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8. Contributors

Author

Barbé, Ferran, primary, Barney, Ryan C., additional, Barrott, Jared, additional, Beltrán-García, Jesús, additional, Berenguer-Pascual, Ester, additional, Cardona-Monzonís, Alejandro, additional, Carretero, Julian, additional, Cervantes, Andrés, additional, Chen, Lin-Yu, additional, Cosín-Roger, Jesús, additional, Crujeiras, Ana B., additional, de Gonzalo-Calvo, David, additional, Deml, Moritz C., additional, Fatema, Kaniz, additional, Ferrer-Buitrago, Minerva, additional, Friedland, Matthew H., additional, Gallagher, William M., additional, García-Giménez, José Luis, additional, Guerra, José M., additional, Hermida, Teresa Bas, additional, Heyneman, Alexandra L., additional, Hitchins, Megan P., additional, Huang, Rui-Lan, additional, Ibáñez-Cabellos, José Santiago, additional, Izquierdo, Andrea G., additional, Jenkins, Timothy G., additional, Jordan, Asia C., additional, Kim, Hong Sun, additional, Kirkham, Matthew, additional, Lai, Hung-Cheng, additional, Lambrou, George I., additional, Laurent-Puig, Pierre, additional, Liew, Phui-Ly, additional, Llorente-Cortés, Vicenta, additional, Lorenzo, Paula M., additional, Luelling, Sarah, additional, Maciel, Valter Luiz, additional, McGee, Jean S., additional, Meeran, Syed Musthapa, additional, Mena-Mollá, Salvador, additional, Mondal, Priya, additional, Natesh, Jagadish, additional, Ortega, Ángel L., additional, Osca-Verdegal, Rebeca, additional, Pallardó, Federico V., additional, Pavek, Adriene, additional, Peiró-Chova, Lorena, additional, Penta, Dhanamjai, additional, Pérez-Machado, Gisselle, additional, Perry, A.S., additional, Pinilla, Lucía, additional, Prencipe, M., additional, Ruiz-Jorro, Miguel, additional, Seco-Cervera, Marta, additional, Shi, Jiaqi, additional, Silva, Romina, additional, Su, Po-Hsuan, additional, Tollefsbol, Trygve O., additional, Tost, Jörg, additional, Ushijima, Toshikazu, additional, Wen, Kuo-Chang, additional, and Yi, Julie Z., additional

Published
2022
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10. A strategy for studying epigenetic diversity in natural populations: proof of concept in poplar and oak.

Author

Lesur, Isabelle, Rogier, Odile, Sow, Mamadou Dia, Boury, Christophe, Duplan, Alexandre, Garnier, Abel, Senhaji-Rachik, Abdeljalil, Civan, Peter, Daron, Josquin, Delaunay, Alain, Duvaux, Ludovic, Benoit, Vanina, Guichoux, Erwan, Provost, Grégoire Le, Sanou, Edmond, Ambroise, Christophe, Plomion, Christophe, Salse, Jérôme, Segura, Vincent, and Tost, Jörg

Subjects
WHOLE genome sequencing, DNA methylation, DURMAST oak, BLACK poplar, BIODIVERSITY
Abstract

In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, taking into account the structural complexity of genomes, their size, and their content in unique coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by sequencing capture bisulfite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea. [ABSTRACT FROM AUTHOR]

Published
2024
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11. An integrated omics approach highlights how epigenetic events can explain and predict response to neoadjuvant chemotherapy and bevacizumab in breast cancer.

Author

Fleischer, Thomas, Haugen, Mads Haugland, Ankill, Jørgen, Silwal‐Pandit, Laxmi, Børresen‐Dale, Anne‐Lise, Hedenfalk, Ingrid, Hatschek, Thomas, Tost, Jörg, Engebraaten, Olav, and Kristensen, Vessela N.

