuroblastoma, breast, lung and ovarian cancer. In combination with standard-of-care, WEHI-7326 induces a remarkable complete response in a mouse model of high-risk neuroblastoma. WEHI-7326 is mechanistically distinct from known microtubule-targeting agents and blocks cells early in mitosis to inhibit cell division, ultimately leading to apoptotic cell death. The compound is simple to produce and possesses favorable pharmacokinetic and toxicity profiles in rodents. It represents a novel class of anti-cancer therapeutics with excellent potential for further development due to the ease of synthesis, simple formulation, moderate side effects and potent in vivo activity. WEHI-7326 has the potential to complement current frontline anti-cancer drugs and to overcome drug resistance in a wide range of cancers.
Published: 2021

3. Population-based targeted sequencing of 54 candidate genes identifies PALB2 as a susceptibility gene for high-grade serous ovarian cancer

Author: Song, H, Dicks, EM, Tyrer, J, Intermaggio, M, Chenevix-Trench, G, Bowtell, DD, Traficante, N, Group, A, Brenton, J, Goranova, T, Hosking, K, Piskorz, A, Van Oudenhove, E, Doherty, J, Harris, HR, Rossing, MA, Duerst, M, Dork, T, Bogdanova, NV, Modugno, F, Moysich, K, Odunsi, K, Ness, R, Karlan, BY, Lester, J, Jensen, A, Krüger Kjaer, S, Høgdall, E, Campbell, IG, Lázaro, C, Pujara, MA, Cunningham, J, Vierkant, R, Winham, SJ, Hildebrandt, M, Huff, C, Li, D, Wu, X, Yu, Y, Permuth, JB, Levine, DA, Schildkraut, JM, Riggan, MJ, Berchuck, A, Webb, PM, Group, OS, Cybulski, C, Gronwald, J, Jakubowska, A, Lubinski, J, Alsop, J, Harrington, P, Chan, I, Menon, U, Pearce, CL, Wu, AH, De Fazio, A, Kennedy, CJ, Goode, E, Ramus, S, Gayther, S, Pharoah, P, Song, H, Dicks, EM, Tyrer, J, Intermaggio, M, Chenevix-Trench, G, Bowtell, DD, Traficante, N, Group, A, Brenton, J, Goranova, T, Hosking, K, Piskorz, A, Van Oudenhove, E, Doherty, J, Harris, HR, Rossing, MA, Duerst, M, Dork, T, Bogdanova, NV, Modugno, F, Moysich, K, Odunsi, K, Ness, R, Karlan, BY, Lester, J, Jensen, A, Krüger Kjaer, S, Høgdall, E, Campbell, IG, Lázaro, C, Pujara, MA, Cunningham, J, Vierkant, R, Winham, SJ, Hildebrandt, M, Huff, C, Li, D, Wu, X, Yu, Y, Permuth, JB, Levine, DA, Schildkraut, JM, Riggan, MJ, Berchuck, A, Webb, PM, Group, OS, Cybulski, C, Gronwald, J, Jakubowska, A, Lubinski, J, Alsop, J, Harrington, P, Chan, I, Menon, U, Pearce, CL, Wu, AH, De Fazio, A, Kennedy, CJ, Goode, E, Ramus, S, Gayther, S, and Pharoah, P
Abstract: Purpose The known epithelial ovarian cancer (EOC) susceptibility genes account for less than 50% of the heritable risk of ovarian cancer suggesting that other susceptibility genes exist. The aim of this study was to evaluate the contribution to ovarian cancer susceptibility of rare deleterious germline variants in a set of candidate genes. Methods We sequenced the coding region of 54 candidate genes in 6385 invasive EOC cases and 6115 controls of broad European ancestry. Genes with an increased frequency of putative deleterious variants in cases versus controls were further examined in an independent set of 14 135 EOC cases and 28 655 controls from the Ovarian Cancer Association Consortium and the UK Biobank. For each gene, we estimated the EOC risks and evaluated associations between germline variant status and clinical characteristics. Results The ORs associated for high-grade serous ovarian cancer were 3.01 for PALB2 (95% CI 1.59 to 5.68; p=0.00068), 1.99 for POLK (95% CI 1.15 to 3.43; p=0.014) and 4.07 for SLX4 (95% CI 1.34 to 12.4; p=0.013). Deleterious mutations in FBXO10 were associated with a reduced risk of disease (OR 0.27, 95% CI 0.07 to 1.00, p=0.049). However, based on the Bayes false discovery probability, only the association for PALB2 in high-grade serous ovarian cancer is likely to represent a true positive. Conclusions We have found strong evidence that carriers of PALB2 deleterious mutations are at increased risk of high-grade serous ovarian cancer. Whether the magnitude of risk is sufficiently high to warrant the inclusion of PALB2 in cancer gene panels for ovarian cancer risk testing is unclear; much larger sample sizes will be needed to provide sufficiently precise estimates for clinical counselling.
Published: 2021

4. On-site genetic analysis for species identification using lab-on-a-chip

Author: Wimbles, R, Melling, LM, Cain, B, Davies, N, Doherty, J, Johnson, B, Shaw, KJ, Wimbles, R, Melling, LM, Cain, B, Davies, N, Doherty, J, Johnson, B, and Shaw, KJ
Abstract: © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.
Published: 2021

5. Population-based targeted sequencing of 54 candidate genes identifies PALB2 as a susceptibility gene for high-grade serous ovarian cancer

Author: Song, H, Dicks, EM, Tyrer, J, Intermaggio, M, Chenevix-Trench, G, Bowtell, DD, Traficante, N, Brenton, J, Goranova, T, Hosking, K, Piskorz, A, van Oudenhove, E, Doherty, J, Harris, HR, Rossing, MA, Duerst, M, Dork, T, Bogdanova, N, Modugno, F, Moysich, K, Odunsi, K, Ness, R, Karlan, BY, Lester, J, Jensen, A, Kruger Kjaer, S, Hogdall, E, Campbell, IG, Lazaro, C, Pujara, MA, Cunningham, J, Vierkant, R, Winham, SJ, Hildebrandt, M, Huff, C, Li, D, Wu, X, Yu, Y, Permuth, JB, Levine, DA, Schildkraut, JM, Riggan, MJ, Berchuck, A, Webb, PM, Cybulski, C, Gronwald, J, Jakubowska, A, Lubinski, J, Alsop, J, Harrington, P, Chan, I, Menon, U, Pearce, CL, Wu, AH, de Fazio, A, Kennedy, CJ, Goode, E, Ramus, S, Gayther, S, Pharoah, P, Song, H, Dicks, EM, Tyrer, J, Intermaggio, M, Chenevix-Trench, G, Bowtell, DD, Traficante, N, Brenton, J, Goranova, T, Hosking, K, Piskorz, A, van Oudenhove, E, Doherty, J, Harris, HR, Rossing, MA, Duerst, M, Dork, T, Bogdanova, N, Modugno, F, Moysich, K, Odunsi, K, Ness, R, Karlan, BY, Lester, J, Jensen, A, Kruger Kjaer, S, Hogdall, E, Campbell, IG, Lazaro, C, Pujara, MA, Cunningham, J, Vierkant, R, Winham, SJ, Hildebrandt, M, Huff, C, Li, D, Wu, X, Yu, Y, Permuth, JB, Levine, DA, Schildkraut, JM, Riggan, MJ, Berchuck, A, Webb, PM, Cybulski, C, Gronwald, J, Jakubowska, A, Lubinski, J, Alsop, J, Harrington, P, Chan, I, Menon, U, Pearce, CL, Wu, AH, de Fazio, A, Kennedy, CJ, Goode, E, Ramus, S, Gayther, S, and Pharoah, P
Abstract: PURPOSE: The known epithelial ovarian cancer (EOC) susceptibility genes account for less than 50% of the heritable risk of ovarian cancer suggesting that other susceptibility genes exist. The aim of this study was to evaluate the contribution to ovarian cancer susceptibility of rare deleterious germline variants in a set of candidate genes. METHODS: We sequenced the coding region of 54 candidate genes in 6385 invasive EOC cases and 6115 controls of broad European ancestry. Genes with an increased frequency of putative deleterious variants in cases versus controls were further examined in an independent set of 14 135 EOC cases and 28 655 controls from the Ovarian Cancer Association Consortium and the UK Biobank. For each gene, we estimated the EOC risks and evaluated associations between germline variant status and clinical characteristics. RESULTS: The ORs associated for high-grade serous ovarian cancer were 3.01 for PALB2 (95% CI 1.59 to 5.68; p=0.00068), 1.99 for POLK (95% CI 1.15 to 3.43; p=0.014) and 4.07 for SLX4 (95% CI 1.34 to 12.4; p=0.013). Deleterious mutations in FBXO10 were associated with a reduced risk of disease (OR 0.27, 95% CI 0.07 to 1.00, p=0.049). However, based on the Bayes false discovery probability, only the association for PALB2 in high-grade serous ovarian cancer is likely to represent a true positive. CONCLUSIONS: We have found strong evidence that carriers of PALB2 deleterious mutations are at increased risk of high-grade serous ovarian cancer. Whether the magnitude of risk is sufficiently high to warrant the inclusion of PALB2 in cancer gene panels for ovarian cancer risk testing is unclear; much larger sample sizes will be needed to provide sufficiently precise estimates for clinical counselling.
Published: 2021

6. Preclinical small molecule WEHI-7326 overcomes drug resistance and elicits response in patient-derived xenograft models of human treatment-refractory tumors

Author: Grohmann, C, Walker, F, Devlin, M, Luo, M-X, Chueh, AC, Doherty, J, Vaillant, F, Ho, G-Y, Wakefield, MJ, Weeden, CE, Kamili, A, Murray, J, Po'uha, ST, Weinstock, J, Kane, SR, Faux, MC, Broekhuizen, E, Zheng, Y, Shield-Artin, K, Kershaw, NJ, Tan, CW, Witchard, HM, Ebert, G, Charman, SA, Street, I, Kavallaris, M, Haber, M, Fletcher, JI, Asselin-Labat, M-L, Scott, CL, Visvader, JE, Lindeman, GJ, Watson, KG, Burgess, AW, Lessene, G, Grohmann, C, Walker, F, Devlin, M, Luo, M-X, Chueh, AC, Doherty, J, Vaillant, F, Ho, G-Y, Wakefield, MJ, Weeden, CE, Kamili, A, Murray, J, Po'uha, ST, Weinstock, J, Kane, SR, Faux, MC, Broekhuizen, E, Zheng, Y, Shield-Artin, K, Kershaw, NJ, Tan, CW, Witchard, HM, Ebert, G, Charman, SA, Street, I, Kavallaris, M, Haber, M, Fletcher, JI, Asselin-Labat, M-L, Scott, CL, Visvader, JE, Lindeman, GJ, Watson, KG, Burgess, AW, and Lessene, G
Abstract: Targeting cell division by chemotherapy is a highly effective strategy to treat a wide range of cancers. However, there are limitations of many standard-of-care chemotherapies: undesirable drug toxicity, side-effects, resistance and high cost. New small molecules which kill a wide range of cancer subtypes, with good therapeutic window in vivo, have the potential to complement the current arsenal of anti-cancer agents and deliver improved safety profiles for cancer patients. We describe results with a new anti-cancer small molecule, WEHI-7326, which causes cell cycle arrest in G2/M, cell death in vitro, and displays efficacious anti-tumor activity in vivo. WEHI-7326 induces cell death in a broad range of cancer cell lines, including taxane-resistant cells, and inhibits growth of human colon, brain, lung, prostate and breast tumors in mice xenografts. Importantly, the compound elicits tumor responses as a single agent in patient-derived xenografts of clinically aggressive, treatment-refractory neuroblastoma, breast, lung and ovarian cancer. In combination with standard-of-care, WEHI-7326 induces a remarkable complete response in a mouse model of high-risk neuroblastoma. WEHI-7326 is mechanistically distinct from known microtubule-targeting agents and blocks cells early in mitosis to inhibit cell division, ultimately leading to apoptotic cell death. The compound is simple to produce and possesses favorable pharmacokinetic and toxicity profiles in rodents. It represents a novel class of anti-cancer therapeutics with excellent potential for further development due to the ease of synthesis, simple formulation, moderate side effects and potent in vivo activity. WEHI-7326 has the potential to complement current frontline anti-cancer drugs and to overcome drug resistance in a wide range of cancers.
Published: 2021

7. Detecting microstructural deviations in individuals with deep diffusion MRI tractometry.

Author: Chamberland, M, Genc, S, Tax, CMW, Shastin, D, Koller, K, Raven, EP, Cunningham, A, Doherty, J, van den Bree, MBM, Parker, GD, Hamandi, K, Gray, WP, Jones, DK, Chamberland, M, Genc, S, Tax, CMW, Shastin, D, Koller, K, Raven, EP, Cunningham, A, Doherty, J, van den Bree, MBM, Parker, GD, Hamandi, K, Gray, WP, and Jones, DK
Abstract: Most diffusion magnetic resonance imaging studies of disease rely on statistical comparisons between large groups of patients and healthy participants to infer altered tissue states in the brain; however, clinical heterogeneity can greatly challenge their discriminative power. There is currently an unmet need to move away from the current approach of group-wise comparisons to methods with the sensitivity to detect altered tissue states at the individual level. This would ultimately enable the early detection and interpretation of microstructural abnormalities in individual patients, an important step towards personalized medicine in translational imaging. To this end, Detect was developed to advance diffusion magnetic resonance imaging tractometry towards single-patient analysis. By operating on the manifold of white-matter pathways and learning normative microstructural features, our framework captures idiosyncrasies in patterns along white-matter pathways. Our approach paves the way from traditional group-based comparisons to true personalized radiology, taking microstructural imaging from the bench to the bedside.
Published: 2021

8. On-site genetic analysis for species identification using lab-on-a-chip

Author: Wimbles, R, Melling, LM, Cain, B, Davies, N, Doherty, J, Johnson, B, Shaw, KJ, Wimbles, R, Melling, LM, Cain, B, Davies, N, Doherty, J, Johnson, B, and Shaw, KJ
Abstract: © 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd This paper presents a microfluidic device capable of performing genetic analysis on dung samples to identify White Rhinoceros (Ceratotherium simum). The development of a microfluidic device, which can be used in the field, offers a portable and cost-effective solution for DNA analysis and species identification to aid conservation efforts. Optimization of the DNA extraction processes produced equivalent yields compared to conventional kit-based methods within just 5 minutes. The use of a color-changing loop-mediated isothermal amplification reaction for simultaneous detection of the cytochrome B sequence of C. simum enabled positive results to be obtained within as little as 30 minutes. Field testing was performed at Knowsley Safari to demonstrate real-world applicability of the microfluidic device for testing of biological samples.
Published: 2021

