TY - STD TI - Ambatipudi S, Cuenin C, Hernandez-Vargas H, Ghantous A, Le Calvez-Kelm F, Kaaks R, Herceg Z. Tobacco smoking-associated genome-wide DNA methylation changes in the EPIC study. Epigenomics. 2016;8(5):599–618. https://doi.org/10.2217/epi-2016-0001. ID - ref1 ER - TY - STD TI - Ambatipudi S, Horvath S, Perrier F, Cuenin C, Hernandez-Vargas H, Le Calvez-Kelm F, Herceg Z. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility. Eur J Cancer. 2017;75:299–307. https://doi.org/10.1016/j.ejca.2017.01.014 ID - ref2 ER - TY - STD TI - Ba Y, Yu H, Liu F, Geng X, Zhu C, Zhu Q, Zhang Y. Relationship of folate, vitamin B12 and methylation of insulin-like growth factor-II in maternal and cord blood. Eur J Clin Nutr. 2011;65(4):480–85. https://doi.org/10.1038/ejcn.2010.294. ID - ref3 ER - TY - JOUR AU - Baglietto, L. AU - English, D. R. AU - Gertig, D. M. AU - Hopper, J. L. AU - Giles, G. G. PY - 2005 DA - 2005// TI - Does dietary folate intake modify effect of alcohol consumption on breast cancer risk? Prospective cohort study JO - Bmj VL - 331 UR - https://doi.org/10.1136/bmj.38551.446470.06 DO - 10.1136/bmj.38551.446470.06 ID - Baglietto2005 ER - TY - STD TI - Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98. https://doi.org/10.1016/j.ygeno.2011.07.007. ID - ref5 ER - TY - STD TI - Bolstad B. M. Probe level quantile normalization of high density oligonucleotide array data. 2001. Retrieved from http://bmbolstad.com/stuff/qnorm.pdf UR - http://bmbolstad.com/stuff/qnorm.pdf ID - ref6 ER - TY - JOUR AU - Bouckaert, K. P. AU - Slimani, N. AU - Nicolas, G. AU - Vignat, J. AU - Wright, A. J. AU - Roe, M. AU - Finglas, P. M. PY - 2011 DA - 2011// TI - Critical evaluation of folate data in European and international databases: recommendations for standardization in international nutritional studies JO - Mol Nutr Food Res VL - 55 UR - https://doi.org/10.1002/mnfr.201000391 DO - 10.1002/mnfr.201000391 ID - Bouckaert2011 ER - TY - STD TI - Candès EJ, Wakin MB, Boyd SP. Enhancing sparsity by reweighted ℓ 1 minimization. J Fourier Anal Appl. 2008;14(5):877–905. https://doi.org/10.1007/s00041-008-9045-x. ID - ref8 ER - TY - STD TI - Chen M, Bresnick AR, O'Connor KL. Coupling S100A4 to Rhotekin alters Rho signaling output in breast cancer cells. Oncogene. 2012;32:3754. https://doi.org/10.1038/onc.2012.383https://www.nature.com/articles/onc2012383#supplementary-information. UR - https://www.nature.com/articles/onc2012383#supplementary-information ID - ref9 ER - TY - STD TI - Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Weksberg R. