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11. Supplementary Tables from DNA Methylation in Peripheral Blood and Risk of Gastric Cancer: A Prospective Nested Case–control Study

Author

Chamberlain, James A, primary, Dugué, Pierre-Antoine, primary, Bassett, Julie K., primary, Milne, Roger L., primary, Joo, Jihoon E., primary, Wong, Ee Ming, primary, Brinkman, Maree T., primary, Stuart, Geoffrey W., primary, Boussioutas, Alex, primary, Southey, Melissa C., primary, Giles, Graham G., primary, Mitchell, Hazel, primary, English, Dallas R., primary, and Hodge, Allison M., primary

Published
2023
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14. Data from DNA Methylation in Peripheral Blood and Risk of Gastric Cancer: A Prospective Nested Case–control Study

Author

Chamberlain, James A, primary, Dugué, Pierre-Antoine, primary, Bassett, Julie K., primary, Milne, Roger L., primary, Joo, Jihoon E., primary, Wong, Ee Ming, primary, Brinkman, Maree T., primary, Stuart, Geoffrey W., primary, Boussioutas, Alex, primary, Southey, Melissa C., primary, Giles, Graham G., primary, Mitchell, Hazel, primary, English, Dallas R., primary, and Hodge, Allison M., primary

Published
2023
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16. Methylation scores for smoking, alcohol consumption, and body mass index and risk of seven types of cancer

Author

Dugué, Pierre‐Antoine, primary, Yu, Chenglong, additional, Hodge, Allison M, additional, Wong, Ee Ming, additional, Joo, JiHoon E, additional, Jung, Chol‐Hee, additional, Schmidt, Daniel, additional, Makalic, Enes, additional, Buchanan, Daniel D, additional, Severi, Gianluca, additional, English, Dallas R, additional, Hopper, John L, additional, Milne, Roger L, additional, Giles, Graham G, additional, and Southey, Melissa C, additional

Published
2023
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20. Association of DNA Methylation-Based Biological Age With Health Risk Factors and Overall and Cause-Specific Mortality

Author

Dugué, Pierre-Antoine, Bassett, Julie K, Joo, JiHoon E, Baglietto, Laura, Jung, Chol-Hee, Wong, Ee Ming, Fiorito, Giovanni, Schmidt, Daniel, Makalic, Enes, Li, Shuai, Moreno-Betancur, Margarita, Buchanan, Daniel D, Vineis, Paolo, English, Dallas R, Hopper, John L, Severi, Gianluca, Southey, Melissa C, Giles, Graham G, and Milne, Roger L

Published
2018
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21. Does genetic predisposition modify the effect of lifestyle-related factors on DNA methylation?

Author

Yu, Chenglong, primary, Hodge, Allison M, additional, Wong, Ee Ming, additional, Joo, Jihoon E, additional, Makalic, Enes, additional, Schmidt, Daniel F, additional, Buchanan, Daniel D, additional, Severi, Gianluca, additional, Hopper, John L, additional, English, Dallas R, additional, Giles, Graham G, additional, Milne, Roger L, additional, Southey, Melissa C, additional, and Dugué, Pierre-Antoine, additional

Published
2022
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22. Smoking Methylation Marks for Prediction of Urothelial Cancer Risk

Author

Yu, Chenglong, primary, Jordahl, Kristina M., additional, Bassett, Julie K., additional, Joo, Jihoon Eric, additional, Wong, Ee Ming, additional, Brinkman, Maree T., additional, Schmidt, Daniel F., additional, Bolton, Damien M., additional, Makalic, Enes, additional, Brasky, Theodore M., additional, Shadyab, Aladdin H., additional, Tinker, Lesley F., additional, Longano, Anthony, additional, Hopper, John L., additional, English, Dallas R., additional, Milne, Roger L., additional, Bhatti, Parveen, additional, Southey, Melissa C., additional, Giles, Graham G., additional, and Dugué, Pierre-Antoine, additional

Published
2021
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24. Does genetic predisposition modify the effect of lifestyle-related factors on DNA methylation?

