Advanced search
Publication Cover
Epigenetics Volume 13, 2018 - Issue 3
Submit an article Journal homepage
2,230
Views
8
CrossRef citations to date
0
Altmetric
Research Paper

Breast cancer family history and allele-specific DNA methylation in the legacy girls study

Hui-Chen WuHerbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY;Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NYView further author information
,
Catherine DoJohn Theurer Cancer Center, Hackensack University Medical Center, HackensackNJView further author information
,
Irene L. AndrulisLunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario;Departments of Molecular Genetics and Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, CanadaView further author information
,
Esther M. JohnCancer Prevention Institute of California, FremontCA;Department of Health Research & Policy (Epidemiology), and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CAView further author information
,
Mary B. DalyDepartment of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PAView further author information
,
Saundra S BuysDepartment of Medicine and, Huntsman Cancer Institute, University of Utah Health Sciences Center, UTView further author information
,
Wendy K. ChungDepartments of Pediatrics; Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NYView further author information
,
Julia A. KnightLunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario;Dalla Lana School of Public Health, University of Toronto, TorontoView further author information
,
Angela R. BradburyDepartments of Medicine, Division of Hematology/Oncology, Department of Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PAView further author information
,
Theresa H. M. KeeganCenter for Oncology Hematology Outcomes Research and Training (COHORT);Division of Hematology and Oncology, University of California Davis School of Medicine, Sacramento, CAView further author information
,
Lisa SchwartzDepartment of Pediatrics, Division of Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA;The Children's Hospital of Philadelphia, Philadelphia, PAView further author information
,
Izabela KrupskaHerbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NYView further author information
,
Rachel L. MillerHerbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY;Departments of Pediatrics; Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NYView further author information
,
Regina M. SantellaHerbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY;Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NYView further author information
,
Benjamin TyckoJohn Theurer Cancer Center, Hackensack University Medical Center, HackensackNJ;Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DCView further author information
&
Mary Beth TerryHerbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY;Department of Environmental Health Sciences, Mailman School of Public Health of Columbia University, New York, NY;Imprints Center, Columbia University Medical Center, New York, NY;Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NYCorrespondence[email protected]
View further author information
 show all
Pages 240-250 | Received 11 Jul 2017, Accepted 17 Jan 2018, Published online: 02 Apr 2018

References

  • Cancer CGoHFiB. Familial breast cancer: collaborative reanalysis of individual data from 52 epidemiological studies including 58 209 women with breast cancer and 101 986 women without the disease. The Lancet. 2001;358:1389–1399. doi:http://dx.doi.org/10.1016/S0140-6736(01)06524-2.
  • Stratton MR. Rahman N. The emerging landscape of breast cancer susceptibility. Nature Genet. 2008;40:17–22. doi:10.1038/ng.2007.53. PMID:18163131.
  • Shiovitz S, Korde LA. Genetics of breast cancer: a topic in evolution. Ann Oncol. 2015;26:1291–1299. doi:10.1093/annonc/mdv022. PMID:25605744
  • Esteller M, Silva JM, Dominguez G, et al. Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors. J Natl Cancer Inst. 2000;92:564–569. doi:10.1093/jnci/92.7.564. PMID:10749912
  • Rice JC, Ozcelik H, Maxeiner P, et al. Methylation of the BRCA1 promoter is associated with decreased BRCA1 mRNA levels in clinical breast cancer specimens. Carcinogenesis. 2000;21:1761–1765. doi:10.1093/carcin/21.9.1761. PMID:10964110
  • Widschwendter M, Jones P. DNA methylation and breast carcinogenesis. Oncogene. 2002;21:5462–5482. doi:10.1038/sj.onc.1205606. PMID:12154408
  • Terry MB, Delgado-Cruzata L, Vin-Raviv N, et al. DNA methylation in white blood cells: association with risk factors in epidemiologic studies. Epigenetics : official journal of the DNA Methylation Society. 2011;6:828–837. doi: 16500 [pii]. PMID: 21636973; PMCID: 3154425. doi:10.4161/epi.6.7.16500.