Abstract

Treatment with the anti‐angiogenic drug bevacizumab in addition to chemotherapy has shown efficacy for breast cancer in some clinical trials, but better biomarkers are needed to optimally select patients for treatment. Here, we present an omics approach where DNA methylation profiles are integrated with gene expression and results from proteomic data in breast cancer patients to predict response to therapy and pinpoint response‐related epigenetic events. Fresh‐frozen tumor biopsies taken before, during, and after treatment from human epidermal growth factor receptor 2 negative non‐metastatic patients receiving neoadjuvant chemotherapy with or without bevacizumab were subjected to molecular profiling. Here, we report that DNA methylation at enhancer CpGs related to cell cycle regulation can predict response to chemotherapy and bevacizumab for the estrogen receptor positive subset of patients (AUC = 0.874), and we validated this observation in an independent patient cohort with a similar treatment regimen (AUC = 0.762). Combining the DNA methylation scores with the scores from a previously published protein signature resulted in a slight increase in the prediction performance (AUC = 0.784). We also show that tumors receiving the combination treatment underwent more extensive epigenetic alterations. Finally, we performed an integrative expression–methylation quantitative trait loci analysis on alterations in DNA methylation and gene expression levels, showing that the epigenetic alterations that occur during treatment are different between responders and non‐responders and that these differences may be explained by the proliferation–epithelial‐to‐mesenchymal transition axis through the activity of grainyhead like transcription factor 2. Using tumor purity computed from copy number data, we developed a method for estimating cancer cell‐specific methylation to confirm that the association to response reflects DNA methylation in cancer cells. Taken together, these results support the potential for clinical benefit of the addition of bevacizumab to chemotherapy when administered to the correct patients. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Molecular Mechanisms of Trophoblast Dysfunction Mediated by Imbalance between STOX1 Isoforms

Author

Ducat, Aurélien, Couderc, Betty, Bouter, Anthony, Biquard, Louise, Aouache, Rajaa, Passet, Bruno, Doridot, Ludivine, Cohen, Marie-Benoîte, Ribaux, Pascale, Apicella, Clara, Gaillard, Irène, Palfray, Sophia, Chen, Yulian, Vargas, Alexandra, Julé, Amélie, Frelin, Léo, Cocquet, Julie, San Martin, Camino Ruano, Jacques, Sébastien, Busato, Florence, Tost, Jorg, Méhats, Céline, Laissue, Paul, Vilotte, Jean-Luc, Miralles, Francisco, and Vaiman, Daniel

Published
2020
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13. DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

Author

Joubert, Bonnie R, Felix, Janine F, Yousefi, Paul, Bakulski, Kelly M, Just, Allan C, Breton, Carrie, Reese, Sarah E, Markunas, Christina A, Richmond, Rebecca C, Xu, Cheng-Jian, Küpers, Leanne K, Oh, Sam S, Hoyo, Cathrine, Gruzieva, Olena, Söderhäll, Cilla, Salas, Lucas A, Baïz, Nour, Zhang, Hongmei, Lepeule, Johanna, Ruiz, Carlos, Ligthart, Symen, Wang, Tianyuan, Taylor, Jack A, Duijts, Liesbeth, Sharp, Gemma C, Jankipersadsing, Soesma A, Nilsen, Roy M, Vaez, Ahmad, Fallin, M Daniele, Hu, Donglei, Litonjua, Augusto A, Fuemmeler, Bernard F, Huen, Karen, Kere, Juha, Kull, Inger, Munthe-Kaas, Monica Cheng, Gehring, Ulrike, Bustamante, Mariona, Saurel-Coubizolles, Marie José, Quraishi, Bilal M, Ren, Jie, Tost, Jörg, Gonzalez, Juan R, Peters, Marjolein J, Håberg, Siri E, Xu, Zongli, van Meurs, Joyce B, Gaunt, Tom R, Kerkhof, Marjan, Corpeleijn, Eva, Feinberg, Andrew P, Eng, Celeste, Baccarelli, Andrea A, Neelon, Sara E Benjamin, Bradman, Asa, Merid, Simon Kebede, Bergström, Anna, Herceg, Zdenko, Hernandez-Vargas, Hector, Brunekreef, Bert, Pinart, Mariona, Heude, Barbara, Ewart, Susan, Yao, Jin, Lemonnier, Nathanaël, Franco, Oscar H, Wu, Michael C, Hofman, Albert, McArdle, Wendy, Van der Vlies, Pieter, Falahi, Fahimeh, Gillman, Matthew W, Barcellos, Lisa F, Kumar, Ashish, Wickman, Magnus, Guerra, Stefano, Charles, Marie-Aline, Holloway, John, Auffray, Charles, Tiemeier, Henning W, Smith, George Davey, Postma, Dirkje, Hivert, Marie-France, Eskenazi, Brenda, Vrijheid, Martine, Arshad, Hasan, Antó, Josep M, Dehghan, Abbas, Karmaus, Wilfried, Annesi-Maesano, Isabella, Sunyer, Jordi, Ghantous, Akram, Pershagen, Göran, Holland, Nina, Murphy, Susan K, DeMeo, Dawn L, Burchard, Esteban G, Ladd-Acosta, Christine, Snieder, Harold, and Nystad, Wenche