Author

Yu, Chenglong, primary, Hodge, Allison M, additional, Wong, Ee Ming, additional, Joo, Jihoon E, additional, Makalic, Enes, additional, Schmidt, Daniel F, additional, Buchanan, Daniel D, additional, Severi, Gianluca, additional, Hopper, John L, additional, English, Dallas R, additional, Giles, Graham G, additional, Milne, Roger L, additional, Southey, Melissa C, additional, and Dugué, Pierre-Antoine, additional

Published
2021
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29. Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance

Author

Hurley, Rachel M, primary, McGehee, Cordelia D, additional, Nesic, Ksenija, additional, Correia, Cristina, additional, Weiskittel, Taylor M, additional, Kelly, Rebecca L, additional, Venkatachalam, Annapoorna, additional, Hou, Xiaonan, additional, Pathoulas, Nicholas M, additional, Meng, X Wei, additional, Kondrashova, Olga, additional, Radke, Marc R, additional, Schneider, Paula A, additional, Flatten, Karen S, additional, Peterson, Kevin L, additional, Becker, Marc A, additional, Wong, Ee Ming, additional, Southey, Melissa S, additional, Dobrovic, Alexander, additional, Lin, Kevin K, additional, Harding, Thomas C, additional, McNeish, Iain, additional, Ross, Christian A, additional, Wagner, Jill M, additional, Wakefield, Matthew J, additional, Scott, Clare L, additional, Haluska, Paul, additional, Wahner Hendrickson, Andrea E, additional, Karnitz, Larry M, additional, Swisher, Elizabeth M, additional, Li, Hu, additional, Weroha, S John, additional, and Kaufmann, Scott H, additional

Published
2021
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30. DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer

Author

Joo, Jihoon E., primary, Clendenning, Mark, additional, Wong, Ee Ming, additional, Rosty, Christophe, additional, Mahmood, Khalid, additional, Georgeson, Peter, additional, Winship, Ingrid M., additional, Preston, Susan G., additional, Win, Aung Ko, additional, Dugué, Pierre-Antoine, additional, Jayasekara, Harindra, additional, English, Dallas, additional, Macrae, Finlay A., additional, Hopper, John L., additional, Jenkins, Mark A., additional, Milne, Roger L., additional, Giles, Graham G., additional, Southey, Melissa C., additional, and Buchanan, Daniel D., additional

Published
2021
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31. Additional file 1 of Repeatability of methylation measures using a QIAseq targeted methyl panel and comparison with the Illumina HumanMethylation450 assay

Author

Yu, Chenglong, Dugué, Pierre-Antoine, Dowty, James G., Hammet, Fleur, Joo, JiHoon E., Wong, Ee Ming, Hosseinpour, Mahnaz, Giles, Graham G., Hopper, John L., Nguyen-Dumont, Tu, MacInnis, Robert J., and Southey, Melissa C.

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, ComputingMilieux_COMPUTERSANDEDUCATION, Data_FILES, ComputerApplications_COMPUTERSINOTHERSYSTEMS
Abstract

Additional file 1: Supplementary Tables and Figures.

Published
2021
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32. Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance

Author

Hurley, Rachel M, McGehee, Cordelia D, Nesic, Ksenija, Correia, Cristina, Weiskittel, Taylor M, Kelly, Rebecca L, Venkatachalam, Annapoorna, Hou, Xiaonan, Pathoulas, Nicholas M, Meng, X Wei, Kondrashova, Olga, Radke, Marc R, Schneider, Paula A, Flatten, Karen S, Peterson, Kevin L, Becker, Marc A, Wong, Ee Ming, Southey, Melissa S, Dobrovic, Alexander, Lin, Kevin K, Harding, Thomas C, McNeish, Iain, Ross, Christian A, Wagner, Jill M, Wakefield, Matthew J, Scott, Clare L, Haluska, Paul, Hendrickson, Andrea E Wahner, Karnitz, Larry M, Swisher, Elizabeth M, Li, Hu, Weroha, S John, and Kaufmann, Scott H