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8(2):203–09. https://doi.org/10.4161/epi.23470. ID - ref10 ER - TY - JOUR AU - Cole, S. R. AU - Platt, R. W. AU - Schisterman, E. F. AU - Chu, H. AU - Westreich, D. AU - Richardson, D. AU - Poole, C. PY - 2010 DA - 2010// TI - Illustrating bias due to conditioning on a collider JO - Int J Epidemiol VL - 39 UR - https://doi.org/10.1093/ije/dyp334 DO - 10.1093/ije/dyp334 ID - Cole2010 ER - TY - STD TI - de Batlle J, Ferrari P, Chajes V, Park J. Y, Slimani N, McKenzie F, Romieu I. Dietary folate intake and breast cancer risk: European prospective investigation into cancer and nutrition. J Natl Cancer Inst. 2015;107(1):367. https://doi.org/10.1093/jnci/dju367. ID - ref12 ER - TY - JOUR AU - Du, P. AU - Kibbe, W. A. AU - Lin, S. M. PY - 2008 DA - 2008// TI - Lumi: a pipeline for processing Illumina microarray JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn224 DO - 10.1093/bioinformatics/btn224 ID - Du2008 ER - TY - JOUR AU - Du, P. AU - Zhang, X. AU - Huang, C. -. C. AU - Jafari, N. AU - Kibbe, W. A. AU - Hou, L. AU - Lin, S. M. PY - 2010 DA - 2010// TI - Comparison of beta-value and M-value methods for quantifying methylation levels by microarray analysis JO - BMC Bioinformatics VL - 11 UR - https://doi.org/10.1186/1471-2105-11-587 DO - 10.1186/1471-2105-11-587 ID - Du2010 ER - TY - STD TI - Fan J, Ma LJ, Xia SJ, Yu L, Fu Q, Wu CQ, Tang XD. Association between clinical characteristics and expression abundance of RTKN gene in human bladder carcinoma tissues from Chinese patients. J Cancer Res Clin Oncol. 2005;131(3):157–62. https://doi.org/10.1007/s00432-004-0638-8. ID - ref15 ER - TY - BOOK AU - Hastie, T. PY - 2009 DA - 2009// TI - The elements of statistical learning: data mining, inference, and prediction UR - https://doi.org/10.1007/978-0-387-84858-7 DO - 10.1007/978-0-387-84858-7 ID - Hastie2009 ER - TY - STD TI - Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A. 2012;109. https://doi.org/10.1073/pnas.1120658109. ID - ref17 ER - TY - JOUR AU - Hino, K. AU - Saito, A. AU - Kido, M. AU - Kanemoto, S. AU - Asada, R. AU - Takai, T. AU - Imaizumi, K. PY - 2014 DA - 2014// TI - Master regulator for chondrogenesis, Sox9, regulates transcriptional activation of the endoplasmic reticulum stress transducer BBF2H7/CREB3L2 in chondrocytes JO - J Biol Chem VL - 289 UR - https://doi.org/10.1074/jbc.M113.543322 DO - 10.1074/jbc.M113.543322 ID - Hino2014 ER - TY - JOUR AU - Horvath, S. AU - Raj, K. PY - 2018 DA - 2018// TI - DNA methylation-based biomarkers and the epigenetic clock theory of ageing JO - Nat Rev Genet VL - 19 UR - https://doi.org/10.1038/s41576-018-0004-3 DO - 10.1038/s41576-018-0004-3 ID - Horvath2018 ER - TY - JOUR AU - Houseman, E. A. AU - Accomando, W. P. AU - Koestler, D. C. AU - Christensen, B. C. AU - Marsit, C. J. AU - Nelson, H. H. AU - Kelsey, K. T. PY - 2012 DA - 2012// TI - DNA methylation arrays as surrogate measures of cell mixture distribution JO - BMC Bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-86 DO - 10.1186/1471-2105-13-86 ID - Houseman2012 ER - TY - STD TI - Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Morgan M. Orchestrating high-throughput genomic analysis with bioconductor. Nat Methods. (2015);12(2):115–21. https://doi.org/10.1038/nmeth.3252. ID - ref21 ER - TY - STD TI - IARC Working Group on the Evaluation of Carcinogenic Risks to Humans. (2012). Personal habits and indoor combustions. Volume 