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Health Sciences, Genetics, Human Genome, Prevention, Tobacco Smoke and Health, Tobacco, Perinatal Period - Conditions Originating in Perinatal Period, Pediatric, Clinical Research, 2.1 Biological and endogenous factors, Reproductive health and childbirth, Respiratory, Good Health and Well Being, Asthma, Child, Child, Preschool, Chromosome Mapping, Cleft Lip, Cleft Palate, DNA Methylation, Epigenesis, Genetic, Female, Genetic Association Studies, Humans, Infant, Infant, Newborn, Pregnancy, Smoking, White People, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Epigenetic modifications, including DNA methylation, represent a potential mechanism for environmental impacts on human disease. Maternal smoking in pregnancy remains an important public health problem that impacts child health in a myriad of ways and has potential lifelong consequences. The mechanisms are largely unknown, but epigenetics most likely plays a role. We formed the Pregnancy And Childhood Epigenetics (PACE) consortium and meta-analyzed, across 13 cohorts (n = 6,685), the association between maternal smoking in pregnancy and newborn blood DNA methylation at over 450,000 CpG sites (CpGs) by using the Illumina 450K BeadChip. Over 6,000 CpGs were differentially methylated in relation to maternal smoking at genome-wide statistical significance (false discovery rate, 5%), including 2,965 CpGs corresponding to 2,017 genes not previously related to smoking and methylation in either newborns or adults. Several genes are relevant to diseases that can be caused by maternal smoking (e.g., orofacial clefts and asthma) or adult smoking (e.g., certain cancers). A number of differentially methylated CpGs were associated with gene expression. We observed enrichment in pathways and processes critical to development. In older children (5 cohorts, n = 3,187), 100% of CpGs gave at least nominal levels of significance, far more than expected by chance (p value < 2.2 × 10(-16)). Results were robust to different normalization methods used across studies and cell type adjustment. In this large scale meta-analysis of methylation data, we identified numerous loci involved in response to maternal smoking in pregnancy with persistence into later childhood and provide insights into mechanisms underlying effects of this important exposure.

Published
2016

16. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus

Author

Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, Maury, Stéphane, Conseil Régional du Centre-Val de Loire, Department of Energy (US), Kohler, Annegret [0000-0002-9575-9567], Sow, Mamadou Dia [0000-0002-2815-4939], Delaunay, Alain [0000-0002-2519-5380], Fauchery, Laure [0000-0002-2571-0274], Barry, Kerrie W. [0000-0002-8999-6785], Keymanesh, Keykhosrow [0000-0001-6019-9443], Singan, Vasanth [0000-0002-9983-5707], Grigoriev, Igor [0000-0002-3136-8903], Fichot, Régis [0000-0001-5527-4103], Conde, Daniel [0000-0001-8362-4190], Perales, Mariano [0000-0002-7351-8439], Tost, Jörg [0000-0002-2683-0817], Martin, Francis M. [0000-0002-4737-3715], Allona, Isabel [0000-0002-7012-2850], Strauss, Steven H. [0000-0001-9670-3082], Veneault-Fourrey, Claire [0000-0001-9778-2659], Maury, Stéphane 0000-0003-0481-0847], Vigneaud, Julien, Kohler, Annegret, Sow, Mamadou Dia, Delaunay, Alain, Fauchery, Laure, Guinet, Frederic, Daviaud, Christian, Barry, Kerrie W., Keymanesh, Keykhosrow, Johnson, Jenifer, Singan, Vasanth, Grigoriev, Igor, Fichot, Régis, Conde, Daniel, Perales, Mariano, Tost, Jörg, Martin, Francis M., Allona, Isabel, Strauss, Steven H., Veneault-Fourrey, Claire, and Maury, Stéphane