  • Ruiz-Hernandez A, Kuo C-C, Rentero-Garrido P, et al. Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence. Clin Epigenetics. 2015;7:55. PMID: doi:10.1186/s13148-015-0055-7. PMID:25984247
  • Wong EM, Southey MC, Fox SB, et al. Constitutional methylation of the BRCA1 promoter is specifically associated with BRCA1 mutation-associated pathology in early-onset breast cancer. Cancer Prev Res. 2011;4:23–33. doi:10.1158/1940-6207.capr-10-0212; PMCID: PMC4030007. PMID:20978112
  • Cho YH, McCullough LE, Gammon MD, et al. Promoter hypermethylation in white blood cell DNA and breast cancer risk. ‎J Cancer. 2015;6:819–824. doi:10.7150/jca.12174. PMID: PMC4532978. PMID:26284132
  • Severi G, Southey MC, English DR, et al. Epigenome-wide methylation in DNA from peripheral blood as a marker of risk for breast cancer. Breast Cancer Res Treat. 2014;148. doi:10.1007/s10549-014-3209-y.
  • van Veldhoven K, Polidoro S, Baglietto L, et al. Epigenome-wide association study reveals decreased average methylation levels years before breast cancer diagnosis. Clin Epigenetics. 2015;7:67. doi:10.1186/s13148-015-0104-2. PMID:26244061
  • Xu Z, Bolick SCE, DeRoo LA, et al. Epigenome-wide association study of breast cancer using prospectively collected sister study samples. JNCI J Natl Cancer Inst. 2013;105:694–700. doi:10.1093/jnci/djt045. PMID: PMC3653821. PMID:23578854
  • Fraser HB, Lam LL, Neumann SM, et al. Population-specificity of human DNA methylation. Genome Biol. 2012;13:R8–R8. doi:10.1186/gb-2012-13-2-r8. PMID: PMC3334571. PMID:22322129
  • Rushton MD, Reynard LN, Young DA, et al. Methylation quantitative trait locus (meQTL) analysis of osteoarthritis links epigenetics with genetic risk. Hum Mol Gen. 2015;24:7432–7444. doi:10.1093/hmg/ddv433. PMID:26464490
  • Bell JT, Pai AA, Pickrell JK, et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011;12:R10–R10. doi:10.1186/gb-2011-12-1-r10. PMID: PMC3091299. PMID:21251332
  • Do C, Lang CF, Lin J, et al. Mechanisms and disease associations of haplotype-dependent allele-specific DNA methylation. ‎Am J Hum Genet. 2016;98:934–955. doi:10.1016/j.ajhg.2016.03.027. PMID: 27153397; PMCID: 4863666. PMID:27153397
  • Tycko B. Mapping allele-specific DNA methylation: a new tool for maximizing information from GWAS. ‎Am J Hum Genet. 2010;86:109–112. doi:10.1016/j.ajhg.2010.01.021. PMID: 20159108; PMCID: 2820186. PMID:20159108
  • Cortijo S, Wardenaar R, Colomé-Tatché M, et al. Mapping the epigenetic basis of complex traits. Science. 2014;343:1145–1148. doi:10.1126/science.1248127. PMID:24505129
  • Wu HC, John EM, Ferris JS, et al. Global DNA methylation levels in girls with and without a family history of breast cancer. Epigenetics : official journal of the DNA Methylation Society. 2011;6:29–33. doi:10.4161/epi.6.1.13393. PMID: 20930546; PMCID: PMC3052913.