9. Parasites are endangered by the conservation of their hosts: Meta-analyses of the effect of host captivity on the odds of parasite infection

Author: Milotic, M., Lymbery, A., Thompson, A., Doherty, J-F, Godfrey, S., Milotic, M., Lymbery, A., Thompson, A., Doherty, J-F, and Godfrey, S.
Published: 2020

10. Parasites are endangered by the conservation of their hosts: Meta-analyses of the effect of host captivity on the odds of parasite infection

Author: Milotic, M., Lymbery, A., Thompson, A., Doherty, J-F, Godfrey, S., Milotic, M., Lymbery, A., Thompson, A., Doherty, J-F, and Godfrey, S.
Published: 2020

11. A compact multi-planet system around a bright nearby star from the Dispersed Matter Planet Project

Author: Staab, D., Haswell, C. A., Barnes, J. R., Anglada-Escudé, G., Fossati, L., Doherty, J. P. J., Cooper, J., Jenkins, J. S., Díaz, M. R., Soto, M. G., Staab, D., Haswell, C. A., Barnes, J. R., Anglada-Escudé, G., Fossati, L., Doherty, J. P. J., Cooper, J., Jenkins, J. S., Díaz, M. R., and Soto, M. G.
Abstract: The Dispersed Matter Planet Project targets stars with anomalously low Ca II H&K chromospheric emission. High precision, high cadence radial velocity measurements of the F8V star HD 38677 / DMPP-1 reveal four short period planets. DMPP-1 has log(R'HK) = -5.16 which probably indicates the presence of circumstellar absorbing gas arising from an ablating hot planet. The planets have P$_{\rm orb}$ ~ 2.9 - 19 d, i.e., a compact planetary system with super-Earth (~3 M$_\oplus$) to Neptune-mass (~24 M$_\oplus$) planets. These irradiated planets may be chthonian: remnant cores of giant planets after mass-loss while crossing the Neptune desert. Modelling the possible long-term activity indicators while searching for Keplerian signals modifies the recovered planetary signals. A priori inferences about the presence of short period planets allowed the efficient discovery of the DMPP-1 planets. They have great potential for novel and informative follow-up characterisation studies., Comment: Accepted for publication by Nature Astronomy on 12th November 2019 (Main article, Methods and Supplementary Information; 24 pages, 10 figures, 3 tables)
Published: 2019
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12. NEW REALITIES for Canada'S PARLIAMENT: A WORKFLOW for PREPARING HERITAGE BIM for GAME ENGINES and VIRTUAL REALITY

Author: Pybus, C. (C.), Graham, K. (K.), Doherty, J. (J.), Arellano, N. (N.), Fai, S. (Stephen), Pybus, C. (C.), Graham, K. (K.), Doherty, J. (J.), Arellano, N. (N.), and Fai, S. (Stephen)
Abstract: With a growing interest in the use of virtual reality (VR) for dissemination of cultural heritage sites, the question of how to leverage existing documentation as content for virtual experiences becomes a potentially valuable opportunity. Notably, as sites are increasingly documented with building information modelling (BIM) for the purposes of conservation, there is potential to give these models a second life as content for public education and promotion. However, although software exist for viewing BIM in VR headsets, they are inadequate for complex mo
Published: 2019
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13. A compact multi-planet system around a bright nearby star from the Dispersed Matter Planet Project

Author: Staab, D., Haswell, C. A., Barnes, J. R., Anglada-Escudé, G., Fossati, L., Doherty, J. P. J., Cooper, J., Jenkins, J. S., Díaz, M. R., Soto, M. G., Staab, D., Haswell, C. A., Barnes, J. R., Anglada-Escudé, G., Fossati, L., Doherty, J. P. J., Cooper, J., Jenkins, J. S., Díaz, M. R., and Soto, M. G.
Abstract: The Dispersed Matter Planet Project targets stars with anomalously low Ca II H&K chromospheric emission. High precision, high cadence radial velocity measurements of the F8V star HD 38677 / DMPP-1 reveal four short period planets. DMPP-1 has log(R'HK) = -5.16 which probably indicates the presence of circumstellar absorbing gas arising from an ablating hot planet. The planets have P$_{\rm orb}$ ~ 2.9 - 19 d, i.e., a compact planetary system with super-Earth (~3 M$_\oplus$) to Neptune-mass (~24 M$_\oplus$) planets. These irradiated planets may be chthonian: remnant cores of giant planets after mass-loss while crossing the Neptune desert. Modelling the possible long-term activity indicators while searching for Keplerian signals modifies the recovered planetary signals. A priori inferences about the presence of short period planets allowed the efficient discovery of the DMPP-1 planets. They have great potential for novel and informative follow-up characterisation studies., Comment: Accepted for publication by Nature Astronomy on 12th November 2019 (Main article, Methods and Supplementary Information; 24 pages, 10 figures, 3 tables)
Published: 2019
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14. Uncertainty of CERES-maize calibration under different irrigation strategies using pest optimization algorithm

Author: Fang, Q, Ma, L, Harmel, RD, Yu, Q, Sima, MW, Bartling, PNS, Malone, RW, Nolan, BT, Doherty, J, Fang, Q, Ma, L, Harmel, RD, Yu, Q, Sima, MW, Bartling, PNS, Malone, RW, Nolan, BT, and Doherty, J
Abstract: © 2019 by the authors. An important but rarely studied aspect of crop modeling is the uncertainty associated with model calibration and its effect on model prediction. Biomass and grain yield data from a four-year maize experiment (2008–2011) with six irrigation treatments were divided into subsets by either treatments (Calibration-by-Treatment) or years (Calibration-by-Year). These subsets were then used to calibrate crop cultivar parameters in CERES (Crop Environment Resource Synthesis)-Maize implemented within RZWQM2 (Root Zone Water Quality Model 2) using the automatic Parameter ESTimation (PEST) algorithm to explore model calibration uncertainties. After calibration for each subset, PEST also generated 300 cultivar parameter sets by assuming a normal distribution of each parameter within their reported values in the literature, using the Latin hypercube sampling (LHS) method. The parameter sets that produced similar goodness of fit (11–164 depending on subset used for calibration) were then used to predict all the treatments and years of the entire dataset. Our results showed that the selection of calibration datasets greatly affected the calibrated crop parameters and their uncertainty, as well as prediction uncertainty of grain yield and biomass. The high variability in model prediction of grain yield and biomass among the six (Calibration-by-Treatment) or the four (Calibration-by-Year) scenarios indicated that parameter uncertainty should be considered in calibrating CERES-Maize with grain yield and biomass data from different irrigation treatments, and model predictions should be provided with confidence intervals.
Published: 2019

15. Uncertainty of CERES-maize calibration under different irrigation strategies using pest optimization algorithm

Author: Fang, Q, Ma, L, Harmel, RD, Yu, Q, Sima, MW, Bartling, PNS, Malone, RW, Nolan, BT, Doherty, J, Fang, Q, Ma, L, Harmel, RD, Yu, Q, Sima, MW, Bartling, PNS, Malone, RW, Nolan, BT, and Doherty, J
Abstract: © 2019 by the authors. An important but rarely studied aspect of crop modeling is the uncertainty associated with model calibration and its effect on model prediction. Biomass and grain yield data from a four-year maize experiment (2008–2011) with six irrigation treatments were divided into subsets by either treatments (Calibration-by-Treatment) or years (Calibration-by-Year). These subsets were then used to calibrate crop cultivar parameters in CERES (Crop Environment Resource Synthesis)-Maize implemented within RZWQM2 (Root Zone Water Quality Model 2) using the automatic Parameter ESTimation (PEST) algorithm to explore model calibration uncertainties. After calibration for each subset, PEST also generated 300 cultivar parameter sets by assuming a normal distribution of each parameter within their reported values in the literature, using the Latin hypercube sampling (LHS) method. The parameter sets that produced similar goodness of fit (11–164 depending on subset used for calibration) were then used to predict all the treatments and years of the entire dataset. Our results showed that the selection of calibration datasets greatly affected the calibrated crop parameters and their uncertainty, as well as prediction uncertainty of grain yield and biomass. The high variability in model prediction of grain yield and biomass among the six (Calibration-by-Treatment) or the four (Calibration-by-Year) scenarios indicated that parameter uncertainty should be considered in calibrating CERES-Maize with grain yield and biomass data from different irrigation treatments, and model predictions should be provided with confidence intervals.
Published: 2019

16. Nephronectin is Correlated with Poor Prognosis in Breast Cancer and Promotes Metastasis via its Integrin-Binding Motifs

Author: Steigedal, TS, Toraskar, J, Redvers, RP, Valla, M, Magnussen, SN, Bofin, AM, Opdahl, S, Lundgren, S, Eckhardt, BL, Lamar, JM, Doherty, J, Hynes, RO, Anderson, RL, Svineng, G, Steigedal, TS, Toraskar, J, Redvers, RP, Valla, M, Magnussen, SN, Bofin, AM, Opdahl, S, Lundgren, S, Eckhardt, BL, Lamar, JM, Doherty, J, Hynes, RO, Anderson, RL, and Svineng, G
Abstract: Most cancer patients with solid tumors who succumb to their illness die of metastatic disease. While early detection and improved treatment have led to reduced mortality, even for those with metastatic cancer, some patients still respond poorly to treatment. Understanding the mechanisms of metastasis is important to improve prognostication, to stratify patients for treatment, and to identify new targets for therapy. We have shown previously that expression of nephronectin (NPNT) is correlated with metastatic propensity in breast cancer cell lines. In the present study, we provide a comprehensive analysis of the expression pattern and distribution of NPNT in breast cancer tissue from 842 patients by immunohistochemical staining of tissue microarrays from a historic cohort. Several patterns of NPNT staining were observed. An association between granular cytoplasmic staining (in <10% of tumor cells) and poor prognosis was found. We suggest that granular cytoplasmic staining may represent NPNT-positive exosomes. We found that NPNT promotes adhesion and anchorage-independent growth via its integrin-binding and enhancer motifs and that enforced expression in breast tumor cells promotes their colonization of the lungs. We propose that NPNT may be a novel prognostic marker in a subgroup of breast cancer patients.
Published: 2018

17. Exploring with student midwives the content and experience of attending an educational training workshop on bereavement care

Author: Doherty, J, Coughlan, B, Casey, B, Lloyd, B, Sheehy, L, McMahon, A, Brosnan, M, Barry, T, Cullen, S, Doherty, J, Coughlan, B, Casey, B, Lloyd, B, Sheehy, L, McMahon, A, Brosnan, M, Barry, T, and Cullen, S
Published: 2018

18. Exploring with student midwives the content and experience of attending an educational training workshop on bereavement care

Author: Doherty, J, Coughlan, B, Casey, B, Lloyd, B, Sheehy, L, McMahon, A, Brosnan, M, Barry, T, Cullen, S, Doherty, J, Coughlan, B, Casey, B, Lloyd, B, Sheehy, L, McMahon, A, Brosnan, M, Barry, T, and Cullen, S
Published: 2018

19. Mixed-layer dynamics in the Nordic Seas during MIS 11: Implications for the AMOC

Author: Doherty, J., Ling, Y. F., Not, Christelle, Bauch, H. A., Paytan , A., Thibodeau, Benoit, Doherty, J., Ling, Y. F., Not, Christelle, Bauch, H. A., Paytan , A., and Thibodeau, Benoit
Abstract: Deep-water formation in the high latitudes partially controls the strength of the Atlantic Meridional Overturning Circulation (AMOC). While recent research has illustrated a reduction in ocean convection likely attributable to enhanced freshwater fluxes in this region, elevated surface freshening of the Nordic Seas occurred in tangent with a strong AMOC during the marine isotope stage (MIS) 11 interglacial, 424,000 – 374,000 ka. It was previously hypothesized that the prolonged introduction of freshwater resulted in a thicker mixed layer relative to other quaternary interglacials, which is supported by bulk nitrogen reconstructions of nutrient utilization. Here, we further investigate the phasing of nutrient utilization during MIS 11 using foraminifera-bound stable nitrogen isotope ratios, which are better protected from diagenetic alteration and thus allow for higher-confidence interpretation. Our record faithfully tracks the global AMOC trend as reconstructed from benthic carbon data, where lower levels of nutrient utilization occur in phase with stronger AMOC conditions. While this may reflect the enhanced advection of nutrient-rich North Atlantic waters into the Nordic Seas, reconstructions of sea surface temperature and salinity suggest that the influence of southern-sourced waters was delayed relative to the observed AMOC and nutrient trends. We therefore hypothesize that the coupling of nutrient utilization and AMOC strength reflects the physical conditions of a deeper mixed layer, allowing for an increased mixing of nutrients from below.
Published: 2018

20. Identification of nine new susceptibility loci for endometrial cancer

Author: O Mara, T., Glubb, D., Amant, F., Annibali, D., Ashton, K., Attia, J., Auer, P., Beckmann, M., Black, A., Bolla, M., Brauch, H., Brenner, H., Brinton, L., Buchanan, D., Burwinkel, B., Chang-Claude, J., Chanock, S., Chen, C., Chen, M., Cheng, T., Clarke, C., Clendenning, M., Cook, L., Couch, F., Cox, A., Crous-Bous, M., Czene, K., Day, F., Dennis, J., Depreeuw, J., Doherty, J., Dörk, T., Dowdy, S., Dürst, M., Ekici, A., Fasching, P., Fridley, B., Friedenreich, C., Fritschi, Lin, Fung, J., García-Closas, M., Gaudet, M., Giles, G., Goode, E., Gorman, M., Haiman, C., Hall, P., Hankison, S., Healey, C., Hein, A., Hillemanns, P., Hodgson, S., Hoivik, E., Holliday, E., Hopper, J., Hunter, D., Jones, A., Krakstad, C., Kristensen, V., Lambrechts, D., Marchand, L., Liang, X., Lindblom, A., Lissowska, J., Long, J., Lu, L., Magliocco, A., Martin, L., McEvoy, M., O Mara, T., Glubb, D., Amant, F., Annibali, D., Ashton, K., Attia, J., Auer, P., Beckmann, M., Black, A., Bolla, M., Brauch, H., Brenner, H., Brinton, L., Buchanan, D., Burwinkel, B., Chang-Claude, J., Chanock, S., Chen, C., Chen, M., Cheng, T., Clarke, C., Clendenning, M., Cook, L., Couch, F., Cox, A., Crous-Bous, M., Czene, K., Day, F., Dennis, J., Depreeuw, J., Doherty, J., Dörk, T., Dowdy, S., Dürst, M., Ekici, A., Fasching, P., Fridley, B., Friedenreich, C., Fritschi, Lin, Fung, J., García-Closas, M., Gaudet, M., Giles, G., Goode, E., Gorman, M., Haiman, C., Hall, P., Hankison, S., Healey, C., Hein, A., Hillemanns, P., Hodgson, S., Hoivik, E., Holliday, E., Hopper, J., Hunter, D., Jones, A., Krakstad, C., Kristensen, V., Lambrechts, D., Marchand, L., Liang, X., Lindblom, A., Lissowska, J., Long, J., Lu, L., Magliocco, A., Martin, L., and McEvoy, M.
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.
Published: 2018