Subjects
Uncategorized
Abstract

Acquired PARP inhibitor (PARPi) resistance in BRCA1- or BRCA2-mutant ovarian cancer often results from secondary mutations that restore expression of functional protein. RAD51C is a less commonly studied ovarian cancer susceptibility gene whose promoter is sometimes methylated, leading to homologous recombination (HR) deficiency and PARPi sensitivity. For this study, the PARPi-sensitive patient-derived ovarian cancer xenograft PH039, which lacks HR gene mutations but harbors RAD51C promoter methylation, was selected for PARPi resistance by cyclical niraparib treatment in vivo. PH039 acquired PARPi resistance by the third treatment cycle and grew through subsequent treatment with either niraparib or rucaparib. Transcriptional profiling throughout the course of resistance development showed widespread pathway level changes along with a marked increase in RAD51C mRNA, which reflected loss of RAD51C promoter methylation. Analysis of ovarian cancer samples from the ARIEL2 Part 1 clinical trial of rucaparib monotherapy likewise indicated an association between loss of RAD51C methylation prior to on-study biopsy and limited response. Interestingly, the PARPi resistant PH039 model remained platinum sensitive. Collectively, these results not only indicate that PARPi treatment pressure can reverse RAD51C methylation and restore RAD51C expression, but also provide a model for studying the clinical observation that PARPi and platinum sensitivity are sometimes dissociated.

Published
2021
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34. Epigenetic Drift Association with Cancer Risk and Survival, and Modification by Sex

Author

Yu, Chenglong, primary, Wong, Ee Ming, additional, Joo, Jihoon Eric, additional, Hodge, Allison M., additional, Makalic, Enes, additional, Schmidt, Daniel, additional, Buchanan, Daniel D., additional, Severi, Gianluca, additional, Hopper, John L., additional, English, Dallas R., additional, Giles, Graham G., additional, Southey, Melissa C., additional, and Dugué, Pierre-Antoine, additional

Published
2021
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35. Methylation scores for smoking, alcohol consumption, and body mass index and risk of seven types of cancer

Author

Dugué, Pierre-Antoine, primary, Yu, Chenglong, additional, Hodge, Allison M, additional, Wong, Ee Ming, additional, Joo, JiHoon E, additional, Jung, Chol-Hee, additional, Schmidt, Daniel, additional, Makalic, Enes, additional, Buchanan, Daniel D, additional, Severi, Gianluca, additional, English, Dallas R, additional, Hopper, John L, additional, Milne, Roger L, additional, Giles, Graham G, additional, and Southey, Melissa C, additional

Published
2021
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36. DNA Methylation in Peripheral Blood and Risk of Gastric Cancer: A Prospective Nested Case–control Study

Author

Chamberlain, James A, primary, Dugué, Pierre-Antoine, additional, Bassett, Julie K., additional, Milne, Roger L., additional, Joo, Jihoon E., additional, Wong, Ee Ming, additional, Brinkman, Maree T., additional, Stuart, Geoffrey W., additional, Boussioutas, Alex, additional, Southey, Melissa C., additional, Giles, Graham G., additional, Mitchell, Hazel, additional, English, Dallas R., additional, and Hodge, Allison M., additional

Published
2021
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38. Biological Aging Measures Based on Blood DNA Methylation and Risk of Cancer: A Prospective Study

Author

Dugué, Pierre-Antoine, primary, Bassett, Julie K, additional, Wong, Ee Ming, additional, Joo, JiHoon E, additional, Li, Shuai, additional, Yu, Chenglong, additional, Schmidt, Daniel F, additional, Makalic, Enes, additional, Doo, Nicole Wong, additional, Buchanan, Daniel D, additional, Hodge, Allison M, additional, English, Dallas R, additional, Hopper, John L, additional, Giles, Graham G, additional, Southey, Melissa C, additional, and Milne, Roger L, additional

Published
2020
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41. Causes of variation in epigenetic aging across the lifespan

Author

Li, Shuai, primary, Nguyen, Tuong, additional, Wong, Ee Ming, additional, Dugué, Pierre-Antoine, additional, Dite, Gillian S, additional, Armstrong, Nicola J, additional, Craig, Jeffrey M, additional, Mather, Karen A, additional, Sachdev, Perminder S, additional, Saffery, Richard, additional, Sung, Joohon, additional, Tan, Qihua, additional, Thalamuthu, Anbupalam, additional, Milne, Roger L, additional, Giles, Graham G, additional, Southey, Melissa C, additional, and Hopper, John L, additional

Published
2020
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42. Overall lack of replication of associations between dietary intake of folate and vitamin B-12 and DNA methylation in peripheral blood

Author

Dugué, Pierre-Antoine, primary, Chamberlain, James A, additional, Bassett, Julie K, additional, Hodge, Allison M, additional, Brinkman, Maree T, additional, Joo, JiHoon E, additional, Jung, Chol-Hee, additional, Wong, Ee Ming, additional, Makalic, Enes, additional, Schmidt, Daniel F, additional, Hopper, John L, additional, Buchanan, Daniel D, additional, English, Dallas R, additional, Milne, Roger L, additional, Southey, Melissa C, additional, and Giles, Graham G, additional