100 E. A review of human carcinogens (1017–1606). Retrieved from https://www.ncbi.nlm.nih.gov/pubmed/23193840, https://www.ncbi.nlm.nih.gov/pmc/PMC4781577/. UR - https://www.ncbi.nlm.nih.gov/pmc/PMC4781577/ ID - ref22 ER - TY - BOOK PY - 2011 DA - 2011// TI - GenomeStudio/BeadStudio Software Methylation Module ID - ref23 ER - TY - JOUR AU - Joehanes, R. AU - Just, A. C. AU - Marioni, R. E. AU - Pilling, L. C. AU - Reynolds, L. M. AU - Mandaviya, P. R. AU - London, S. J. PY - 2016 DA - 2016// TI - Epigenetic signatures of cigarette smoking JO - Circ Cardiovasc Genet VL - 9 UR - https://doi.org/10.1161/circgenetics.116.001506 DO - 10.1161/circgenetics.116.001506 ID - Joehanes2016 ER - TY - JOUR AU - Joubert, B. R. AU - Dekker, H. T. AU - Felix, J. F. AU - Bohlin, J. AU - Ligthart, S. AU - Beckett, E. AU - London, S. J. PY - 2016 DA - 2016// TI - Maternal plasma folate impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms10577 DO - 10.1038/ncomms10577 ID - Joubert2016 ER - TY - STD TI - Kok DE, Dhonukshe-Rutten RA, Lute C, Heil SG, Uitterlinden AG, van der Velde N, Steegenga WT. The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects. Clin Epigenetics. 2015;7;121. https://doi.org/10.1186/s13148-015-0154-5. ID - ref26 ER - TY - JOUR AU - Kruman, I. I. AU - Fowler, A. K. PY - 2014 DA - 2014// TI - Impaired one carbon metabolism and DNA methylation in alcohol toxicity JO - J Neurochem VL - 129 UR - https://doi.org/10.1111/jnc.12677 DO - 10.1111/jnc.12677 ID - Kruman2014 ER - TY - JOUR AU - Lee, M. P. AU - Brandenburg, S. AU - Landes, G. M. AU - Adams, M. AU - Miller, G. AU - Feinberg, A. P. PY - 1999 DA - 1999// TI - Two novel genes in the center of the 11p15 imprinted domain escape genomic imprinting JO - Hum Mol Genet VL - 8 UR - https://doi.org/10.1093/hmg/8.4.683 DO - 10.1093/hmg/8.4.683 ID - Lee1999 ER - TY - JOUR AU - Leek, J. T. AU - Johnson, W. E. AU - Parker, H. S. AU - Jaffe, A. E. AU - Storey, J. D. PY - 2012 DA - 2012// TI - The sva package for removing batch effects and other unwanted variation in high-throughput experiments JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts034 DO - 10.1093/bioinformatics/bts034 ID - Leek2012 ER - TY - STD TI - Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3. https://doi.org/10.1371/journal.pgen.0030161. ID - ref30 ER - TY - JOUR AU - Leek, J. T. AU - Storey, J. D. PY - 2008 DA - 2008// TI - A general framework for multiple testing dependence JO - Proc Natl Acad Sci U S A VL - 105 UR - https://doi.org/10.1073/pnas.0808709105 DO - 10.1073/pnas.0808709105 ID - Leek2008 ER - TY - STD TI - Liu C, Marioni RE, Hedman AK, Pfeiffer L, Tsai PC, Reynolds LM, Levy D. A DNA methylation biomarker of alcohol consumption. Mol Psychiatry. 