Abstract

Ectomycorrhizas are an intrinsic component of tree nutrition and responses to environmental variations. How epigenetic mechanisms might regulate these mutualistic interactions is unknown. By manipulating the level of expression of the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1) and two demethylases DEMETER-LIKE (DML) in Populus tremula × Populus alba lines, we examined how host DNA methylation modulates multiple parameters of the responses to root colonization with the mutualistic fungus Laccaria bicolor. We compared the ectomycorrhizas formed between transgenic and wild-type (WT) trees and analyzed their methylomes and transcriptomes. The poplar lines displaying lower mycorrhiza formation rate corresponded to hypomethylated overexpressing DML or RNAi-ddm1 lines. We found 86 genes and 288 transposable elements (TEs) differentially methylated between WT and hypomethylated lines (common to both OX-dml and RNAi-ddm1) and 120 genes/1441 TEs in the fungal genome suggesting a host-induced remodeling of the fungal methylome. Hypomethylated poplar lines displayed 205 differentially expressed genes (cis and trans effects) in common with 17 being differentially methylated (cis). Our findings suggest a central role of host and fungal DNA methylation in the ability to form ectomycorrhizas including not only poplar genes involved in root initiation, ethylene and jasmonate-mediated pathways, and immune response but also terpenoid metabolism.

Published
2023

17. A General Framework for Interrogation of mRNA Stability Programs Identifies RNA-Binding Proteins that Govern Cancer Transcriptomes

Author

Perron, Gabrielle, Jandaghi, Pouria, Solanki, Shraddha, Safisamghabadi, Maryam, Storoz, Cristina, Karimzadeh, Mehran, Papadakis, Andreas I., Arseneault, Madeleine, Scelo, Ghislaine, Banks, Rosamonde E., Tost, Jorg, Lathrop, Mark, Tanguay, Simon, Brazma, Alvis, Huang, Sidong, Brimo, Fadi, Najafabadi, Hamed S., and Riazalhosseini, Yasser

Published
2018
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20. Specific association of extracellular vesicles-derived miRNA-17 and -106a clusters with pathomechanims of obesity-associated low type-2 asthma

Author

Alhamdan, Fahd, primary, Greulich, Timm, additional, Daviaud, Christian, additional, Marsh, Leigh M., additional, Pedersen, Frauke, additional, Thölken, Clemens, additional, Pfefferle, Petra I., additional, Bahmer, Thomas, additional, Potaczek, Daniel P., additional, Tost, Jörg, additional, and Garn, Holger, additional

Published
2023
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21. Placental DNA methylation signatures of prenatal air pollution exposure and potential effects on birth outcomes: an analysis of three prospective cohorts

Author

Broséus, Lucile, Guilbert, Ariane, Hough, Ian, Kloog, Itai, Chauvaud, Anath, Seyve, Emie, Vaiman, Daniel, Heude, Barbara, Chevrier, Cécile, Tost, Jörg, Slama, Rémy, and Lepeule, Johanna

Abstract

Pregnancy air pollution exposure (PAPE) has been linked to a wide range of adverse birth and childhood outcomes, but there is a paucity of data on its influence on the placental epigenome, which can regulate the programming of physiological functions and affect child development. This study aimed to investigate the association between prenatal air pollutant exposure concentrations and changes in placental DNA methylation patterns, and to explore the potential windows of susceptibility and sex-specific alterations.