Published
2020
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43. Genome-wide association study of peripheral blood DNA methylation and conventional mammographic density measures

Author

Shuai, Li, Dugué, Pierre-Antoine, Baglietto, Laura, Severi, Gianluca, Wong, Ee Ming, Nguyen, Tuong L., Stone, Jennifer, English, Dallas R., Southey, Melissa C., Giles, Graham G., Hopper, John L., and Milne, Roger L.

Subjects
Adult, Cancer Research, Blood Cells, epigenetics, mammographic density, Siblings, Australia, Twins, DNA Methylation, Middle Aged, Body Mass Index, Epigenesis, Genetic, breast cancer, Oncology, DNA methylation, Case-Control Studies, Humans, Female, Aged, Breast Density, Genome-Wide Association Study, Mammography
Abstract

Age- and body mass index (BMI)-adjusted mammographic density is one of the strongest breast cancer risk factors. DNA methylation is a molecular mechanism that could underlie inter-individual variation in mammographic density. We aimed to investigate the association between breast cancer risk-predicting mammographic density measures and blood DNA methylation. For 436 women from the Australian Mammographic Density Twins and Sisters Study and 591 women from the Melbourne Collaborative Cohort Study, mammographic density (dense area, nondense area and percentage dense area) defined by the conventional brightness threshold was measured using the CUMULUS software, and peripheral blood DNA methylation was measured using the HumanMethylation450 (HM450) BeadChip assay. Associations between DNA methylation at400,000 sites and mammographic density measures adjusted for age and BMI were assessed within each cohort and pooled using fixed-effect meta-analysis. Associations with methylation at genetic loci known to be associated with mammographic density were also examined. We found no genome-wide significant (p 10

Published
2018

44. Smoking and blood DNA methylation: an epigenome-wide association study and assessment of reversibility

Author

Dugué, Pierre-Antoine, primary, Jung, Chol-Hee, additional, Joo, Jihoon E, additional, Wang, Xiaochuan, additional, Wong, Ee Ming, additional, Makalic, Enes, additional, Schmidt, Daniel F, additional, Baglietto, Laura, additional, Severi, Gianluca, additional, Southey, Melissa C, additional, English, Dallas R, additional, Giles, Graham G, additional, and Milne, Roger L, additional

Published
2019
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45. Smoking and blood DNA methylation: novel associations, replication of previous findings and assessment of reversibility

Author

Dugué, Pierre-Antoine, primary, Jung, Chol-Hee, additional, Joo, JiHoon E, additional, Wang, Xiaochuan, additional, Wong, Ee Ming, additional, Makalic, Enes, additional, Schmidt, Daniel F, additional, Baglietto, Laura, additional, Severi, Gianluca, additional, Southey, Melissa C, additional, English, Dallas R, additional, Giles, Graham G, additional, and Milne, Roger L, additional

Published
2019
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46. Genome-wide association study of peripheral blood DNA methylation and conventional mammographic density measures

Author

Li, Shuai, primary, Dugué, Pierre-Antoine, additional, Baglietto, Laura, additional, Severi, Gianluca, additional, Wong, Ee Ming, additional, Nguyen, Tuong L., additional, Stone, Jennifer, additional, English, Dallas R., additional, Southey, Melissa C., additional, Giles, Graham G., additional, Hopper, John L., additional, and Milne, Roger L., additional

Published
2019
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47. Genome-wide association study of peripheral blood DNA methylation and conventional mammographic density measures

Author

Li, Shuai, primary, Dugué, Pierre-Antoine, additional, Baglietto, Laura, additional, Severi, Gianluca, additional, Wong, Ee Ming, additional, Nguyen, Tuong L., additional, Stone, Jennifer, additional, English, Dallas R., additional, Southey, Melissa C., additional, Giles, Graham G., additional, Hopper, John L., additional, and Milne, Roger L., additional

Published
2018
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48. Methylation marks of prenatal exposure to maternal smoking and risk of cancer in adulthood.