21. Incorporating chemical shrinkage volume into Gibson’s solution

Author: Walske, Megan, Doherty, J., Walske, Megan, and Doherty, J.
Abstract: Rapid filling of low-permeability cemented paste backfill (CPB) into underground stopes results in the generation of significant excess pore pressures. These are dissipated through conventional consolidation and shrinkage due to cement hydration. Gibson’s solution for excess pore pressures in an accreting sediment can be used to assess the self-weight consolidation of CPB in a stope. In this paper, numerical modelling is used to determine the chemical shrinkage-induced pore pressure response for hydration of CPB for an accreting material and the results presented in a series of dimensionless design charts. It is shown that superposition can be used to combine Gibson’s solution with the newly developed charts for chemical shrinkage- induced pore pressures. This allows a qualitative assessment of potential pore pressure development in a CPB backfilled stope.
Published: 2018

22. Using tree ring data as a proxy for transpiration to reduce predictive uncertainty of a model simulating groundwater–surface water–vegetation interactions

Author: Schilling, O. S, Doherty, J, Kinzelbach, W, Wang, H, Yang, P. N, Brunner, Philip, Schilling, O. S, Doherty, J, Kinzelbach, W, Wang, H, Yang, P. N, and Brunner, Philip
Abstract: Summary The interactions between surface water, the vadose zone, groundwater, and vegetation are governed by complex feedback mechanisms. Numerical models simulating these interactions are essential in quantifying these processes. However, the notorious lack of field observations results in highly uncertain parameterizations. We suggest a new type of observation data to be included in the calibration data set for hydrological models simulating interactions with vegetation: Tree rings as a proxy for transpiration. We use the lower Tarim River as an example site for our approach. In order to forestall the loss of riparian ecosystems from reduced flow over a 300 km reach of the lower Tarim River, the Chinese government initiated periodical, ecological water releases. The water exchange processes in this region were simulated for a cross-section on the lower reaches of the Tarim River using a numerical model (Hydro-GeoSphere) calibrated against observations of water tables, as well as transpiration estimated from tree ring growth. A predictive uncertainty analysis quantifying the worth of different components of the observation dataset in reducing the uncertainty of model predictions was carried out. The flow of information from elements of the calibration dataset to the different parameters employed by the model was also evaluated. The flow of information and the uncertainty analysis demonstrate that tree ring records can significantly improve confidence in modeling ecosystem dynamics, even if these transpiration estimates are uncertain. To use the full potential of the historical information encapsulated in the Tarim River tree rings, however, the relationship between tree ring growth and transpiration rates has to be studied further.
Published: 2017

23. Uncertainty assessment and implications for data acquisition in support of integrated hydrologic models

Author: Brunner, Philip, Doherty, J, Simmons, Craig T, Brunner, Philip, Doherty, J, and Simmons, Craig T
Abstract: The data set used for calibration of regional numerical models which simulate groundwater flow and vadose zone processes is often dominated by head observations. It is to be expected therefore, that parameters describing vadose zone processes are poorly constrained. A number of studies on small spatial scales explored how additional data types used in calibration constrain vadose zone parameters or reduce predictive uncertainty. However, available studies focused on subsets of observation types and did not jointly account for different measurement accuracies or different hydrologic conditions. In this study, parameter identifiability and predictive uncertainty are quantified in simulation of a 1-D vadose zone soil system driven by infiltration, evaporation and transpiration. The worth of different types of observation data (employed individually, in combination, and with different measurement accuracies) is evaluated by using a linear methodology and a nonlinear Pareto-based methodology under different hydrological conditions. Our main conclusions are (1) Linear analysis provides valuable information on comparative parameter and predictive uncertainty reduction accrued through acquisition of different data types. Its use can be supplemented by nonlinear methods. (2) Measurements of water table elevation can support future water table predictions, even if such measurements inform the individual parameters of vadose zone models to only a small degree. (3) The benefits of including ET and soil moisture observations in the calibration data set are heavily dependent on depth to groundwater. (4) Measurements of groundwater levels, measurements of vadose ET or soil moisture poorly constrain regional groundwater system forcing functions.
Published: 2017

24. Association of vitamin D levels and risk of ovarian cancer: a Mendelian randomization study

Author: Ong, J.S., Cuellar-Partida, G., Lu, Y., Fasching, P.A., Hein, A., Burghaus, S., Beckmann, M.W., Lambrechts, D., Nieuwenhuysen, E. Van, Vergote, I., Vanderstichele, A., Doherty, J., Rossing, M. Anne, Chang-Claude, J., Eilber, U., Rudolph, A., Wang-Gohrke, S., Goodman, M.T., Bogdanova, N., Dork, T., Durst, M., Hillemanns, P., Runnebaum, I.B., Antonenkova, N., Butzow, R., Leminen, A., Nevanlinna, H., Pelttari, L.M., Edwards, R.P., Kelley, J.L., Modugno, F., Moysich, K.B., Ness, R.B., Cannioto, R., Hogdall, E., Hogdall, C.K., Jensen, A., Giles, G.G., Bruinsma, F., Kjaer, S.K., Hildebrandt, M.A.T., Liang, D., Lu, K.H., Wu, X., Bisogna, M., Dao, F., Levine, D.A., Cramer, D.W, Terry, K.L., Tworoger, S.S., Stampfer, M., Missmer, S., Bjorge, L., Salvesen, H.B., Kopperud, R.K., Bischof, K., Aben, K.K.H., Kiemeney, L.A.L.M., Massuger, L.F.A.G., Brooks-Wilson, A., Olson, S.H., McGuire, V., Rothstein, J.H., Sieh, W., Whittemore, A.S., Cook, L.S., Le, N.D., Gilks, C.B., Gronwald, J., Jakubowska, A., Lubinski, J., Kluz, T., Song, H., Tyrer, J.P., Wentzensen, N., Brinton, L., Trabert, B., Lissowska, J., McLaughlin, J.R., Narod, S.A., Phelan, C., Anton-Culver, H., Ziogas, A., Eccles, D., Campbell, I., Gayther, S.A., Gentry-Maharaj, A., Menon, U., Ramus, S.J., Wu, A.H., Dansonka-Mieszkowska, A., Kupryjanczyk, J., Timorek, A., Szafron, L., Cunningham, J.M., Fridley, B.L., Winham, S.J., Bandera, E.V., Poole, E.M., Morgan, T.K., Ong, J.S., Cuellar-Partida, G., Lu, Y., Fasching, P.A., Hein, A., Burghaus, S., Beckmann, M.W., Lambrechts, D., Nieuwenhuysen, E. Van, Vergote, I., Vanderstichele, A., Doherty, J., Rossing, M. Anne, Chang-Claude, J., Eilber, U., Rudolph, A., Wang-Gohrke, S., Goodman, M.T., Bogdanova, N., Dork, T., Durst, M., Hillemanns, P., Runnebaum, I.B., Antonenkova, N., Butzow, R., Leminen, A., Nevanlinna, H., Pelttari, L.M., Edwards, R.P., Kelley, J.L., Modugno, F., Moysich, K.B., Ness, R.B., Cannioto, R., Hogdall, E., Hogdall, C.K., Jensen, A., Giles, G.G., Bruinsma, F., Kjaer, S.K., Hildebrandt, M.A.T., Liang, D., Lu, K.H., Wu, X., Bisogna, M., Dao, F., Levine, D.A., Cramer, D.W, Terry, K.L., Tworoger, S.S., Stampfer, M., Missmer, S., Bjorge, L., Salvesen, H.B., Kopperud, R.K., Bischof, K., Aben, K.K.H., Kiemeney, L.A.L.M., Massuger, L.F.A.G., Brooks-Wilson, A., Olson, S.H., McGuire, V., Rothstein, J.H., Sieh, W., Whittemore, A.S., Cook, L.S., Le, N.D., Gilks, C.B., Gronwald, J., Jakubowska, A., Lubinski, J., Kluz, T., Song, H., Tyrer, J.P., Wentzensen, N., Brinton, L., Trabert, B., Lissowska, J., McLaughlin, J.R., Narod, S.A., Phelan, C., Anton-Culver, H., Ziogas, A., Eccles, D., Campbell, I., Gayther, S.A., Gentry-Maharaj, A., Menon, U., Ramus, S.J., Wu, A.H., Dansonka-Mieszkowska, A., Kupryjanczyk, J., Timorek, A., Szafron, L., Cunningham, J.M., Fridley, B.L., Winham, S.J., Bandera, E.V., Poole, E.M., and Morgan, T.K.
Abstract: Contains fulltext : 171904.pdf (publisher's version ) (Closed access), BACKGROUND: In vitro and observational epidemiological studies suggest that vitamin D may play a role in cancer prevention. However, the relationship between vitamin D and ovarian cancer is uncertain, with observational studies generating conflicting findings. A potential limitation of observational studies is inadequate control of confounding. To overcome this problem, we used Mendelian randomization (MR) to evaluate the association between single nucleotide polymorphisms (SNPs) associated with circulating 25-hydroxyvitamin D [25(OH)D] concentration and risk of ovarian cancer. METHODS: We employed SNPs with well-established associations with 25(OH)D concentration as instrumental variables for MR: rs7944926 (DHCR7), rs12794714 (CYP2R1) and rs2282679 (GC). We included 31 719 women of European ancestry (10 065 cases, 21 654 controls) from the Ovarian Cancer Association Consortium, who were genotyped using customized Illumina Infinium iSelect (iCOGS) arrays. A two-sample (summary data) MR approach was used and analyses were performed separately for all ovarian cancer (10 065 cases) and for high-grade serous ovarian cancer (4121 cases). RESULTS: The odds ratio for epithelial ovarian cancer risk (10 065 cases) estimated by combining the individual SNP associations using inverse variance weighting was 1.27 (95% confidence interval: 1.06 to 1.51) per 20 nmol/L decrease in 25(OH)D concentration. The estimated odds ratio for high-grade serous epithelial ovarian cancer (4121 cases) was 1.54 (1.19, 2.01). CONCLUSIONS: Genetically lowered 25-hydroxyvitamin D concentrations were associated with higher ovarian cancer susceptibility in Europeans. These findings suggest that increasing plasma vitamin D levels may reduce risk of ovarian cancer.
Published: 2016

25. Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome

Author: Machiela, MJ, Zhou, W, Karlins, E, Sampson, JN, Freedman, ND, Yang, Q, Hicks, B, Dagnall, C, Hautman, C, Jacobs, KB, Abnet, CC, Aldrich, MC, Amos, C, Amundadottir, LT, Arslan, AA, Beane-Freeman, LE, Berndt, SI, Black, A, Blot, WJ, Bock, CH, Bracci, PM, Brinton, LA, Bueno-de-Mesquita, HB, Burdett, L, Buring, JE, Butler, MA, Canzian, F, Carreon, T, Chaffee, KG, Chang, I-S, Chatterjee, N, Chen, C, Chen, K, Chung, CC, Cook, LS, Bou, MC, Cullen, M, Davis, FG, De Vivo, I, Ding, T, Doherty, J, Duell, EJ, Epstein, CG, Fan, J-H, Figueroa, JD, Fraumeni, JF, Friedenreich, CM, Fuchs, CS, Gallinger, S, Gao, Y-T, Gapstur, SM, Garcia-Closas, M, Gaudet, MM, Gaziano, JM, Giles, GG, Gillanders, EM, Giovannucci, EL, Goldin, L, Goldstein, AM, Haiman, CA, Hallmans, G, Hankinson, SE, Harris, CC, Henriksson, R, Holly, EA, Hong, Y-C, Hoover, RN, Hsiung, CA, Hu, N, Hu, W, Hunter, DJ, Hutchinson, A, Jenab, M, Johansen, C, Khaw, K-T, Kim, HN, Kim, YH, Kim, YT, Klein, AP, Klein, R, Koh, W-P, Kolonel, LN, Kooperberg, C, Kraft, P, Krogh, V, Kurtz, RC, LaCroix, A, Lan, Q, Landi, MT, Le Marchand, L, Li, D, Liang, X, Liao, LM, Lin, D, Liu, J, Lissowska, J, Lu, L, Magliocco, AM, Malats, N, Matsuo, K, McNeill, LH, McWilliams, RR, Melin, BS, Mirabello, L, Moore, L, Olson, SH, Orlow, I, Park, JY, Patino-Garcia, A, Peplonska, B, Peters, U, Petersen, GM, Pooler, L, Prescott, J, Prokunina-Olsson, L, Purdue, MP, Qiao, Y-L, Rajaraman, P, Real, FX, Riboli, E, Risch, HA, Rodriguez-Santiago, B, Ruder, AM, Savage, SA, Schumacher, F, Schwartz, AG, Schwartz, KL, Seow, A, Setiawan, VW, Severi, G, Shen, H, Sheng, X, Shin, M-H, Shu, X-O, Silverman, DT, Spitz, MR, Stevens, VL, Stolzenberg-Solomon, R, Stram, D, Tang, Z-Z, Taylor, PR, Teras, LR, Tobias, GS, Van den Berg, D, Visvanathan, K, Wacholder, S, Wang, J-C, Wang, Z, Wentzensen, N, Wheeler, W, White, E, Wiencke, JK, Wolpin, BM, Wong, MP, Wu, C, Wu, T, Wu, X, Wu, Y-L, Wunder, JS, Xia, L, Yang, HP, Yang, P-C, Yu, K, Zanetti, KA, Zeleniuch-Jacquotte, A, Zheng, W, Zhou, B, Ziegler, RG, Perez-Jurado, LA, Caporaso, NE, Rothman, N, Tucker, M, Dean, MC, Yeager, M, Chanock, SJ, Machiela, MJ, Zhou, W, Karlins, E, Sampson, JN, Freedman, ND, Yang, Q, Hicks, B, Dagnall, C, Hautman, C, Jacobs, KB, Abnet, CC, Aldrich, MC, Amos, C, Amundadottir, LT, Arslan, AA, Beane-Freeman, LE, Berndt, SI, Black, A, Blot, WJ, Bock, CH, Bracci, PM, Brinton, LA, Bueno-de-Mesquita, HB, Burdett, L, Buring, JE, Butler, MA, Canzian, F, Carreon, T, Chaffee, KG, Chang, I-S, Chatterjee, N, Chen, C, Chen, K, Chung, CC, Cook, LS, Bou, MC, Cullen, M, Davis, FG, De Vivo, I, Ding, T, Doherty, J, Duell, EJ, Epstein, CG, Fan, J-H, Figueroa, JD, Fraumeni, JF, Friedenreich, CM, Fuchs, CS, Gallinger, S, Gao, Y-T, Gapstur, SM, Garcia-Closas, M, Gaudet, MM, Gaziano, JM, Giles, GG, Gillanders, EM, Giovannucci, EL, Goldin, L, Goldstein, AM, Haiman, CA, Hallmans, G, Hankinson, SE, Harris, CC, Henriksson, R, Holly, EA, Hong, Y-C, Hoover, RN, Hsiung, CA, Hu, N, Hu, W, Hunter, DJ, Hutchinson, A, Jenab, M, Johansen, C, Khaw, K-T, Kim, HN, Kim, YH, Kim, YT, Klein, AP, Klein, R, Koh, W-P, Kolonel, LN, Kooperberg, C, Kraft, P, Krogh, V, Kurtz, RC, LaCroix, A, Lan, Q, Landi, MT, Le Marchand, L, Li, D, Liang, X, Liao, LM, Lin, D, Liu, J, Lissowska, J, Lu, L, Magliocco, AM, Malats, N, Matsuo, K, McNeill, LH, McWilliams, RR, Melin, BS, Mirabello, L, Moore, L, Olson, SH, Orlow, I, Park, JY, Patino-Garcia, A, Peplonska, B, Peters, U, Petersen, GM, Pooler, L, Prescott, J, Prokunina-Olsson, L, Purdue, MP, Qiao, Y-L, Rajaraman, P, Real, FX, Riboli, E, Risch, HA, Rodriguez-Santiago, B, Ruder, AM, Savage, SA, Schumacher, F, Schwartz, AG, Schwartz, KL, Seow, A, Setiawan, VW, Severi, G, Shen, H, Sheng, X, Shin, M-H, Shu, X-O, Silverman, DT, Spitz, MR, Stevens, VL, Stolzenberg-Solomon, R, Stram, D, Tang, Z-Z, Taylor, PR, Teras, LR, Tobias, GS, Van den Berg, D, Visvanathan, K, Wacholder, S, Wang, J-C, Wang, Z, Wentzensen, N, Wheeler, W, White, E, Wiencke, JK, Wolpin, BM, Wong, MP, Wu, C, Wu, T, Wu, X, Wu, Y-L, Wunder, JS, Xia, L, Yang, HP, Yang, P-C, Yu, K, Zanetti, KA, Zeleniuch-Jacquotte, A, Zheng, W, Zhou, B, Ziegler, RG, Perez-Jurado, LA, Caporaso, NE, Rothman, N, Tucker, M, Dean, MC, Yeager, M, and Chanock, SJ
Abstract: To investigate large structural clonal mosaicism of chromosome X, we analysed the SNP microarray intensity data of 38,303 women from cancer genome-wide association studies (20,878 cases and 17,425 controls) and detected 124 mosaic X events >2 Mb in 97 (0.25%) women. Here we show rates for X-chromosome mosaicism are four times higher than mean autosomal rates; X mosaic events more often include the entire chromosome and participants with X events more likely harbour autosomal mosaic events. X mosaicism frequency increases with age (0.11% in 50-year olds; 0.45% in 75-year olds), as reported for Y and autosomes. Methylation array analyses of 33 women with X mosaicism indicate events preferentially involve the inactive X chromosome. Our results provide further evidence that the sex chromosomes undergo mosaic events more frequently than autosomes, which could have implications for understanding the underlying mechanisms of mosaic events and their possible contribution to risk for chronic diseases.
Published: 2016

26. Association of vitamin D levels and risk of ovarian cancer: a Mendelian randomization study

Author: Ong, J.S., Cuellar-Partida, G., Lu, Y., Fasching, P.A., Hein, A., Burghaus, S., Beckmann, M.W., Lambrechts, D., Nieuwenhuysen, E. Van, Vergote, I., Vanderstichele, A., Doherty, J., Rossing, M. Anne, Chang-Claude, J., Eilber, U., Rudolph, A., Wang-Gohrke, S., Goodman, M.T., Bogdanova, N., Dork, T., Durst, M., Hillemanns, P., Runnebaum, I.B., Antonenkova, N., Butzow, R., Leminen, A., Nevanlinna, H., Pelttari, L.M., Edwards, R.P., Kelley, J.L., Modugno, F., Moysich, K.B., Ness, R.B., Cannioto, R., Hogdall, E., Hogdall, C.K., Jensen, A., Giles, G.G., Bruinsma, F., Kjaer, S.K., Hildebrandt, M.A.T., Liang, D., Lu, K.H., Wu, X., Bisogna, M., Dao, F., Levine, D.A., Cramer, D.W, Terry, K.L., Tworoger, S.S., Stampfer, M., Missmer, S., Bjorge, L., Salvesen, H.B., Kopperud, R.K., Bischof, K., Aben, K.K.H., Kiemeney, L.A.L.M., Massuger, L.F.A.G., Brooks-Wilson, A., Olson, S.H., McGuire, V., Rothstein, J.H., Sieh, W., Whittemore, A.S., Cook, L.S., Le, N.D., Gilks, C.B., Gronwald, J., Jakubowska, A., Lubinski, J., Kluz, T., Song, H., Tyrer, J.P., Wentzensen, N., Brinton, L., Trabert, B., Lissowska, J., McLaughlin, J.R., Narod, S.A., Phelan, C., Anton-Culver, H., Ziogas, A., Eccles, D., Campbell, I., Gayther, S.A., Gentry-Maharaj, A., Menon, U., Ramus, S.J., Wu, A.H., Dansonka-Mieszkowska, A., Kupryjanczyk, J., Timorek, A., Szafron, L., Cunningham, J.M., Fridley, B.L., Winham, S.J., Bandera, E.V., Poole, E.M., Morgan, T.K., Ong, J.S., Cuellar-Partida, G., Lu, Y., Fasching, P.A., Hein, A., Burghaus, S., Beckmann, M.W., Lambrechts, D., Nieuwenhuysen, E. Van, Vergote, I., Vanderstichele, A., Doherty, J., Rossing, M. Anne, Chang-Claude, J., Eilber, U., Rudolph, A., Wang-Gohrke, S., Goodman, M.T., Bogdanova, N., Dork, T., Durst, M., Hillemanns, P., Runnebaum, I.B., Antonenkova, N., Butzow, R., Leminen, A., Nevanlinna, H., Pelttari, L.M., Edwards, R.P., Kelley, J.L., Modugno, F., Moysich, K.B., Ness, R.B., Cannioto, R., Hogdall, E., Hogdall, C.K., Jensen, A., Giles, G.G., Bruinsma, F., Kjaer, S.K., Hildebrandt, M.A.T., Liang, D., Lu, K.H., Wu, X., Bisogna, M., Dao, F., Levine, D.A., Cramer, D.W, Terry, K.L., Tworoger, S.S., Stampfer, M., Missmer, S., Bjorge, L., Salvesen, H.B., Kopperud, R.K., Bischof, K., Aben, K.K.H., Kiemeney, L.A.L.M., Massuger, L.F.A.G., Brooks-Wilson, A., Olson, S.H., McGuire, V., Rothstein, J.H., Sieh, W., Whittemore, A.S., Cook, L.S., Le, N.D., Gilks, C.B., Gronwald, J., Jakubowska, A., Lubinski, J., Kluz, T., Song, H., Tyrer, J.P., Wentzensen, N., Brinton, L., Trabert, B., Lissowska, J., McLaughlin, J.R., Narod, S.A., Phelan, C., Anton-Culver, H., Ziogas, A., Eccles, D., Campbell, I., Gayther, S.A., Gentry-Maharaj, A., Menon, U., Ramus, S.J., Wu, A.H., Dansonka-Mieszkowska, A., Kupryjanczyk, J., Timorek, A., Szafron, L., Cunningham, J.M., Fridley, B.L., Winham, S.J., Bandera, E.V., Poole, E.M., and Morgan, T.K.
Abstract: Contains fulltext : 171904.pdf (publisher's version ) (Closed access), BACKGROUND: In vitro and observational epidemiological studies suggest that vitamin D may play a role in cancer prevention. However, the relationship between vitamin D and ovarian cancer is uncertain, with observational studies generating conflicting findings. A potential limitation of observational studies is inadequate control of confounding. To overcome this problem, we used Mendelian randomization (MR) to evaluate the association between single nucleotide polymorphisms (SNPs) associated with circulating 25-hydroxyvitamin D [25(OH)D] concentration and risk of ovarian cancer. METHODS: We employed SNPs with well-established associations with 25(OH)D concentration as instrumental variables for MR: rs7944926 (DHCR7), rs12794714 (CYP2R1) and rs2282679 (GC). We included 31 719 women of European ancestry (10 065 cases, 21 654 controls) from the Ovarian Cancer Association Consortium, who were genotyped using customized Illumina Infinium iSelect (iCOGS) arrays. A two-sample (summary data) MR approach was used and analyses were performed separately for all ovarian cancer (10 065 cases) and for high-grade serous ovarian cancer (4121 cases). RESULTS: The odds ratio for epithelial ovarian cancer risk (10 065 cases) estimated by combining the individual SNP associations using inverse variance weighting was 1.27 (95% confidence interval: 1.06 to 1.51) per 20 nmol/L decrease in 25(OH)D concentration. The estimated odds ratio for high-grade serous epithelial ovarian cancer (4121 cases) was 1.54 (1.19, 2.01). CONCLUSIONS: Genetically lowered 25-hydroxyvitamin D concentrations were associated with higher ovarian cancer susceptibility in Europeans. These findings suggest that increasing plasma vitamin D levels may reduce risk of ovarian cancer.
Published: 2016