Published
2024
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25. Identification of extracellular vesicle microRNA signatures specifically linked to inflammatory and metabolic mechanisms in obesity‐associated low type‐2 asthma

Author

Alhamdan, Fahd, primary, Greulich, Timm, additional, Daviaud, Christian, additional, Marsh, Leigh M., additional, Pedersen, Frauke, additional, Thölken, Clemens, additional, Pfefferle, Petra Ina, additional, Bahmer, Thomas, additional, Potaczek, Daniel P., additional, Tost, Jörg, additional, and Garn, Holger, additional

Published
2023
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26. Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age

Author

Nakamura, Aurélie, primary, Broséus, Lucile, additional, Tost, Jörg, additional, Vaiman, Daniel, additional, Martins, Silvia, additional, Keyes, Katherine, additional, Bonello, Kim, additional, Fekom, Mathilde, additional, Strandberg-Larsen, Katrine, additional, Sutter-Dallay, Anne-Laure, additional, Heude, Barbara, additional, Melchior, Maria, additional, and Lepeule, Johanna, additional

Published
2023
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27. Tunable DNMT1 degradation reveals cooperation of DNMT1 and DNMT3B in regulating DNA methylation dynamics and genome organization

Author

Scelfo, Andrea, primary, Barra, Viviana, additional, Abdennur, Nezar, additional, Spracklin, George, additional, Busato, Florence, additional, Salinas-Luypaert, Catalina, additional, Bonaiti, Elena, additional, Velasco, Guillaume, additional, Chipont, Anna, additional, Guerin, Coralie, additional, Tijhuis, Andrea, additional, Spierings, Diana C.J., additional, Francastel, Claire, additional, Fooijer, Floris, additional, Tost, Jörg, additional, Mirny, Leonid A., additional, and Fachinetti, Daniele, additional

Published
2023
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31. Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age

Author

Nakamura, Aurélie, Broséus, Lucile, Tost, Jörg, Vaiman, Daniel, Martins, Silvia, Keyes, Katherine, Bonello, Kim, Fekom, Mathilde, Strandberg-Larsen, Katrine, Sutter-Dallay, Anne Laure, Heude, Barbara, Melchior, Maria, Lepeule, Johanna, Nakamura, Aurélie, Broséus, Lucile, Tost, Jörg, Vaiman, Daniel, Martins, Silvia, Keyes, Katherine, Bonello, Kim, Fekom, Mathilde, Strandberg-Larsen, Katrine, Sutter-Dallay, Anne Laure, Heude, Barbara, Melchior, Maria, and Lepeule, Johanna

Abstract

The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother–child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment. Keywords: EWAS; DNA methylation; DOHAD; placenta; child behavior; pregnancy; epidemiology, The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother–child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment.

Published
2023

32. Supplementary Methods S1 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Vasudev, Naveen S., primary, Scelo, Ghislaine, primary, Glennon, Kate I., primary, Wilson, Michelle, primary, Letourneau, Louis, primary, Eveleigh, Robert, primary, Nourbehesht, Nazanin, primary, Arseneault, Madeleine, primary, Paccard, Antoine, primary, Egevad, Lars, primary, Viksna, Juris, primary, Celms, Edgars, primary, Jackson, Sharon M., primary, Abedi-Ardekani, Behnoush, primary, Warren, Anne Y., primary, Selby, Peter J., primary, Trainor, Sebastian, primary, Kimuli, Michael, primary, Cartledge, Jon, primary, Soomro, Naeem, primary, Adeyoju, Adebanji, primary, Patel, Poulam M., primary, Wozniak, Magdalena B., primary, Holcatova, Ivana, primary, Brisuda, Antonin, primary, Janout, Vladimir, primary, Chanudet, Estelle, primary, Zaridze, David, primary, Moukeria, Anush, primary, Shangina, Oxana, primary, Foretova, Lenka, primary, Navratilova, Marie, primary, Mates, Dana, primary, Jinga, Viorel, primary, Bogdanovic, Ljiljana, primary, Kovacevic, Bozidar, primary, Cambon-Thomsen, Anne, primary, Bourque, Guillaume, primary, Brazma, Alvis, primary, Tost, Jörg, primary, Brennan, Paul, primary, Lathrop, Mark, primary, Riazalhosseini, Yasser, primary, and Banks, Rosamonde E., primary