  • Do C, Shearer A, Suzuki M, et al. Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol. 2017;18:120. doi:10.1186/s13059-017-1250-y. PMID: PMC5477265. PMID:28629478
  • Dunning AM, Michailidou K, Kuchenbaecker KB, et al. Breast cancer risk variants at 6q25 display different phenotype associations and regulate ESR1, RMND1 and CCDC170. Nature Genet. 2016;48:374–386. doi:10.1038/ng.3521. PMID: PMC4938803. PMID:26928228
  • Stone A, Zotenko E, Locke WJ, et al. DNA methylation of oestrogen-regulated enhancers defines endocrine sensitivity in breast cancer. ‎Nat Commun. 2015;6:7758. doi:10.1038/ncomms8758. http://www.nature.com/articles/ncomms8758#supplementary-information. PMID:26169690
  • Koch A, De Meyer T, Jeschke J, et al. MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data. BMC Genomics. 2015;16:636. doi:10.1186/s12864-015-1847-z. PMID: PMC4549898. PMID:26306699
  • Jeffy BD, Chirnomas RB, Romagnolo DF. Epigenetics of breast cancer: polycyclic aromatic hydrocarbons as risk factors. Environ Mol Mutagen. 2002;39:235–244. doi:10.1002/em.10051. PMID:11921194
  • Li T, Zhao J, Yang J, et al. A Meta-Analysis of the Association between ESR1 genetic variants and the risk of breast cancer. PloS one. 2016;11:e0153314. doi:10.1371/journal.pone.0153314. PMID: PMC4829239. PMID:27070141
  • MacArthur J, Bowler E, Cerezo M, et al. The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog). Nucleic Acids Res. 2017;45:D896–D901. doi:10.1093/nar/gkw1133. PMID:27899670
  • Thorleifsson G, Walters GB, Gudbjartsson DF, et al. Genome-wide association yields new sequence variants at seven loci that associate with measures of obesity. Nat Genet. 2009;41:18–24. doi: http://www.nature.com/ng/journal/v41/n1/suppinfo/ng.274_S1.html. doi:10.1038/ng.274. PMID:19079260
  • The Genomes Project C. A global reference for human genetic variation. Nature. 2015;526:68–74. doi:10.1038/nature15393. PMID: PMC4750478. PMID:26432245
  • Day K, Waite LL, Alonso A, et al. Heritable DNA Methylation in CD4(+) cells among complex families displays genetic and non-genetic effects. PloS one. 2016;11:e0165488. doi:10.1371/journal.pone.0165488. PMID: PMC5085095. PMID:27792787
  • Zhai Y, Zhou G, Deng G, et al. Estrogen receptor α polymorphisms associated with susceptibility to hepatocellular carcinoma in hepatitis B birus carriers. Gastroenterology. 2009;130:2001–2009. doi:10.1053/j.gastro.2006.02.030.
  • Kundakovic M, Gudsnuk K, Franks B, et al. Sex-specific epigenetic disruption and behavioral changes following low-dose in utero bisphenol A exposure. Proc Natl Acad Sci USA. 2013;110:9956–9961. doi:10.1073/pnas.1214056110. PMID: PMC3683772. PMID:23716699
  • Joubert Bonnie R, Felix Janine F, Yousefi P, et al. DNA methylation in newborns and maternal smoking in pregnancy: genome-wide consortium meta-analysis. ‎Am J Hum Genet. 2016;98:680–696. doi: http://dx.doi.org/10.1016/j.ajhg.2016.02.019. PMID:27040690
  • Dvornyk V. Waqar-ul-Haq. Genetics of age at menarche: a systematic review. Hum Reprod Update. 2012;18:198–210. doi:10.1093/humupd/dmr050. PMID:22258758
  • Lv D, Zhang D-D, Wang H, et al. Genetic variations in SEC16B, MC4R, MAP2K5 and KCTD15 were associated with childhood obesity and interacted with dietary behaviors in Chinese school-age population. Gene. 2015;560:149–155. doi:http://dx.doi.org/10.1016/j.gene.2015.01.054. PMID:25637721
  • Leslie R, O'Donnell CJ, Johnson AD. GRASP: analysis of genotype–phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics (Oxford, England). 2014;30:i185–i194. doi:10.1093/bioinformatics/btu273. PMID: PMC4072913. PMID:24931982
  • Lonsdale J, Thomas J, Salvatore M, et al. The Genotype-Tissue Expression (GTEx) project. Nature Genet. 2013;45:580–585. doi:10.1038/ng.2653. http://www.nature.com/ng/journal/v45/n6/abs/ng.2653.html#supplementary-information. PMID:23715323
  • Choi J, Cha YJ, Koo JS. Adipocyte biology in breast cancer: from silent bystander to active facilitator. Prog Lipid Res. 2018;69:11–20. doi:https://doi.org/10.1016/j.plipres.2017.11.002.