27. PALB2, CHEK2 and ATM rare variants and cancer risk:data from COGS

Author: Southey, M. C. (Melissa C.), Goldgar, D. E. (David E.), Winqvist, R. (Robert), Pylkäs, K. (Katri), Couch, F. (Fergus), Tischkowitz, M. (Marc), Foulkes, W. D. (William D.), Dennis, J. (Joe), Michailidou, K. (Kyriaki), van Rensburg, E. J. (Elizabeth J.), Heikkinen, T. (Tuomas), Nevanlinna, H. (Heli), Hopper, J. L. (John L.), Doerk, T. (Thilo), Claes, K. B. (Kathleen B. M.), Reis-Filho, J. (Jorge), Teo, Z. L. (Zhi Ling), Radice, P. (Paolo), Catucci, I. (Irene), Peterlongo, P. (Paolo), Tsimiklis, H. (Helen), Odefrey, F. A. (Fabrice A.), Dowty, J. G. (James G.), Schmidt, M. K. (Marjanka K.), Broeks, A. (Annegien), Hogervorst, F. B. (Frans B.), Verhoef, S. (Senno), Carpenter, J. (Jane), Clarke, C. (Christine), Scott, R. J. (Rodney J.), Fasching, P. A. (Peter A.), Haeberle, L. (Lothar), Ekici, A. B. (Arif B.), Beckmann, M. W. (Matthias W.), Peto, J. (Julian), dos-Santos-Silva, I. (Isabel), Fletcher, O. (Olivia), Johnson, N. (Nichola), Bolla, M. K. (Manjeet K.), Sawyer, E. J. (Elinor J.), Tomlinson, I. (Ian), Kerin, M. J. (Michael J.), Miller, N. (Nicola), Marme, F. (Federik), Burwinkel, B. (Barbara), Yang, R. (Rongxi), Guenel, P. (Pascal), . (), Menegaux, F. (Florence), Sanchez, M. (Marie), Bojesen, S. (Stig), Nielsen, S. F. (Sune F.), Flyger, H. (Henrik), Benitez, J. (Javier), Pilar Zamora, M. (M.), Arias Perez, J. I. (Jose Ignacio), Menendez, P. (Primitiva), Anton-Culver, H. (Hoda), Neuhausen, S. (Susan), Ziogas, A. (Argyrios), Clarke, C. A. (Christina A.), Brenner, H. (Hermann), Arndt, V. (Volker), Stegmaier, C. (Christa), Brauch, H. (Hiltrud), Bruening, T. (Thomas), Ko, Y.-D. (Yon-Dschun), Muranen, T. A. (Taru A.), Aittomaki, K. (Kristiina), Blomqvist, C. (Carl), Bogdanova, N. V. (Natalia V.), Antonenkova, N. N. (Natalia N.), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kataja, V. (Vesa), Kosma, V.-M. (Veli-Matti), Hartikainen, J. M. (Jaana M.), Spurdle, A. B. (Amanda B.), Wauters, E. (Els), Smeets, D. (Dominiek), Beuselinck, B. (Benoit), Floris, G. (Giuseppe), Chang-Claude, J. (Jenny), Rudolph, A. (Anja), Seibold, P. (Petra), Flesch-Janys, D. (Dieter), Olson, J. E. (Janet E.), Vachon, C. (Celine), Pankratz, V. S. (Vernon S.), McLean, C. (Catriona), Haiman, C. A. (Christopher A.), Henderson, B. E. (Brian E.), Schumacher, F. (Fredrick), Le Marchand, L. (Loic), Kristensen, V. (Vessela), Alnaes, G. G. (Grethe Grenaker), Zheng, W. (Wei), Hunter, D. J. (David J.), Lindstrom, S. (Sara), Hankinson, S. E. (Susan E.), Kraft, P. (Peter), Andrulis, I. (Irene), Knight, J. A. (Julia A.), Glendon, G. (Gord), Mulligan, A. M. (Anna Marie), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Kauppila, S. (Saila), Devilee, P. (Peter), Tollenaar, R. A. (Robert A. E. M.), Seynaeve, C. (Caroline), Hollestelle, A. (Antoinette), Garcia-Closas, M. (Montserrat), Figueroa, J. (Jonine), Chanock, S. J. (Stephen J.), Lissowska, J. (Jolanta), Czene, K. (Kamila), Darabi, H. (Hatef), Eriksson, M. (Mikael), Eccles, D. M. (Diana M.), Rafiq, S. (Sajjad), Tapper, W. J. (William J.), Gerty, S. M. (Sue M.), Hooning, M. J. (Maartje J.), Martens, J. W. (John W. M.), Collee, J. M. (J. Margriet), Tilanus-Linthorst, M. (Madeleine), Hall, P. (Per), Li, J. (Jingmei), Brand, J. S. (Judith S.), Humphreys, K. (Keith), Cox, A. (Angela), Reed, M. W. (Malcolm W. R.), Luccarini, C. (Craig), Baynes, C. (Caroline), Dunning, A. M. (Alison M.), Hamann, U. (Ute), Torres, D. (Diana), Ulmer, H. U. (Hans Ulrich), Ruediger, T. (Thomas), Jakubowska, A. (Anna), Lubinski, J. (Jan), Jaworska, K. (Katarzyna), Durda, K. (Katarzyna), Slager, S. (Susan), Toland, A. E. (Amanda E.), Ambrosone, C. B. (Christine B.), Yannoukakos, D. (Drakoulis), Swerdlow, A. (Anthony), Ashworth, A. (Alan), Orr, N. (Nick), Jones, M. (Michael), Gonzalez-Neira, A. (Anna), Pita, G. (Guillermo), Rosario Alonso, M. (M.), Alvarez, N. (Nuria), Herrero, D. (Daniel), Tessier, D. C. (Daniel C.), Vincent, D. (Daniel), Bacot, F. (Francois), Simard, J. (Jacques), Dumont, M. (Martine), Soucy, P. (Penny), Eeles, R. (Rosalind), Muir, K. (Kenneth), Wiklund, F. (Fredrik), Gronberg, H. (Henrik), Schleutker, J. (Johanna), Nordestgaard, B. G. (Borge G.), Weischer, M. (Maren), Travis, R. C. (Ruth C.), Neal, D. (David), Donovan, J. L. (Jenny L.), Hamdy, F. C. (Freddie C.), Khaw, K.-T. (Kay-Tee), Stanford, J. L. (Janet L.), Blot, W. J. (William J.), Thibodeau, S. (Stephen), Schaid, D. J. (Daniel J.), Kelley, J. L. (Joseph L.), Maier, C. (Christiane), Kibel, A. S. (Adam S.), Cybulski, C. (Cezary), Cannon-Albright, L. (Lisa), Butterbach, K. (Katja), Park, J. (Jong), Kaneva, R. (Radka), Batra, J. (Jyotsna), Teixeira, M. R. (Manuel R.), Kote-Jarai, Z. (Zsofia), Al Olama, A. A. (Ali Amin), Benlloch, S. (Sara), Renner, S. P. (Stefan P.), Hartmann, A. (Arndt), Hein, A. (Alexander), Ruebner, M. (Matthias), Lambrechts, D. (Diether), Van Nieuwenhuysen, E. (Els), Vergote, I. (Ignace), Lambretchs, S. (Sandrina), Doherty, J. A. (Jennifer A.), Rossing, M. A. (Mary Anne), Nickels, S. (Stefan), Eilber, U. (Ursula), Wang-Gohrke, S. (Shan), Odunsi, K. (Kunle), Sucheston-Campbell, L. E. (Lara E.), Friel, G. (Grace), Lurie, G. (Galina), Killeen, J. L. (Jeffrey L.), Wilkens, L. R. (Lynne R.), Goodman, M. T. (Marc T.), Runnebaum, I. (Ingo), Hillemanns, P. A. (Peter A.), Pelttari, L. M. (Liisa M.), Butzow, R. (Ralf), Modugno, F. (Francesmary), Edwards, R. P. (Robert P.), Ness, R. B. (Roberta B.), Moysich, K. B. (Kirsten B.), du Bois, A. (Andreas), Heitz, F. (Florian), Harter, P. (Philipp), Kommoss, S. (Stefan), Karlan, B. Y. (Beth Y.), Walsh, C. (Christine), Lester, J. (Jenny), Jensen, A. (Allan), Kjaer, S. K. (Susanne Kruger), Hogdall, E. (Estrid), Peissel, B. (Bernard), Bonanni, B. (Bernardo), Bernard, L. (Loris), Goode, E. L. (Ellen L.), Fridley, B. L. (Brooke L.), Vierkant, R. A. (Robert A.), Cunningham, J. M. (Julie M.), Larson, M. C. (Melissa C.), Fogarty, Z. C. (Zachary C.), Kalli, K. R. (Kimberly R.), Liang, D. (Dong), Lu, K. H. (Karen H.), Hildebrandt, M. A. (Michelle A. T.), Wu, X. (Xifeng), Levine, D. A. (Douglas A.), Dao, F. (Fanny), Bisogna, M. (Maria), Berchuck, A. (Andrew), Iversen, E. S. (Edwin S.), Marks, J. R. (Jeffrey R.), Akushevich, L. (Lucy), Cramer, D. W. (Daniel W.), Schildkraut, J. (Joellen), Terry, K. L. (Kathryn L.), Poole, E. M. (Elizabeth M.), Stampfer, M. (Meir), Tworoger, S. S. (Shelley S.), Bandera, E. V. (Elisa V.), Orlow, I. (Irene), Olson, S. H. (Sara H.), Bjorge, L. (Line), Salvesen, H. B. (Helga B.), van Altena, A. M. (Anne M.), Aben, K. K. (Katja K. H.), Kiemeney, L. A. (Lambertus A.), Massuger, L. F. (Leon F. A. G.), Pejovic, T. (Tanja), Bean, Y. (Yukie), Brooks-Wilson, A. (Angela), Kelemen, L. E. (Linda E.), Cook, L. S. (Linda S.), Le, N. D. (Nhu D.), Grski, B. (Bohdan), Gronwald, J. (Jacek), Menkiszak, J. (Janusz), Hogdall, C. K. (Claus K.), Lundvall, L. (Lene), Nedergaard, L. (Lotte), Engelholm, S. A. (Svend Aage), Dicks, E. (Ed), Tyrer, J. (Jonathan), Campbell, I. (Ian), McNeish, I. (Iain), Paul, J. (James), Siddiqui, N. (Nadeem), Glasspool, R. (Rosalind), Whittemore, A. S. (Alice S.), Rothstein, J. H. (Joseph H.), McGuire, V. (Valerie), Sieh, W. (Weiva), Cai, H. (Hui), Shu, X.-O. (Xiao-Ou), Teten, R. T. (Rachel T.), Sutphen, R. (Rebecca), McLaughlin, J. R. (John R.), Narod, S. A. (Steven A.), Phelan, C. M. (Catherine M.), Monteiro, A. N. (Alvaro N.), Fenstermacher, D. (David), Lin, H.-Y. (Hui-Yi), Permuth, J. B. (Jennifer B.), Sellers, T. A. (Thomas A.), Chen, Y. A. (Y. Ann), Tsai, Y.-Y. (Ya-Yu), Chen, Z. (Zhihua), Gentry-Maharaj, A. (Aleksandra), Gayther, S. A. (Simon A.), Ramus, S. J. (Susan J.), Menon, U. (Usha), Wu, A. H. (Anna H.), Pearce, C. L. (Celeste L.), Van den Berg, D. (David), Pike, M. C. (Malcolm C.), Dansonka-Mieszkowska, A. (Agnieszka), Plisiecka-Halasa, J. (Joanna), Moes-Sosnowska, J. (Joanna), Kupryjanczyk, J. (Jolanta), Pharoah, P. D. (Paul D. P.), Song, H. (Honglin), Winship, I. (Ingrid), Chenevix-Trench, G. (Georgia), Giles, G. G. (Graham G.), Tavtigian, S. V. (Sean V.), Easton, D. F. (Doug F.), Milne, R. L. (Roger L.), Southey, M. C. (Melissa C.), Goldgar, D. E. (David E.), Winqvist, R. (Robert), Pylkäs, K. (Katri), Couch, F. (Fergus), Tischkowitz, M. (Marc), Foulkes, W. D. (William D.), Dennis, J. (Joe), Michailidou, K. (Kyriaki), van Rensburg, E. J. (Elizabeth J.), Heikkinen, T. (Tuomas), Nevanlinna, H. (Heli), Hopper, J. L. (John L.), Doerk, T. (Thilo), Claes, K. B. (Kathleen B. M.), Reis-Filho, J. (Jorge), Teo, Z. L. (Zhi Ling), Radice, P. (Paolo), Catucci, I. (Irene), Peterlongo, P. (Paolo), Tsimiklis, H. (Helen), Odefrey, F. A. (Fabrice A.), Dowty, J. G. (James G.), Schmidt, M. K. (Marjanka K.), Broeks, A. (Annegien), Hogervorst, F. B. (Frans B.), Verhoef, S. (Senno), Carpenter, J. (Jane), Clarke, C. (Christine), Scott, R. J. (Rodney J.), Fasching, P. A. (Peter A.), Haeberle, L. (Lothar), Ekici, A. B. (Arif B.), Beckmann, M. W. (Matthias W.), Peto, J. (Julian), dos-Santos-Silva, I. (Isabel), Fletcher, O. (Olivia), Johnson, N. (Nichola), Bolla, M. K. (Manjeet K.), Sawyer, E. J. (Elinor J.), Tomlinson, I. (Ian), Kerin, M. J. (Michael J.), Miller, N. (Nicola), Marme, F. (Federik), Burwinkel, B. (Barbara), Yang, R. (Rongxi), Guenel, P. (Pascal), . (), Menegaux, F. (Florence), Sanchez, M. (Marie), Bojesen, S. (Stig), Nielsen, S. F. (Sune F.), Flyger, H. (Henrik), Benitez, J. (Javier), Pilar Zamora, M. (M.), Arias Perez, J. I. (Jose Ignacio), Menendez, P. (Primitiva), Anton-Culver, H. (Hoda), Neuhausen, S. (Susan), Ziogas, A. (Argyrios), Clarke, C. A. (Christina A.), Brenner, H. (Hermann), Arndt, V. (Volker), Stegmaier, C. (Christa), Brauch, H. (Hiltrud), Bruening, T. (Thomas), Ko, Y.-D. (Yon-Dschun), Muranen, T. A. (Taru A.), Aittomaki, K. (Kristiina), Blomqvist, C. (Carl), Bogdanova, N. V. (Natalia V.), Antonenkova, N. N. (Natalia N.), Lindblom, A. (Annika), Margolin, S. (Sara), Mannermaa, A. (Arto), Kataja, V. (Vesa), Kosma, V.-M. (Veli-Matti), Hartikainen, J. M. (Jaana M.), Spurdle, A. B. (Amanda B.), Wauters, E. (Els), Smeets, D. (Dominiek), Beuselinck, B. (Benoit), Floris, G. (Giuseppe), Chang-Claude, J. (Jenny), Rudolph, A. (Anja), Seibold, P. (Petra), Flesch-Janys, D. (Dieter), Olson, J. E. (Janet E.), Vachon, C. (Celine), Pankratz, V. S. (Vernon S.), McLean, C. (Catriona), Haiman, C. A. (Christopher A.), Henderson, B. E. (Brian E.), Schumacher, F. (Fredrick), Le Marchand, L. (Loic), Kristensen, V. (Vessela), Alnaes, G. G. (Grethe Grenaker), Zheng, W. (Wei), Hunter, D. J. (David J.), Lindstrom, S. (Sara), Hankinson, S. E. (Susan E.), Kraft, P. (Peter), Andrulis, I. (Irene), Knight, J. A. (Julia A.), Glendon, G. (Gord), Mulligan, A. M. (Anna Marie), Jukkola-Vuorinen, A. (Arja), Grip, M. (Mervi), Kauppila, S. (Saila), Devilee, P. (Peter), Tollenaar, R. A. (Robert A. E. M.), Seynaeve, C. (Caroline), Hollestelle, A. (Antoinette), Garcia-Closas, M. (Montserrat), Figueroa, J. (Jonine), Chanock, S. J. (Stephen J.), Lissowska, J. (Jolanta), Czene, K. (Kamila), Darabi, H. (Hatef), Eriksson, M. (Mikael), Eccles, D. M. (Diana M.), Rafiq, S. (Sajjad), Tapper, W. J. (William J.), Gerty, S. M. (Sue M.), Hooning, M. J. (Maartje J.), Martens, J. W. (John W. M.), Collee, J. M. (J. Margriet), Tilanus-Linthorst, M. (Madeleine), Hall, P. (Per), Li, J. (Jingmei), Brand, J. S. (Judith S.), Humphreys, K. (Keith), Cox, A. (Angela), Reed, M. W. (Malcolm W. R.), Luccarini, C. (Craig), Baynes, C. (Caroline), Dunning, A. M. (Alison M.), Hamann, U. (Ute), Torres, D. (Diana), Ulmer, H. U. (Hans Ulrich), Ruediger, T. (Thomas), Jakubowska, A. (Anna), Lubinski, J. (Jan), Jaworska, K. (Katarzyna), Durda, K. (Katarzyna), Slager, S. (Susan), Toland, A. E. (Amanda E.), Ambrosone, C. B. (Christine B.), Yannoukakos, D. (Drakoulis), Swerdlow, A. (Anthony), Ashworth, A. (Alan), Orr, N. (Nick), Jones, M. (Michael), Gonzalez-Neira, A. (Anna), Pita, G. (Guillermo), Rosario Alonso, M. (M.), Alvarez, N. (Nuria), Herrero, D. (Daniel), Tessier, D. C. (Daniel C.), Vincent, D. (Daniel), Bacot, F. (Francois), Simard, J. (Jacques), Dumont, M. (Martine), Soucy, P. (Penny), Eeles, R. (Rosalind), Muir, K. (Kenneth), Wiklund, F. (Fredrik), Gronberg, H. (Henrik), Schleutker, J. (Johanna), Nordestgaard, B. G. (Borge G.), Weischer, M. (Maren), Travis, R. C. (Ruth C.), Neal, D. (David), Donovan, J. L. (Jenny L.), Hamdy, F. C. (Freddie C.), Khaw, K.-T. (Kay-Tee), Stanford, J. L. (Janet L.), Blot, W. J. (William J.), Thibodeau, S. (Stephen), Schaid, D. J. (Daniel J.), Kelley, J. L. (Joseph L.), Maier, C. (Christiane), Kibel, A. S. (Adam S.), Cybulski, C. (Cezary), Cannon-Albright, L. (Lisa), Butterbach, K. (Katja), Park, J. (Jong), Kaneva, R. (Radka), Batra, J. (Jyotsna), Teixeira, M. R. (Manuel R.), Kote-Jarai, Z. (Zsofia), Al Olama, A. A. (Ali Amin), Benlloch, S. (Sara), Renner, S. P. (Stefan P.), Hartmann, A. (Arndt), Hein, A. (Alexander), Ruebner, M. (Matthias), Lambrechts, D. (Diether), Van Nieuwenhuysen, E. (Els), Vergote, I. (Ignace), Lambretchs, S. (Sandrina), Doherty, J. A. (Jennifer A.), Rossing, M. A. (Mary Anne), Nickels, S. (Stefan), Eilber, U. (Ursula), Wang-Gohrke, S. (Shan), Odunsi, K. (Kunle), Sucheston-Campbell, L. E. (Lara E.), Friel, G. (Grace), Lurie, G. (Galina), Killeen, J. L. (Jeffrey L.), Wilkens, L. R. (Lynne R.), Goodman, M. T. (Marc T.), Runnebaum, I. (Ingo), Hillemanns, P. A. (Peter A.), Pelttari, L. M. (Liisa M.), Butzow, R. (Ralf), Modugno, F. (Francesmary), Edwards, R. P. (Robert P.), Ness, R. B. (Roberta B.), Moysich, K. B. (Kirsten B.), du Bois, A. (Andreas), Heitz, F. (Florian), Harter, P. (Philipp), Kommoss, S. (Stefan), Karlan, B. Y. (Beth Y.), Walsh, C. (Christine), Lester, J. (Jenny), Jensen, A. (Allan), Kjaer, S. K. (Susanne Kruger), Hogdall, E. (Estrid), Peissel, B. (Bernard), Bonanni, B. (Bernardo), Bernard, L. (Loris), Goode, E. L. (Ellen L.), Fridley, B. L. (Brooke L.), Vierkant, R. A. (Robert A.), Cunningham, J. M. (Julie M.), Larson, M. C. (Melissa C.), Fogarty, Z. C. (Zachary C.), Kalli, K. R. (Kimberly R.), Liang, D. (Dong), Lu, K. H. (Karen H.), Hildebrandt, M. A. (Michelle A. T.), Wu, X. (Xifeng), Levine, D. A. (Douglas A.), Dao, F. (Fanny), Bisogna, M. (Maria), Berchuck, A. (Andrew), Iversen, E. S. (Edwin S.), Marks, J. R. (Jeffrey R.), Akushevich, L. (Lucy), Cramer, D. W. (Daniel W.), Schildkraut, J. (Joellen), Terry, K. L. (Kathryn L.), Poole, E. M. (Elizabeth M.), Stampfer, M. (Meir), Tworoger, S. S. (Shelley S.), Bandera, E. V. (Elisa V.), Orlow, I. (Irene), Olson, S. H. (Sara H.), Bjorge, L. (Line), Salvesen, H. B. (Helga B.), van Altena, A. M. (Anne M.), Aben, K. K. (Katja K. H.), Kiemeney, L. A. (Lambertus A.), Massuger, L. F. (Leon F. A. G.), Pejovic, T. (Tanja), Bean, Y. (Yukie), Brooks-Wilson, A. (Angela), Kelemen, L. E. (Linda E.), Cook, L. S. (Linda S.), Le, N. D. (Nhu D.), Grski, B. (Bohdan), Gronwald, J. (Jacek), Menkiszak, J. (Janusz), Hogdall, C. K. (Claus K.), Lundvall, L. (Lene), Nedergaard, L. (Lotte), Engelholm, S. A. (Svend Aage), Dicks, E. (Ed), Tyrer, J. (Jonathan), Campbell, I. (Ian), McNeish, I. (Iain), Paul, J. (James), Siddiqui, N. (Nadeem), Glasspool, R. (Rosalind), Whittemore, A. S. (Alice S.), Rothstein, J. H. (Joseph H.), McGuire, V. (Valerie), Sieh, W. (Weiva), Cai, H. (Hui), Shu, X.-O. (Xiao-Ou), Teten, R. T. (Rachel T.), Sutphen, R. (Rebecca), McLaughlin, J. R. (John R.), Narod, S. A. (Steven A.), Phelan, C. M. (Catherine M.), Monteiro, A. N. (Alvaro N.), Fenstermacher, D. (David), Lin, H.-Y. (Hui-Yi), Permuth, J. B. (Jennifer B.), Sellers, T. A. (Thomas A.), Chen, Y. A. (Y. Ann), Tsai, Y.-Y. (Ya-Yu), Chen, Z. (Zhihua), Gentry-Maharaj, A. (Aleksandra), Gayther, S. A. (Simon A.), Ramus, S. J. (Susan J.), Menon, U. (Usha), Wu, A. H. (Anna H.), Pearce, C. L. (Celeste L.), Van den Berg, D. (David), Pike, M. C. (Malcolm C.), Dansonka-Mieszkowska, A. (Agnieszka), Plisiecka-Halasa, J. (Joanna), Moes-Sosnowska, J. (Joanna), Kupryjanczyk, J. (Jolanta), Pharoah, P. D. (Paul D. P.), Song, H. (Honglin), Winship, I. (Ingrid), Chenevix-Trench, G. (Georgia), Giles, G. G. (Graham G.), Tavtigian, S. V. (Sean V.), Easton, D. F. (Doug F.), and Milne, R. L. (Roger L.)
Abstract: Background: The rarity of mutations in PALB2, CHEK2 and ATM make it difficult to estimate precisely associated cancer risks. Population-based family studies have provided evidence that at least some of these mutations are associated with breast cancer risk as high as those associated with rare BRCA2 mutations. We aimed to estimate the relative risks associated with specific rare variants in PALB2, CHEK2 and ATM via a multicentre case-control study. Methods: We genotyped 10 rare mutations using the custom iCOGS array: PALB2 c.1592delT, c.2816T>G and c.3113G>A, CHEK2 c.349A>G, c.538C>T, c.715G>A, c.1036C>T, c.1312G>T, and c.1343T>G and ATM c.7271T>G. We assessed associations with breast cancer risk (42 671 cases and 42 164 controls), as well as prostate (22 301 cases and 22 320 controls) and ovarian (14 542 cases and 23 491 controls) cancer risk, for each variant. Results: For European women, strong evidence of association with breast cancer risk was observed for PALB2 c.1592delT OR 3.44 (95% CI 1.39 to 8.52, p = 7.1 × 10⁻⁵), PALB2 c.3113G>A OR 4.21 (95% CI 1.84 to 9.60, p = 6.9 × 10⁻⁸) and ATM c.7271T>G OR 11.0 (95% CI 1.42 to 85.7, p = 0.0012). We also found evidence of association with breast cancer risk for three variants in CHEK2, c.349A>G OR 2.26 (95% CI 1.29 to 3.95), c.1036C>T OR 5.06 (95% CI 1.09 to 23.5) and c.538C>T OR 1.33 (95% CI 1.05 to 1.67) (p ≤ 0.017). Evidence for prostate cancer risk was observed for CHEK2 c.1343T>G OR 3.03 (95% CI 1.53 to 6.03, p = 0.0006) for African men and CHEK2 c.1312G>T OR 2.21 (95% CI 1.06 to 4.63, p = 0.030) for European men. No evidence of association with ovarian cancer was found for any of these variants. Conclusions: This report adds to accumulating evidence that at least some variants in these genes are associated with an increased risk of breast cancer that is clinically important.
Published: 2016