Author

Dugué, Pierre-Antoine, Hodge, Allison M, Wong, Ee Ming, Joo, JiHoon E, Jung, Chol-Hee, Hopper, John L, English, Dallas R, Giles, Graham G, Milne, Roger L, and Southey, Melissa C

Subjects
MATERNAL exposure, METHYLATION, SMOKING, DNA methylation, TRANSITIONAL cell carcinoma, UROTHELIUM, ADENOMATOUS polyps, P16 gene, PRENATAL exposure delayed effects, TUMORS, LONGITUDINAL method
Abstract

Background: Prenatal exposure to maternal smoking is detrimental to child health but its association with risk of cancer has seldom been investigated. Maternal smoking induces widespread and long-lasting DNA methylation changes, which we study here for association with risk of cancer in adulthood.Methods: Eight prospective case-control studies nested within the Melbourne Collaborative Cohort Study were used to assess associations between maternal-smoking-associated methylation marks in blood and risk of several cancers: breast (n = 406 cases), colorectal (n = 814), gastric (n = 166), kidney (n = 139), lung (n = 327), prostate (n = 847) and urothelial (n = 404) cancer and B-cell lymphoma (n = 426). We used conditional logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between cancer and five methylation scores calculated as weighted averages for 568, 19, 15, 28 and 17 CpG sites. Models were adjusted for confounders, including personal smoking history (smoking status, pack-years, age at starting and quitting) and methylation scores for personal smoking.Results: All methylation scores for maternal smoking were strongly positively associated with risk of urothelial cancer. Risk estimates were only slightly attenuated after adjustment for smoking history, other potential confounders and methylation scores for personal smoking. Potential negative associations were observed with risk of lung cancer and B-cell lymphoma. No associations were observed for other cancers.Conclusions: We found that methylation marks of prenatal exposure to maternal smoking are associated with increased risk of urothelial cancer. Our study demonstrates the potential for using DNA methylation to investigate the impact of early-life, unmeasured exposures on later-life cancer risk. [ABSTRACT FROM AUTHOR]

Published
2021
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49. Reply to: Comments on "Methylation scores for smoking, alcohol consumption and body mass index and risk of seven types of cancer".

Author

Dugué, Pierre‐Antoine, Yu, Chenglong, Hodge, Allison M., Wong, Ee Ming, Joo, JiHoon E., Jung, Chol‐Hee, Schmidt, Daniel, Makalic, Enes, Buchanan, Daniel D., Severi, Gianluca, English, Dallas R., Hopper, John L., Milne, Roger L., Giles, Graham G., and Southey, Melissa C.

Subjects
BODY mass index, ALCOHOL drinking, METHYLATION, SMOKING, BLADDER cancer, DISEASE risk factors
Abstract

Our study aimed to assess the value of DNA methylation for prediction purposes, whereas the main points raised by Meng relate to the aetiology of lung and bladder cancer using "causal methods". Biological aging measures based on blood DNA methylation and risk of cancer: a prospective study. [Extracted from the article]

Published
2023
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50. Heritable DNA methylation marks associated with susceptibility to breast cancer

Author

Joo, Jihoon, Dowty, James, Milne, Roger, Wong, Ee Ming, Dugue, Pierre-Antoine, English, Dallas, Hopper, John, Goldgar, David, Giles, Graham, Southey, Melissa, Duijf, Pascal, other, and, Joo, Jihoon, Dowty, James, Milne, Roger, Wong, Ee Ming, Dugue, Pierre-Antoine, English, Dallas, Hopper, John, Goldgar, David, Giles, Graham, Southey, Melissa, Duijf, Pascal, and other, and

Abstract

Mendelian-like inheritance of germline DNA methylation in cancer susceptibility genes has been previously reported. We aimed to scan the genome for heritable methylation marks associated with breast cancer susceptibility by studying 25 Australian multiple-case breast cancer families. Here we report genome-wide DNA methylation measured in 210 peripheral blood DNA samples provided by family members using the Infinium HumanMethylation450. We develop and apply a new statistical method to identify heritable methylation marks based on complex segregation analysis. We estimate carrier probabilities for the 1000 most heritable methylation marks based on family structure, and we use Cox proportional hazards survival analysis to identify 24 methylation marks with corresponding carrier probabilities significantly associated with breast cancer. We replicate an association with breast cancer risk for four of the 24 marks using an independent nested case–control study. Here, we report a novel approach for identifying heritable DNA methylation marks associated with breast cancer risk.

Published
2018

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