  • Jia H, Truica CI, Wang B, et al. Immunotherapy for triple-negative breast cancer: existing challenges and exciting prospects. Drug Resist Updat. 2017;32:1–15. doi:https://doi.org/10.1016/j.drup.2017.07.002. PMID:29145974
  • Almstrup K, Lindhardt Johansen M, Busch AS, et al. Pubertal development in healthy children is mirrored by DNA methylation patterns in peripheral blood. Sci Rep. 2016;6:28657. doi:10.1038/srep28657. http://www.nature.com/articles/srep28657#supplementary-information. PMID:27349168
  • Flanagan JM, Munoz-Alegre M, Henderson S, et al. Gene-body hypermethylation of ATM in peripheral blood DNA of bilateral breast cancer patients. Hum Mol Gen. 2009;18:1332–1342. doi:10.1093/hmg/ddp033. PMID:19153073
  • Reinius LE, Acevedo N, Joerink M, et al. Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PloS one. 2012;7:e41361. doi:10.1371/journal.pone.0041361. PMID:22848472
  • John EM, Terry MB, Keegan THM, et al. The LEGACY girls study: examining early-life exposures, growth and development, and psychosocial well-being in the context of breast cancer family history. Epidemiology. 2016;27:438–448. doi:10.1097/EDE.0000000000000456. PMID:26829160
  • Terry MB, Goldberg M, Schechter S, et al. Comparison of clinical, maternal, and self pubertal assessments: implications for health studies. Pediatrics. 2016;138. doi:10.1542/peds.2015-4571. PMID:27544347
  • Wu H-C, Wang Q, Chung WK, et al. Correlation of DNA methylation levels in blood and saliva DNA in young girls of the LEGACY Girls study. Epigenetics : official journal of the DNA Methylation Society. 2014;9:929–933. doi:10.4161/epi.28902; PMCID: PMC4143407.
  • Purrington KS, Slager S, Eccles D, et al. Genome-wide association study identifies 25 known breast cancer susceptibility loci as risk factors for triple-negative breast cancer. Carcinogenesis. 2014;35:1012–1019. doi:10.1093/carcin/bgt404. PMID: PMC4004200. PMID:24325915
  • Welter D, MacArthur J, Morales J, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014;42(Database issue):D1001–D1006. doi:10.1093/nar/gkt1229. PMID: PMC3965119. PMID:24316577
  • Horikoshi M, Yaghootkar H, Mook-Kanamori DO, et al. New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism. Nature Genet. 2013;45:76–82. doi:10.1038/ng.2477. PMID: PMC3605762. PMID:23202124
  • Engel SM, Joubert BR, Wu MC, et al. Neonatal genome-wide methylation patterns in relation to birth weight in the norwegian mother and child cohort. Am J Epidemiol. 2014;179:834–842. doi:10.1093/aje/kwt433. PMID:24561991
  • Ernst J, Kheradpour P, Mikkelsen TS, et al. Systematic analysis of chromatin state dynamics in nine human cell types. Nature. 2011;473:43–49. doi:10.1038/nature09906. PMID: PMC3088773. PMID:21441907
  • Karolchik D, Hinrichs AS, Kent WJ. The UCSC genome browser. Curr Protoc Bioinformatics. 2009;CHAPTER:Unit1.4–Unit1.4. doi:10.1002/0471250953.bi0104s28. PMID: PMC2834533.
  • Robertson KD. DNA methylation and human disease. Nat Rev Genet. 2005;6:597–610. doi: http://www.nature.com/nrg/journal/v6/n8/suppinfo/nrg1655_S1.html. doi:10.1038/nrg1655. PMID:16136652
  • Li Y, Tollefsbol TO. DNA methylation detection: Bisulfite genomic sequencing analysis. Methods Mol Biol (Clifton, NJ). 2011;791:11–21. doi:10.1007/978-1-61779-316-5_2. PMID: PMC3233226.
  • Antoniou AC, Pharoah PPD, Smith P, et al. The BOADICEA model of genetic susceptibility to breast and ovarian cancer. Br ‎J Cancer. 2004;91:1580–1590. doi:10.1038/sj.bjc.6602175. PMID: PMC2409934. PMID:15381934
  • Terry MB, Keegan THM, Houghton LC, et al. Pubertal development in girls by breast cancer family history: the LEGACY girls cohort. Breast Cancer Res: BCR. 2017;19:69. doi:10.1186/s13058-017-0849-y. PMID: PMC5465536. PMID:28595647

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.