Published
2023
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33. Figure S3 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Vasudev, Naveen S., primary, Scelo, Ghislaine, primary, Glennon, Kate I., primary, Wilson, Michelle, primary, Letourneau, Louis, primary, Eveleigh, Robert, primary, Nourbehesht, Nazanin, primary, Arseneault, Madeleine, primary, Paccard, Antoine, primary, Egevad, Lars, primary, Viksna, Juris, primary, Celms, Edgars, primary, Jackson, Sharon M., primary, Abedi-Ardekani, Behnoush, primary, Warren, Anne Y., primary, Selby, Peter J., primary, Trainor, Sebastian, primary, Kimuli, Michael, primary, Cartledge, Jon, primary, Soomro, Naeem, primary, Adeyoju, Adebanji, primary, Patel, Poulam M., primary, Wozniak, Magdalena B., primary, Holcatova, Ivana, primary, Brisuda, Antonin, primary, Janout, Vladimir, primary, Chanudet, Estelle, primary, Zaridze, David, primary, Moukeria, Anush, primary, Shangina, Oxana, primary, Foretova, Lenka, primary, Navratilova, Marie, primary, Mates, Dana, primary, Jinga, Viorel, primary, Bogdanovic, Ljiljana, primary, Kovacevic, Bozidar, primary, Cambon-Thomsen, Anne, primary, Bourque, Guillaume, primary, Brazma, Alvis, primary, Tost, Jörg, primary, Brennan, Paul, primary, Lathrop, Mark, primary, Riazalhosseini, Yasser, primary, and Banks, Rosamonde E., primary

Published
2023
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34. Supplementary Tables S3-S13 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Vasudev, Naveen S., primary, Scelo, Ghislaine, primary, Glennon, Kate I., primary, Wilson, Michelle, primary, Letourneau, Louis, primary, Eveleigh, Robert, primary, Nourbehesht, Nazanin, primary, Arseneault, Madeleine, primary, Paccard, Antoine, primary, Egevad, Lars, primary, Viksna, Juris, primary, Celms, Edgars, primary, Jackson, Sharon M., primary, Abedi-Ardekani, Behnoush, primary, Warren, Anne Y., primary, Selby, Peter J., primary, Trainor, Sebastian, primary, Kimuli, Michael, primary, Cartledge, Jon, primary, Soomro, Naeem, primary, Adeyoju, Adebanji, primary, Patel, Poulam M., primary, Wozniak, Magdalena B., primary, Holcatova, Ivana, primary, Brisuda, Antonin, primary, Janout, Vladimir, primary, Chanudet, Estelle, primary, Zaridze, David, primary, Moukeria, Anush, primary, Shangina, Oxana, primary, Foretova, Lenka, primary, Navratilova, Marie, primary, Mates, Dana, primary, Jinga, Viorel, primary, Bogdanovic, Ljiljana, primary, Kovacevic, Bozidar, primary, Cambon-Thomsen, Anne, primary, Bourque, Guillaume, primary, Brazma, Alvis, primary, Tost, Jörg, primary, Brennan, Paul, primary, Lathrop, Mark, primary, Riazalhosseini, Yasser, primary, and Banks, Rosamonde E., primary