28. Detailed Building Measurement - Volume 2

Author: Smith, PV, Best, R, Doherty, J, Smith, PV, Best, R, and Doherty, J
Published: 2016

29. Detailed Building Measurement - Volume 2

Author: Smith, PV, Best, R, Doherty, J, Smith, PV, Best, R, and Doherty, J
Published: 2016

30. Deposition and self-weight consolidation of a shrinking fill

Author: Wood, D., Doherty, J., Walske, Megan, Wood, D., Doherty, J., and Walske, Megan
Abstract: Rapid filling of low-permeability cemented paste backfill into underground stopes results in the generation of significant excess pore pressures that are modified by the volume shrinkage accompanying the process of cement hydration. Gibson produced results of an analysis of the excess pore pressures in a simultaneously accreting and consolidating sediment. The dimensionless governing equation lends itself to finite-difference solution: results are presented for a typical rate of volumetric shrinkage and compared with Gibson's original isochrones of excess pore pressure to account for simultaneous conventional consolidation and chemical-induced volume changes in accreting sediment. The effect of time-dependent volume shrinkage can be directly added to Gibson's results for linear problems. The solution technique can be adapted to increase realism by allowing the stiffness of the backfill to increase or permeability to fall as a consequence of the shrinkage. Making a few idealisations, an apparently complex problem can be analysed with rather simple computational resources. Benchmark results can be provided against which more complex methods of analysis (such as finite-element analysis) can be validated.
Published: 2016

31. Early prediction of typical outcome and mild developmental delay for prioritisation of service delivery for very preterm and very low birthweight infants: A study protocol

Author: Caesar, R., Boyd, Roslyn, Colditz, P., Cioni, G., Ware, R., Salthouse, K., Doherty, J., Jackson, M., Matthews, L., Hurley, T., Morosini, A., Thomas, C., Camadoo, L., Baer, E., Caesar, R., Boyd, Roslyn, Colditz, P., Cioni, G., Ware, R., Salthouse, K., Doherty, J., Jackson, M., Matthews, L., Hurley, T., Morosini, A., Thomas, C., Camadoo, L., and Baer, E.
Abstract: Introduction: Over 80% of very preterm (<32 weeks) and very low birthweight (<1500 g) infants will have either typical development (TD) or mild developmental delay (MDD) in multiple domains. As differentiation between TD and MDD can be difficult, infants with MDD often miss opportunities for intervention. For many clinicians, the ongoing challenge is early detection of MDD without over servicing the population. This study aims to: (1) identify early clinical biomarkers for use in this population to predict and differentiate between TD and MDD at 24 months corrected age. (2) Determine the extent to which family and caregiver factors will contribute to neurodevelopmental and behavioural outcomes. Methods and analysis: Participants will be a prospective cohort of 90 infants (<32 weeks and/or <1500 g). Between 34 weeks gestational age and 16 weeks post-term, infants will have a series of 5 neurological, neuromotor, neurobehavioural and perceptual assessments including General Movement Assessment at preterm, writhing and fidgety age. Primary caregivers will complete questionnaires to identify social risk, maternal depression and family strain. Extensive perinatal data will be collected from the medical record. At 24 months, corrected age (c.a) infants will be assessed using standardised tools including the Bayley Scales of Infant and Toddler Development-Third Edition (Bayley III). Longitudinal trajectories of early assessment findings will be examined to determine any predictive relationship with motor and cognitive outcomes at 24 months c.a. Published data of a cohort of Australian children assessed with the Bayley III at 24 months c.a will provide a reference group of term-born controls. Ethics: Ethical approval has been obtained from the Queensland Children's Health Services Human Research Ethics Committee (HREC/13/QRCH/66), the University of Queensland (2013001019) and the Sunshine Coast Hospital and Health Service, SC-Research Governance (SSA/13/QNB/66).
Published: 2016

32. Influence of curing temperature and stress conditions on mechanical properties of cementing paste backfill

Author: Walske, Megan, McWilliam, H., Doherty, J., Fourie, A., Walske, Megan, McWilliam, H., Doherty, J., and Fourie, A.
Abstract: © 2015, National Research Council of Canada. All rights reserved. Cemented paste backfill (CPB) has been observed to achieve greater cemented strength when cured in situ compared with equivalent mixes cured and tested in a laboratory environment. This is in part due to the development of effective stress and generation of elevated temperatures by exothermic cement hydration reactions occurring during curing in a typical underground stope environment. This differs from curing in typical laboratory environments, where little or no effective stresses are generated and curing occurs under constant-temperature conditions. This paper outlines the development, calibration, and testing of a temperature-controlled hydration cell that provides closer representation of in situ conditions by controlling the rate and final amount of specimen temperature increase, in addition to curing under effective stress. The temperature-controlled hydration cell was used to examine the effect of curing under combined effective stress and temperature conditions on the development of small-strain stiffness over a 7 day curing period and the unconfined compressive strength at the end of this period. Curing with both elevated temperature and effective stress was found to significantly increase the mechanical properties of CPB compared with curing at elevated effective stress or ambient temperatures alone.
Published: 2015