2016. https://doi.org/10.1038/mp.2016.192. ID - ref32 ER - TY - JOUR AU - Mason, J. B. AU - Choi, S. -. W. PY - 2005 DA - 2005// TI - Effects of alcohol on folate metabolism: implications for carcinogenesis JO - Alcohol VL - 35 UR - https://doi.org/10.1016/j.alcohol.2005.03.012 DO - 10.1016/j.alcohol.2005.03.012 ID - Mason2005 ER - TY - JOUR AU - Matejcic, M. AU - Batlle, J. AU - Ricci, C. AU - Biessy, C. AU - Perrier, F. AU - Huybrechts, I. AU - Chajes, V. PY - 2017 DA - 2017// TI - Biomarkers of folate and vitamin B12 and breast cancer risk: report from the EPIC cohort JO - Int J Cancer VL - 140 UR - https://doi.org/10.1002/ijc.30536 DO - 10.1002/ijc.30536 ID - Matejcic2017 ER - TY - STD TI - Niculescu MD, Haggarty P. Nutrition in epigenetics: Wiley; 2011. ID - ref35 ER - TY - JOUR AU - O'Leary, N. A. AU - Wright, M. W. AU - Brister, J. R. AU - Ciufo, S. AU - Haddad, D. AU - McVeigh, R. AU - Pruitt, K. D. PY - 2016 DA - 2016// TI - Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation JO - Nucleic Acids Res VL - 44 UR - https://doi.org/10.1093/nar/gkv1189 DO - 10.1093/nar/gkv1189 ID - O'Leary2016 ER - TY - JOUR AU - Panagopoulos, I. AU - Storlazzi, C. T. AU - Fletcher, C. D. AU - Fletcher, J. A. AU - Nascimento, A. AU - Domanski, H. A. AU - Mertens, F. PY - 2004 DA - 2004// TI - The chimeric FUS/CREB3l2 gene is specific for low-grade fibromyxoid sarcoma JO - Genes Chromosomes Cancer VL - 40 UR - https://doi.org/10.1002/gcc.20037 DO - 10.1002/gcc.20037 ID - Panagopoulos2004 ER - TY - JOUR AU - Patel, R. M. AU - Downs-Kelly, E. AU - Dandekar, M. N. AU - Fanburg-Smith, J. C. AU - Billings, S. D. AU - Tubbs, R. R. AU - Goldblum, J. R. PY - 2011 DA - 2011// TI - FUS (16p11) gene rearrangement as detected by fluorescence in-situ hybridization in cutaneous low-grade fibromyxoid sarcoma: a potential diagnostic tool JO - Am J Dermatopathol VL - 33 UR - https://doi.org/10.1097/IAE.0b013e318176de80 DO - 10.1097/IAE.0b013e318176de80 ID - Patel2011 ER - TY - JOUR AU - Peltomaki, P. AU - Chapelle, A. PY - 1997 DA - 1997// TI - Mutations predisposing to hereditary nonpolyposis colorectal cancer JO - Adv Cancer Res VL - 71 UR - https://doi.org/10.1016/S0065-230X(08)60097-4 DO - 10.1016/S0065-230X(08)60097-4 ID - Peltomaki1997 ER - TY - JOUR AU - Perrier, F. AU - Novoloaca, A. AU - Ambatipudi, S. AU - Baglietto, L. AU - Ghantous, A. AU - Perduca, V. AU - Ferrari, P. PY - 2018 DA - 2018// TI - Identifying and correcting epigenetics measurements for systematic sources of variation JO - Clin Epigenetics VL - 10 UR - https://doi.org/10.1186/s13148-018-0471-6 DO - 10.1186/s13148-018-0471-6 ID - Perrier2018 ER - TY - JOUR AU - Peters, T. J. AU - Buckley, M. J. AU - Statham, A. L. AU - Pidsley, R. AU - Samaras, K. AU - V Lord, R. AU - Molloy, P. L. PY - 2015 DA - 2015// TI - De novo identification of differentially methylated regions in the human genome JO - Epigenetics Chromatin VL - 8 UR - https://doi.org/10.1186/1756-8935-8-6 DO - 10.1186/1756-8935-8-6 ID - Peters2015 ER - TY - STD TI - Pochini L, Scalise M, Galluccio M, Indiveri C. Membrane transporters for the special amino acid glutamine: structure/function relationships and relevance to human health. Frontiers Chem. 2014;2(61). https://doi.org/10.3389/fchem.2014.00061. ID - ref42 ER - TY - JOUR AU - Riboli, E. AU - Hunt, K. J. AU - Slimani, N. AU - Ferrari, P. AU - Norat, T. AU - Fahey, M. AU - Saracci, R. PY - 2002 DA - 2002// TI - European Prospective Investigation into Cancer and Nutrition (EPIC): study populations and data collection JO - Public Health Nutr VL - 5 UR - https://doi.org/10.1079/phn2002394 DO - 10.1079/phn2002394 ID - Riboli2002 ER - TY - JOUR AU - Saeki, N. AU - Usui, T. AU - Aoyagi, K. AU - Kim, D. H. AU - Sato, M. AU - Mabuchi, T. AU - Sasaki, H. PY - 2009 DA - 2009// TI - Distinctive expression and function of four GSDM family genes (GSDMA-D) in normal and malignant upper gastrointestinal epithelium JO - Genes Chromosomes Cancer VL - 48 UR - https://doi.org/10.1002/gcc.20636 DO - 10.1002/gcc.20636 ID - Saeki2009 ER - TY - STD TI - Satterthwaite FE. An approximate distribution of estimates of variance components. Biometrics. 1946;2. https://doi.org/10.2307/3002019. ID - ref45 ER - TY - JOUR AU - Seifert, A. AU - Werheid, D. F. AU - Knapp, S. M. AU - Tobiasch, E. PY - 2015 DA - 2015// TI - Role of Hox genes in stem cell differentiation JO - World J Stem Cells VL - 7 UR - https://doi.org/10.4252/wjsc.v7.i3.583 DO - 10.4252/wjsc.v7.i3.583 ID - Seifert2015 ER - TY - JOUR AU - Shah, N. AU - Sukumar, S. PY - 2010 DA - 2010// TI - The Hox genes and their roles in oncogenesis JO - Nat Rev Cancer VL - 10 UR - https://doi.org/10.1038/nrc2826 DO - 10.1038/nrc2826 ID - Shah2010 ER - TY - JOUR AU - Sieri, S. AU - Agudo, A. AU - Kesse, E. AU - Klipstein-Grobusch, K. AU - San-Jose, B. AU - Welch, A. A. AU - Slimani, N. PY - 2002 DA - 2002// TI - Patterns of alcohol consumption in 10 European countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC) project JO - Public Health Nutr VL - 5 UR - https://doi.org/10.1079/phn2002405 DO - 10.1079/phn2002405 ID - Sieri2002 ER - TY - JOUR AU - Slimani, N. AU - Deharveng, G. AU - Unwin, I. AU - Southgate, D. A. AU - Vignat, J. AU - Skeie, G. AU - Riboli, E. PY - 2007 DA - 2007// TI - The EPIC nutrient database project (ENDB): a first attempt to standardize nutrient databases across the 10 European countries participating in the EPIC study JO - Eur J Clin Nutr VL - 61 UR - https://doi.org/10.1038/sj.ejcn.1602679 DO - 10.1038/sj.ejcn.1602679 ID - Slimani2007 ER - TY - JOUR AU - Slimani, N. AU - Kaaks, R. AU - Ferrari, P. AU - Casagrande, C. AU - Clavel-Chapelon, F. AU - Lotze, G. AU - Riboli, E. PY - 2007 DA - 2007// TI - European Prospective Investigation into Cancer and nutrition (EPIC) calibration study: rationale, design and population characteristics JO - Public Health Nutr VL - 5 UR - https://doi.org/10.1079/PHN2002395 DO - 10.1079/PHN2002395 ID - Slimani2007 ER - TY - STD TI - Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet and Mol Biol. 2004;3. ID - ref51 ER - TY - CHAP AU - Smyth, G. K. ED - Gentleman, R. ED - Carey, V. ED - Dudoit, S. ED - Irizarry, R. ED - Huber, W. PY - 2005 DA - 2005// TI - Limma: linear models for microarray data BT - Bioinformatics and computational biology