Published
2023
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35. Supplementary Table S2 from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Vasudev, Naveen S., primary, Scelo, Ghislaine, primary, Glennon, Kate I., primary, Wilson, Michelle, primary, Letourneau, Louis, primary, Eveleigh, Robert, primary, Nourbehesht, Nazanin, primary, Arseneault, Madeleine, primary, Paccard, Antoine, primary, Egevad, Lars, primary, Viksna, Juris, primary, Celms, Edgars, primary, Jackson, Sharon M., primary, Abedi-Ardekani, Behnoush, primary, Warren, Anne Y., primary, Selby, Peter J., primary, Trainor, Sebastian, primary, Kimuli, Michael, primary, Cartledge, Jon, primary, Soomro, Naeem, primary, Adeyoju, Adebanji, primary, Patel, Poulam M., primary, Wozniak, Magdalena B., primary, Holcatova, Ivana, primary, Brisuda, Antonin, primary, Janout, Vladimir, primary, Chanudet, Estelle, primary, Zaridze, David, primary, Moukeria, Anush, primary, Shangina, Oxana, primary, Foretova, Lenka, primary, Navratilova, Marie, primary, Mates, Dana, primary, Jinga, Viorel, primary, Bogdanovic, Ljiljana, primary, Kovacevic, Bozidar, primary, Cambon-Thomsen, Anne, primary, Bourque, Guillaume, primary, Brazma, Alvis, primary, Tost, Jörg, primary, Brennan, Paul, primary, Lathrop, Mark, primary, Riazalhosseini, Yasser, primary, and Banks, Rosamonde E., primary

Published
2023
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36. Data from Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma

Author

Vasudev, Naveen S., primary, Scelo, Ghislaine, primary, Glennon, Kate I., primary, Wilson, Michelle, primary, Letourneau, Louis, primary, Eveleigh, Robert, primary, Nourbehesht, Nazanin, primary, Arseneault, Madeleine, primary, Paccard, Antoine, primary, Egevad, Lars, primary, Viksna, Juris, primary, Celms, Edgars, primary, Jackson, Sharon M., primary, Abedi-Ardekani, Behnoush, primary, Warren, Anne Y., primary, Selby, Peter J., primary, Trainor, Sebastian, primary, Kimuli, Michael, primary, Cartledge, Jon, primary, Soomro, Naeem, primary, Adeyoju, Adebanji, primary, Patel, Poulam M., primary, Wozniak, Magdalena B., primary, Holcatova, Ivana, primary, Brisuda, Antonin, primary, Janout, Vladimir, primary, Chanudet, Estelle, primary, Zaridze, David, primary, Moukeria, Anush, primary, Shangina, Oxana, primary, Foretova, Lenka, primary, Navratilova, Marie, primary, Mates, Dana, primary, Jinga, Viorel, primary, Bogdanovic, Ljiljana, primary, Kovacevic, Bozidar, primary, Cambon-Thomsen, Anne, primary, Bourque, Guillaume, primary, Brazma, Alvis, primary, Tost, Jörg, primary, Brennan, Paul, primary, Lathrop, Mark, primary, Riazalhosseini, Yasser, primary, and Banks, Rosamonde E., primary

Published
2023
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37. Supplementary Figure 2 from DNA Methylation Status of Key Cell-Cycle Regulators Such as CDKNA2/p16 and CCNA1 Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors

Author

Klajic, Jovana, primary, Busato, Florence, primary, Edvardsen, Hege, primary, Touleimat, Nizar, primary, Fleischer, Thomas, primary, Bukholm, Ida, primary, Børresen-Dale, Anne-Lise, primary, Lønning, Per Eystein, primary, Tost, Jörg, primary, and Kristensen, Vessela N., primary

Published
2023
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38. Supplementary Table 1-6 from DNA Methylation Status of Key Cell-Cycle Regulators Such as CDKNA2/p16 and CCNA1 Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors

Author

Klajic, Jovana, primary, Busato, Florence, primary, Edvardsen, Hege, primary, Touleimat, Nizar, primary, Fleischer, Thomas, primary, Bukholm, Ida, primary, Børresen-Dale, Anne-Lise, primary, Lønning, Per Eystein, primary, Tost, Jörg, primary, and Kristensen, Vessela N., primary

Published
2023
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39. Supplementary Figure 1 from DNA Methylation Status of Key Cell-Cycle Regulators Such as CDKNA2/p16 and CCNA1 Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors

Author

Klajic, Jovana, primary, Busato, Florence, primary, Edvardsen, Hege, primary, Touleimat, Nizar, primary, Fleischer, Thomas, primary, Bukholm, Ida, primary, Børresen-Dale, Anne-Lise, primary, Lønning, Per Eystein, primary, Tost, Jörg, primary, and Kristensen, Vessela N., primary

Published
2023
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40. Supplementary Figure legends from DNA Methylation Status of Key Cell-Cycle Regulators Such as CDKNA2/p16 and CCNA1 Correlates with Treatment Response to Doxorubicin and 5-Fluorouracil in Locally Advanced Breast Tumors

Author

Klajic, Jovana, primary, Busato, Florence, primary, Edvardsen, Hege, primary, Touleimat, Nizar, primary, Fleischer, Thomas, primary, Bukholm, Ida, primary, Børresen-Dale, Anne-Lise, primary, Lønning, Per Eystein, primary, Tost, Jörg, primary, and Kristensen, Vessela N., primary

Published
2023
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41. Supplementary Table 1 from GSTP1 Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas

Author

Rønneberg, Jo Anders, primary, Tost, Jörg, primary, Solvang, Hiroko K., primary, Alnaes, Grethe I.G., primary, Johansen, Fredrik E., primary, Brendeford, Elen M., primary, Yakhini, Zohar, primary, Gut, Ivo G., primary, Lønning, Per Eystein, primary, Børresen-Dale, Anne-Lise, primary, Gabrielsen, Odd S., primary, and Kristensen, Vessela N., primary

Published
2023
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42. Supplementary Figure 3 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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43. Data from GSTP1 Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas

Author

Rønneberg, Jo Anders, primary, Tost, Jörg, primary, Solvang, Hiroko K., primary, Alnaes, Grethe I.G., primary, Johansen, Fredrik E., primary, Brendeford, Elen M., primary, Yakhini, Zohar, primary, Gut, Ivo G., primary, Lønning, Per Eystein, primary, Børresen-Dale, Anne-Lise, primary, Gabrielsen, Odd S., primary, and Kristensen, Vessela N., primary

Published
2023
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44. Supplementary Table 3 from GSTP1 Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas

Author

Rønneberg, Jo Anders, primary, Tost, Jörg, primary, Solvang, Hiroko K., primary, Alnaes, Grethe I.G., primary, Johansen, Fredrik E., primary, Brendeford, Elen M., primary, Yakhini, Zohar, primary, Gut, Ivo G., primary, Lønning, Per Eystein, primary, Børresen-Dale, Anne-Lise, primary, Gabrielsen, Odd S., primary, and Kristensen, Vessela N., primary

Published
2023
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45. Supplementary Figure 1 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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46. Supplementary Figure 1 from GSTP1 Promoter Haplotypes Affect DNA Methylation Levels and Promoter Activity in Breast Carcinomas

Author

Rønneberg, Jo Anders, primary, Tost, Jörg, primary, Solvang, Hiroko K., primary, Alnaes, Grethe I.G., primary, Johansen, Fredrik E., primary, Brendeford, Elen M., primary, Yakhini, Zohar, primary, Gut, Ivo G., primary, Lønning, Per Eystein, primary, Børresen-Dale, Anne-Lise, primary, Gabrielsen, Odd S., primary, and Kristensen, Vessela N., primary

Published
2023
Full Text
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47. Supplementary Table 2 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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48. Supplementary Table 1 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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49. Supplementary Figure 2 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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50. Supplementary Figure 4 from Quantitative Analysis of DNA Methylation Profiles in Lung Cancer Identifies Aberrant DNA Methylation of Specific Genes and Its Association with Gender and Cancer Risk Factors

Author

Vaissière, Thomas, primary, Hung, Rayjean J., primary, Zaridze, David, primary, Moukeria, Anush, primary, Cuenin, Cyrille, primary, Fasolo, Virginie, primary, Ferro, Gilles, primary, Paliwal, Anupam, primary, Hainaut, Pierre, primary, Brennan, Paul, primary, Tost, Jörg, primary, Boffetta, Paolo, primary, and Herceg, Zdenko, primary

Published
2023
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