33. In-stope measurements at two Western Australian mine sites.

Author: Hasan A., Paste 2014, proceedings of the 17th international seminar on paste and thickened tailings Vancouver, Canada 08-Jun-1412-Jun-14, Doherty J., Fourie A.B., Suazo G., Hasan A., Paste 2014, proceedings of the 17th international seminar on paste and thickened tailings Vancouver, Canada 08-Jun-1412-Jun-14, Doherty J., Fourie A.B., and Suazo G.
Abstract: In situ pore pressure and total horizontal stress measurements were made during and after the backfilling of two stopes at the Raleigh gold mine and the Lanfranchi nickel mine, respectively. The Raleigh mine uses longhole stoping and underhand longhole bench stoping with paste fill methods and the Lanfranchi mine uses longhole open stoping with paste backfill. Both sites employed cemented paste backfill and a staged filling strategy, but the stope geometry and cemented paste backfill particle size distributions varied significantly between the two sites. In order to compare the results for the two sites, the measurements were converted to total stress ratio (TSR) and pore pressure ratio (PPR). At one location the Raleigh stope showed a maximum PPR of 0.7 after the slurry reached a height of 1.5 m above the sensor in 0.4 days, while the Lanfranchi stope exhibited a maximum PPR of 1 after the sensor experienced 0.4 m of embedment in 0.06 days. The backfill rate at Raleigh was faster but generated lower PPR. Short rest periods of 0.8 and 1.24 h in the Lanfranchi stope generated temporary perturbations in the PPR curves, but when filling resumed the PPR rebounded to almost the same value as before the rest periods. During post-plug filling the Lanfranchi curve was erratic due to multiple rest periods and changes in paste fill rate, while no rest period occurred at Raleigh and the paste fill rate was constant until the end of monitoring. Backfilling of the plug fill at Raleigh showed overall lower TSR and PPR, indicating that arching is more pronounced at the Raleigh stope, consistent with the more slender geometry of the stope., In situ pore pressure and total horizontal stress measurements were made during and after the backfilling of two stopes at the Raleigh gold mine and the Lanfranchi nickel mine, respectively. The Raleigh mine uses longhole stoping and underhand longhole bench stoping with paste fill methods and the Lanfranchi mine uses longhole open stoping with paste backfill. Both sites employed cemented paste backfill and a staged filling strategy, but the stope geometry and cemented paste backfill particle size distributions varied significantly between the two sites. In order to compare the results for the two sites, the measurements were converted to total stress ratio (TSR) and pore pressure ratio (PPR). At one location the Raleigh stope showed a maximum PPR of 0.7 after the slurry reached a height of 1.5 m above the sensor in 0.4 days, while the Lanfranchi stope exhibited a maximum PPR of 1 after the sensor experienced 0.4 m of embedment in 0.06 days. The backfill rate at Raleigh was faster but generated lower PPR. Short rest periods of 0.8 and 1.24 h in the Lanfranchi stope generated temporary perturbations in the PPR curves, but when filling resumed the PPR rebounded to almost the same value as before the rest periods. During post-plug filling the Lanfranchi curve was erratic due to multiple rest periods and changes in paste fill rate, while no rest period occurred at Raleigh and the paste fill rate was constant until the end of monitoring. Backfilling of the plug fill at Raleigh showed overall lower TSR and PPR, indicating that arching is more pronounced at the Raleigh stope, consistent with the more slender geometry of the stope.
Published: 2014

34. Detailed Building Measurement - Volume 1

Author: Smith, PV, Best, R, Doherty, J, Smith, PV, Best, R, and Doherty, J
Published: 2014

35. Detailed Building Measurement - Volume 1

Author: Smith, PV, Best, R, Doherty, J, Smith, PV, Best, R, and Doherty, J
Published: 2014

36. LIM kinase inhibition reduces breast cancer growth and invasiveness but systemic inhibition does not reduce metastasis in mice

Author: Li, R, Doherty, J, Antonipillai, J, Chen, S, Devlin, M, Visser, K, Baell, J, Street, I, Anderson, RL, Bernard, O, Li, R, Doherty, J, Antonipillai, J, Chen, S, Devlin, M, Visser, K, Baell, J, Street, I, Anderson, RL, and Bernard, O
Abstract: Metastasis is the major cause of morbidity and mortality in cancer patients. An understanding of the genes that regulate metastasis and development of therapies to target these genes is needed urgently. Since members of the LIM kinase (LIMK) family are key regulators of the actin cytoskeleton and are involved in cell motility and invasion, LIMK is considered to be a good therapeutic target for metastatic disease. Here we investigated the consequences of LIMK inhibition on growth and metastasis of human and mouse mammary tumors. LIMK activity was reduced in tumor cells by expression of dominant-negative LIMK1, by RNA interference or with a selective LIMK inhibitor. The extent of phosphorylation of the LIMK substrate, cofilin, of proliferation and invasion in 2D and 3D culture and of tumor growth and metastasis in mice were assessed. Inhibition of LIMK activity efficiently reduced the pro-invasive properties of tumor cells in vitro. Tumors expressing dominant-negative LIMK1 grew more slowly and were less metastatic in mice. However, systemic administration of a LIMK inhibitor did not reduce either primary tumor growth or spontaneous metastasis. Surprisingly, metastasis to the liver was increased after administration of the inhibitor. These data raise a concern about the use of systemic LIMK inhibitors for the treatment of metastatic breast cancer.
Published: 2013

37. Social Mixing as a Cure for Negative Neighbourhood Effects: Evidence Based Policy or Urban Myth? (discussion paper)

Author: Manley, D. (author), Van Ham, M. (author), Doherty, J. (author), Manley, D. (author), Van Ham, M. (author), and Doherty, J. (author)
Abstract: In this paper, we review the evidence base for social mixing in neighbourhoods, which is used as a strategy to tackle assumed negative neighbourhood effects. We discuss in detail the theoretical links between neighbourhood characteristics, and outcomes of individuals living in concentrations of poverty. Through this we identify the theoretical case for promoting socially mixed communities. We then review the empirical evidence base, focusing on outcomes of the American poverty deconcentration initiatives including the Moving to Opportunity and HOPE VI programs. We identify that the evidence from these programs is at best inconclusive. Turning to the European experience we identify problems associated with using observational data to assess individual outcomes in relation to their neighbourhood context. We conclude by suggesting that the evidence base for social mixing is far from robust, and that many of the current empirical papers suffer from serious analytical shortcomings. Ultimately, the process of creating more socially mixed neighbourhoods is unlikely to create more opportunities in life for the original residents. Socially mixing neighbourhoods through tenure mixing will only change the population composition of neighbourhoods, increasing average incomes because more affluent (and employed) residents will move into the owner occupied housing replacing social housing., OTB Research Institute for the Built Environment
Published: 2011

38. Social Mixing as a Cure for Negative Neighbourhood Effects: Evidence Based Policy or Urban Myth? (discussion paper)

Author: Manley, D. (author), Van Ham, M. (author), Doherty, J. (author), Manley, D. (author), Van Ham, M. (author), and Doherty, J. (author)
Abstract: In this paper, we review the evidence base for social mixing in neighbourhoods, which is used as a strategy to tackle assumed negative neighbourhood effects. We discuss in detail the theoretical links between neighbourhood characteristics, and outcomes of individuals living in concentrations of poverty. Through this we identify the theoretical case for promoting socially mixed communities. We then review the empirical evidence base, focusing on outcomes of the American poverty deconcentration initiatives including the Moving to Opportunity and HOPE VI programs. We identify that the evidence from these programs is at best inconclusive. Turning to the European experience we identify problems associated with using observational data to assess individual outcomes in relation to their neighbourhood context. We conclude by suggesting that the evidence base for social mixing is far from robust, and that many of the current empirical papers suffer from serious analytical shortcomings. Ultimately, the process of creating more socially mixed neighbourhoods is unlikely to create more opportunities in life for the original residents. Socially mixing neighbourhoods through tenure mixing will only change the population composition of neighbourhoods, increasing average incomes because more affluent (and employed) residents will move into the owner occupied housing replacing social housing., OTB Research Institute for the Built Environment
Published: 2011

39. Common variants at 19p13 are associated with susceptibility to ovarian cancer.

Author: Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., Birrer, M.J., Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., and Birrer, M.J.
Abstract: Contains fulltext : 89441.pdf (publisher's version ) (Closed access)
Published: 2010

40. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.

Author: Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K., Birrer, M.J., Berchuck, A., Schildkraut, J., Tomlinson, I.P., Kiemeney, L.A.L.M., Cook, L.S., Gronwald, J., Garcia-Closas, M., Gore, M.E., Campbell, I., Whittemore, A.S., Sutphen, R., Phelan, C.M., Anton-Culver, H., Pearce, C.L., Lambrechts, D., Rossing, M.A., Chang-Claude, J., Moysich, K.B., Goodman, M.T., Dork, T., Nevanlinna, H., Ness, R.B., Rafnar, T., Hogdall, E., Fridley, B.L., Cunningham, J.M., Sieh, W., McGuire, V., Godwin, A.K., Cramer, D.W, Hernandez, D., Levine, D., Lu, K., Iversen, E.S., Palmieri, R.T., Houlston, R.S., Altena, A.M. van, Aben, K.K.H., Massuger, L.F.A.G., Brooks-Wilson, A., Kelemen, L.E., Le, N.D., Jakubowska, A., Lubinski, J., Medrek, K., Stafford, A., Easton, D.F., Tyrer, J.P., Bolton, K.L., Harrington, P., Eccles, D., Chen, A., Molina, A.N., Davila, B.N., Arango, H., Tsai, Y.Y., Chen, Z., Risch, H.A., McLaughlin, J., Narod, S., Ziogas, A., Brewster, W., Gentry-Maharaj, A., Menon, U., Wu, A.H., Stram, D.O., Pike, M.C., Beesley, J., Webb, P.M., Chen, X., Ekici, A.B., Thiel, F.C., Beckmann, M.W., Yang, H., Wentzensen, N., Lissowska, J., Fasching, P.A., Despierre, E., Amant, F., Vergote, I., Doherty, J., Hein, R., Wang-Gohrke, S., Lurie, G., Carney, M.E., Thompson, P., Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K., Birrer, M.J., Berchuck, A., Schildkraut, J., Tomlinson, I.P., Kiemeney, L.A.L.M., Cook, L.S., Gronwald, J., Garcia-Closas, M., Gore, M.E., Campbell, I., Whittemore, A.S., Sutphen, R., Phelan, C.M., Anton-Culver, H., Pearce, C.L., Lambrechts, D., Rossing, M.A., Chang-Claude, J., Moysich, K.B., Goodman, M.T., Dork, T., Nevanlinna, H., Ness, R.B., Rafnar, T., Hogdall, E., Fridley, B.L., Cunningham, J.M., Sieh, W., McGuire, V., Godwin, A.K., Cramer, D.W, Hernandez, D., Levine, D., Lu, K., Iversen, E.S., Palmieri, R.T., Houlston, R.S., Altena, A.M. van, Aben, K.K.H., Massuger, L.F.A.G., Brooks-Wilson, A., Kelemen, L.E., Le, N.D., Jakubowska, A., Lubinski, J., Medrek, K., Stafford, A., Easton, D.F., Tyrer, J.P., Bolton, K.L., Harrington, P., Eccles, D., Chen, A., Molina, A.N., Davila, B.N., Arango, H., Tsai, Y.Y., Chen, Z., Risch, H.A., McLaughlin, J., Narod, S., Ziogas, A., Brewster, W., Gentry-Maharaj, A., Menon, U., Wu, A.H., Stram, D.O., Pike, M.C., Beesley, J., Webb, P.M., Chen, X., Ekici, A.B., Thiel, F.C., Beckmann, M.W., Yang, H., Wentzensen, N., Lissowska, J., Fasching, P.A., Despierre, E., Amant, F., Vergote, I., Doherty, J., Hein, R., Wang-Gohrke, S., Lurie, G., Carney, M.E., and Thompson, P.
Abstract: Contains fulltext : 89180.pdf (publisher's version ) (Closed access)
Published: 2010

41. Common variants at 19p13 are associated with susceptibility to ovarian cancer.

Author: Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., Birrer, M.J., Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., and Birrer, M.J.
Abstract: Contains fulltext : 89441.pdf (publisher's version ) (Closed access)
Published: 2010

42. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24.

Author: Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K., Birrer, M.J., Berchuck, A., Schildkraut, J., Tomlinson, I.P., Kiemeney, L.A.L.M., Cook, L.S., Gronwald, J., Garcia-Closas, M., Gore, M.E., Campbell, I., Whittemore, A.S., Sutphen, R., Phelan, C.M., Anton-Culver, H., Pearce, C.L., Lambrechts, D., Rossing, M.A., Chang-Claude, J., Moysich, K.B., Goodman, M.T., Dork, T., Nevanlinna, H., Ness, R.B., Rafnar, T., Hogdall, E., Fridley, B.L., Cunningham, J.M., Sieh, W., McGuire, V., Godwin, A.K., Cramer, D.W, Hernandez, D., Levine, D., Lu, K., Iversen, E.S., Palmieri, R.T., Houlston, R.S., Altena, A.M. van, Aben, K.K.H., Massuger, L.F.A.G., Brooks-Wilson, A., Kelemen, L.E., Le, N.D., Jakubowska, A., Lubinski, J., Medrek, K., Stafford, A., Easton, D.F., Tyrer, J.P., Bolton, K.L., Harrington, P., Eccles, D., Chen, A., Molina, A.N., Davila, B.N., Arango, H., Tsai, Y.Y., Chen, Z., Risch, H.A., McLaughlin, J., Narod, S., Ziogas, A., Brewster, W., Gentry-Maharaj, A., Menon, U., Wu, A.H., Stram, D.O., Pike, M.C., Beesley, J., Webb, P.M., Chen, X., Ekici, A.B., Thiel, F.C., Beckmann, M.W., Yang, H., Wentzensen, N., Lissowska, J., Fasching, P.A., Despierre, E., Amant, F., Vergote, I., Doherty, J., Hein, R., Wang-Gohrke, S., Lurie, G., Carney, M.E., Thompson, P., Goode, E.L., Chenevix-Trench, G., Song, H., Ramus, S.J., Notaridou, M., Lawrenson, K., Widschwendter, M., Vierkant, R.A., Larson, M.C., Kjaer, S.K., Birrer, M.J., Berchuck, A., Schildkraut, J., Tomlinson, I.P., Kiemeney, L.A.L.M., Cook, L.S., Gronwald, J., Garcia-Closas, M., Gore, M.E., Campbell, I., Whittemore, A.S., Sutphen, R., Phelan, C.M., Anton-Culver, H., Pearce, C.L., Lambrechts, D., Rossing, M.A., Chang-Claude, J., Moysich, K.B., Goodman, M.T., Dork, T., Nevanlinna, H., Ness, R.B., Rafnar, T., Hogdall, E., Fridley, B.L., Cunningham, J.M., Sieh, W., McGuire, V., Godwin, A.K., Cramer, D.W, Hernandez, D., Levine, D., Lu, K., Iversen, E.S., Palmieri, R.T., Houlston, R.S., Altena, A.M. van, Aben, K.K.H., Massuger, L.F.A.G., Brooks-Wilson, A., Kelemen, L.E., Le, N.D., Jakubowska, A., Lubinski, J., Medrek, K., Stafford, A., Easton, D.F., Tyrer, J.P., Bolton, K.L., Harrington, P., Eccles, D., Chen, A., Molina, A.N., Davila, B.N., Arango, H., Tsai, Y.Y., Chen, Z., Risch, H.A., McLaughlin, J., Narod, S., Ziogas, A., Brewster, W., Gentry-Maharaj, A., Menon, U., Wu, A.H., Stram, D.O., Pike, M.C., Beesley, J., Webb, P.M., Chen, X., Ekici, A.B., Thiel, F.C., Beckmann, M.W., Yang, H., Wentzensen, N., Lissowska, J., Fasching, P.A., Despierre, E., Amant, F., Vergote, I., Doherty, J., Hein, R., Wang-Gohrke, S., Lurie, G., Carney, M.E., and Thompson, P.
Abstract: Contains fulltext : 89180.pdf (publisher's version ) (Closed access)
Published: 2010