solutions using R. and bioconductor PB - Springer CY - New York ID - Smyth2005 ER - TY - JOUR AU - Szyf, M. PY - 2011 DA - 2011// TI - The implications of DNA methylation for toxicology: toward toxicomethylomics, the toxicology of DNA methylation JO - Toxicol Sci VL - 120 UR - https://doi.org/10.1093/toxsci/kfr024 DO - 10.1093/toxsci/kfr024 ID - Szyf2011 ER - TY - JOUR AU - Teegarden, D. AU - Romieu, I. AU - Lelievre, S. A. PY - 2012 DA - 2012// TI - Redefining the impact of nutrition on breast cancer incidence: is epigenetics involved? JO - Nutr Res Rev VL - 25 UR - https://doi.org/10.1017/s0954422411000199 DO - 10.1017/s0954422411000199 ID - Teegarden2012 ER - TY - STD TI - Teo WW, Merino VF, Cho S, Korangath P, Liang X, Wu Rc, Sukumar S. HOXA5 determines cell fate transition and impedes tumor initiation and progression in breast cancer through regulation of E-cadherin and CD24. Oncogene. 2016;35(42):5539–51. https://doi.org/10.1038/onc.2016.95. ID - ref55 ER - TY - JOUR AU - Teschendorff, A. E. AU - Marabita, F. AU - Lechner, M. AU - Bartlett, T. AU - Tegner, J. AU - Gomez-Cabrero, D. AU - Beck, S. PY - 2013 DA - 2013// TI - A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts680 DO - 10.1093/bioinformatics/bts680 ID - Teschendorff2013 ER - TY - JOUR AU - Tibshirani, R. AU - Saunders, M. AU - Rosset, S. AU - Zhu, J. AU - Knight, K. PY - 2005 DA - 2005// TI - Sparsity and smoothness via the fused lasso JO - J. R. Stat. Soc. Ser. B Stat Methodol VL - 67 UR - https://doi.org/10.1111/j.1467-9868.2005.00490.x DO - 10.1111/j.1467-9868.2005.00490.x ID - Tibshirani2005 ER - TY - JOUR AU - Wareham, N. J. AU - Jakes, R. W. AU - Rennie, K. L. AU - Schuit, J. AU - Mitchell, J. AU - Hennings, S. AU - Day, N. E. PY - 2003 DA - 2003// TI - Validity and repeatability of a simple index derived from the short physical activity questionnaire used in the European Prospective Investigation into Cancer and Nutrition (EPIC) study JO - Public Health Nutr VL - 6 UR - https://doi.org/10.1079/phn2002439 DO - 10.1079/phn2002439 ID - Wareham2003 ER - TY - STD TI - World Cancer Research Fund International, & American Institue for Cancer Research. (2017). Continuous update project report: diet, nutrition, physical activity and breast cancer. Retrieved from https://www.wcrf.org/sites/default/files/Breast-Cancer-2017-Report.pdf UR - https://www.wcrf.org/sites/default/files/Breast-Cancer-2017-Report.pdf ID - ref59 ER - TY - JOUR AU - Zhang, S. AU - Hunter, D. J. AU - Hankinson, S. E. AU - Giovannucci, E. L. AU - Rosner, B. A. AU - Colditz, G. A. AU - Willett, W. C. PY - 1999 DA - 1999// TI - A prospective study of folate intake and the risk of breast cancer JO - JAMA VL - 281 UR - https://doi.org/10.1001/jama.281.17.1632 DO - 10.1001/jama.281.17.1632 ID - Zhang1999 ER - TY - JOUR AU - Zou, H. PY - 2006 DA - 2006// TI - The adaptive lasso and its oracle properties JO - J Am Stat Assoc VL - 101 UR - https://doi.org/10.1198/016214506000000735 DO - 10.1198/016214506000000735 ID - Zou2006 ER -