43. Common variants at 19p13 are associated with susceptibility to ovarian cancer.

Author: Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., Birrer, M.J., Bolton, K.L., Tyrer, J.P., Song, H., Ramus, S.J., Notaridou, M., Jones, C., Sher, T., Gentry-Maharaj, A., Wozniak, E., Tsai, Y.Y., Weidhaas, J., Paik, D., Berg, D.P.G. van den, Stram, D.O., Pearce, C.L., Wu, A.H., Brewster, W., Anton-Culver, H., Ziogas, A., Narod, S., Levine, D.A., Kaye, S.B., Brown, R., Paul, J., Flanagan, J., Sieh, W., McGuire, V., Whittemore, A.S., Campbell, I., Gore, M.E., Lissowska, J., Yang, H.P., Medrek, K., Gronwald, J., Lubinski, J., Jakubowska, A., Le, N.D., Cook, L.S., Keleman, L.E., Brook-Wilson, A., Massuger, L.F.A.G., Kiemeney, L.A.L.M., Aben, K.K.H., Altena, A.M. van, Houlston, R.S., Tomlinson, I., Palmieri, R.T., Moorman, P.G., Schildkraut, J., Iversen, E.S., Phelan, C.M., Vierkant, R.A., Cunningham, J.M., Goode, E.L., Fridley, B.L., Kruger-Kjaer, S., Blaeker, J., Hogdall, E., Hogdall, C., Gross, J., Karlan, B.Y., Ness, R.B., Edwards, R.P., Odunsi, K., Moyisch, K.B., Baker, J.A., Modugno, F., Heikkinenen, T., Butzow, R., Nevanlinna, H., Leminen, A., Bogdanova, N., Antonenkova, N., Doerk, T., Hillemanns, P., Durst, M., Runnebaum, I., Thompson, P.J., Carney, M.E., Goodman, M.T., Lurie, G., Wang-Gohrke, S., Hein, R., Chang-Claude, J., Rossing, M.A., Cushing-Haugen, K.L., Doherty, J., Chen, C., Rafnar, T., Besenbacher, S., Sulem, P., Stefansson, K., and Birrer, M.J.
Abstract: Contains fulltext : 89441.pdf (publisher's version ) (Closed access)
Published: 2010

44. Validating genetic risk associations for ovarian cancer through the international Ovarian Cancer Association Consortium

Author: Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, Brewster, W, Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, and Brewster, W
Abstract: Udgivelsesdato: 2009-Jan-27, The search for genetic variants associated with ovarian cancer risk has focused on pathways including sex steroid hormones, DNA repair, and cell cycle control. The Ovarian Cancer Association Consortium (OCAC) identified 10 single-nucleotide polymorphisms (SNPs) in genes in these pathways, which had been genotyped by Consortium members and a pooled analysis of these data was conducted. Three of the 10 SNPs showed evidence of an association with ovarian cancer at P< or =0.10 in a log-additive model: rs2740574 in CYP3A4 (P=0.011), rs1805386 in LIG4 (P=0.007), and rs3218536 in XRCC2 (P=0.095). Additional genotyping in other OCAC studies was undertaken and only the variant in CYP3A4, rs2740574, continued to show an association in the replication data among homozygous carriers: OR(homozygous(hom))=2.50 (95% CI 0.54-11.57, P=0.24) with 1406 cases and 2827 controls. Overall, in the combined data the odds ratio was 2.81 among carriers of two copies of the minor allele (95% CI 1.20-6.56, P=0.017, p(het) across studies=0.42) with 1969 cases and 3491 controls. There was no association among heterozygous carriers. CYP3A4 encodes a key enzyme in oestrogen metabolism and our finding between rs2740574 and risk of ovarian cancer suggests that this pathway may be involved in ovarian carcinogenesis. Additional follow-up is warranted.
Published: 2009

45. Validating genetic risk associations for ovarian cancer through the international Ovarian Cancer Association Consortium

Author: Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, Brewster, W, Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, and Brewster, W
Abstract: Udgivelsesdato: 2009-Jan-27, The search for genetic variants associated with ovarian cancer risk has focused on pathways including sex steroid hormones, DNA repair, and cell cycle control. The Ovarian Cancer Association Consortium (OCAC) identified 10 single-nucleotide polymorphisms (SNPs) in genes in these pathways, which had been genotyped by Consortium members and a pooled analysis of these data was conducted. Three of the 10 SNPs showed evidence of an association with ovarian cancer at P< or =0.10 in a log-additive model: rs2740574 in CYP3A4 (P=0.011), rs1805386 in LIG4 (P=0.007), and rs3218536 in XRCC2 (P=0.095). Additional genotyping in other OCAC studies was undertaken and only the variant in CYP3A4, rs2740574, continued to show an association in the replication data among homozygous carriers: OR(homozygous(hom))=2.50 (95% CI 0.54-11.57, P=0.24) with 1406 cases and 2827 controls. Overall, in the combined data the odds ratio was 2.81 among carriers of two copies of the minor allele (95% CI 1.20-6.56, P=0.017, p(het) across studies=0.42) with 1969 cases and 3491 controls. There was no association among heterozygous carriers. CYP3A4 encodes a key enzyme in oestrogen metabolism and our finding between rs2740574 and risk of ovarian cancer suggests that this pathway may be involved in ovarian carcinogenesis. Additional follow-up is warranted.
Published: 2009

46. Tagging single-nucleotide polymorphisms in candidate oncogenes and susceptibility to ovarian cancer

Author: Quaye, L, Song, H, Ramus, S J, Gentry-Maharaj, A, Høgdall, E, DiCioccio, R A, McGuire, V, Wu, A H, Van Den Berg, D J, Pike, M C, Wozniak, E, Doherty, J A, Rossing, M A, Ness, R B, Moysich, K B, Høgdall, C, Blaakaer, J, Easton, D F, Ponder, B A J, Jacobs, I J, Menon, U, Whittemore, A S, Krüger-Kjaer, S, Pearce, C L, Pharoah, P D P, Gayther, S A, Quaye, L, Song, H, Ramus, S J, Gentry-Maharaj, A, Høgdall, E, DiCioccio, R A, McGuire, V, Wu, A H, Van Den Berg, D J, Pike, M C, Wozniak, E, Doherty, J A, Rossing, M A, Ness, R B, Moysich, K B, Høgdall, C, Blaakaer, J, Easton, D F, Ponder, B A J, Jacobs, I J, Menon, U, Whittemore, A S, Krüger-Kjaer, S, Pearce, C L, Pharoah, P D P, and Gayther, S A
Abstract: Udgivelsesdato: 2009-Mar-24, Low-moderate risk alleles that are relatively common in the population may explain a significant proportion of the excess familial risk of ovarian cancer (OC) not attributed to highly penetrant genes. In this study, we evaluated the risks of OC associated with common germline variants in five oncogenes (BRAF, ERBB2, KRAS, NMI and PIK3CA) known to be involved in OC development. Thirty-four tagging SNPs in these genes were genotyped in approximately 1800 invasive OC cases and 3000 controls from population-based studies in Denmark, the United Kingdom and the United States. We found no evidence of disease association for SNPs in BRAF, KRAS, ERBB2 and PIK3CA when OC was considered as a single disease phenotype; but after stratification by histological subtype, we found borderline evidence of association for SNPs in KRAS and BRAF with mucinous OC and in ERBB2 and PIK3CA with endometrioid OC. For NMI, we identified a SNP (rs11683487) that was associated with a decreased risk of OC (unadjusted P(dominant)=0.004). We then genotyped rs11683487 in another 1097 cases and 1792 controls from an additional three case-control studies from the United States. The combined odds ratio was 0.89 (95% confidence interval (CI): 0.80-0.99) and remained statistically significant (P(dominant)=0.032). We also identified two haplotypes in ERBB2 associated with an increased OC risk (P(global)=0.034) and a haplotype in BRAF that had a protective effect (P(global)=0.005). In conclusion, these data provide borderline evidence of association for common allelic variation in the NMI with risk of epithelial OC.
Published: 2009

47. Validating genetic risk associations for ovarian cancer through the international Ovarian Cancer Association Consortium

Author: Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, Brewster, W, Pearce, C L, Near, A M, Van Den Berg, D J, Ramus, S J, Gentry-Maharaj, A, Menon, U, Gayther, S A, Anderson, A R, Edlund, C K, Wu, A H, Chen, X, Beesley, J, Webb, P M, Holt, S K, Chen, C, Doherty, J A, Rossing, M A, Whittemore, A S, McGuire, V, DiCioccio, R A, Goodman, M T, Lurie, G, Carney, M E, Wilkens, L R, Ness, R B, Moysich, K B, Edwards, R, Jennison, E, Kjær, Susanne Krüger, Hogdall, E, Hogdall, C K, Goode, E L, Sellers, T A, Vierkant, R A, Cunningham, J M, Cunningham, J C, Schildkraut, J M, Berchuck, A, Moorman, P G, Iversen, E S, Cramer, D W, Terry, K L, Vitonis, A F, Titus-Ernstoff, L, Song, H, Pharoah, P D P, Spurdle, A B, Anton-Culver, H, Ziogas, A, and Brewster, W
Abstract: Udgivelsesdato: 2009-Jan-27, The search for genetic variants associated with ovarian cancer risk has focused on pathways including sex steroid hormones, DNA repair, and cell cycle control. The Ovarian Cancer Association Consortium (OCAC) identified 10 single-nucleotide polymorphisms (SNPs) in genes in these pathways, which had been genotyped by Consortium members and a pooled analysis of these data was conducted. Three of the 10 SNPs showed evidence of an association with ovarian cancer at P< or =0.10 in a log-additive model: rs2740574 in CYP3A4 (P=0.011), rs1805386 in LIG4 (P=0.007), and rs3218536 in XRCC2 (P=0.095). Additional genotyping in other OCAC studies was undertaken and only the variant in CYP3A4, rs2740574, continued to show an association in the replication data among homozygous carriers: OR(homozygous(hom))=2.50 (95% CI 0.54-11.57, P=0.24) with 1406 cases and 2827 controls. Overall, in the combined data the odds ratio was 2.81 among carriers of two copies of the minor allele (95% CI 1.20-6.56, P=0.017, p(het) across studies=0.42) with 1969 cases and 3491 controls. There was no association among heterozygous carriers. CYP3A4 encodes a key enzyme in oestrogen metabolism and our finding between rs2740574 and risk of ovarian cancer suggests that this pathway may be involved in ovarian carcinogenesis. Additional follow-up is warranted.
Published: 2009

48. Tagging single-nucleotide polymorphisms in candidate oncogenes and susceptibility to ovarian cancer

Author: Quaye, L, Song, H, Ramus, S J, Gentry-Maharaj, A, Høgdall, E, DiCioccio, R A, McGuire, V, Wu, A H, Van Den Berg, D J, Pike, M C, Wozniak, E, Doherty, J A, Rossing, M A, Ness, R B, Moysich, K B, Høgdall, C, Blaakaer, J, Easton, D F, Ponder, B A J, Jacobs, I J, Menon, U, Whittemore, A S, Krüger-Kjaer, S, Pearce, C L, Pharoah, P D P, Gayther, S A, Quaye, L, Song, H, Ramus, S J, Gentry-Maharaj, A, Høgdall, E, DiCioccio, R A, McGuire, V, Wu, A H, Van Den Berg, D J, Pike, M C, Wozniak, E, Doherty, J A, Rossing, M A, Ness, R B, Moysich, K B, Høgdall, C, Blaakaer, J, Easton, D F, Ponder, B A J, Jacobs, I J, Menon, U, Whittemore, A S, Krüger-Kjaer, S, Pearce, C L, Pharoah, P D P, and Gayther, S A
Abstract: Udgivelsesdato: 2009-Mar-24, Low-moderate risk alleles that are relatively common in the population may explain a significant proportion of the excess familial risk of ovarian cancer (OC) not attributed to highly penetrant genes. In this study, we evaluated the risks of OC associated with common germline variants in five oncogenes (BRAF, ERBB2, KRAS, NMI and PIK3CA) known to be involved in OC development. Thirty-four tagging SNPs in these genes were genotyped in approximately 1800 invasive OC cases and 3000 controls from population-based studies in Denmark, the United Kingdom and the United States. We found no evidence of disease association for SNPs in BRAF, KRAS, ERBB2 and PIK3CA when OC was considered as a single disease phenotype; but after stratification by histological subtype, we found borderline evidence of association for SNPs in KRAS and BRAF with mucinous OC and in ERBB2 and PIK3CA with endometrioid OC. For NMI, we identified a SNP (rs11683487) that was associated with a decreased risk of OC (unadjusted P(dominant)=0.004). We then genotyped rs11683487 in another 1097 cases and 1792 controls from an additional three case-control studies from the United States. The combined odds ratio was 0.89 (95% confidence interval (CI): 0.80-0.99) and remained statistically significant (P(dominant)=0.032). We also identified two haplotypes in ERBB2 associated with an increased OC risk (P(global)=0.034) and a haplotype in BRAF that had a protective effect (P(global)=0.005). In conclusion, these data provide borderline evidence of association for common allelic variation in the NMI with risk of epithelial OC.
Published: 2009

49. Thinking skills and the context of higher education teaching today. What is known?

Author: Doherty, J and Doherty, J
Published: 2008

50. Thinking skills and the context of higher education teaching today. What is known?

Author: Doherty, J and Doherty, J
Published: 2008

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