Michailidou K, Lindstrom S, Dennis J, Beesley J, Hui S, Kar S, et al. Association analysis identifies 65 new breast cancer risk loci. Nature. 2017;551(7678):92–4.
Article
PubMed
PubMed Central
CAS
Google Scholar
Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindstrom S, et al. Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer. Nat Genet. 2017;49(12):1767–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hu C, Hart SN, Gnanaolivu R, Huang H, Lee KY, Na J, et al. A population-based study of genes previously implicated in breast cancer. N Engl J Med. 2021.
Breast Cancer Association C, Dorling L, Carvalho S, Allen J, Gonzalez-Neira A, Luccarini C, et al. Breast Cancer Risk Genes—Association Analysis in More than 113,000 Women. N Engl J Med. 2021;384(5):428–39.
Feng H, Gusev A, Pasaniuc B, Wu L, Long J, Abu-Full Z, et al. Transcriptome-wide association study of breast cancer risk by estrogen-receptor status. Genet Epidemiol. 2020;44(5):442–68.
Article
PubMed
PubMed Central
Google Scholar
Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomaki K, Andrulis IL, Anton-Culver H, et al. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nat Commun. 2019;10(1):1741.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gao G, Pierce BL, Olopade OI, Im HK, Huo D. Trans-ethnic predicted expression genome-wide association analysis identifies a gene for estrogen receptor-negative breast cancer. PLoS Genet. 2017;13(9):e1006727.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hoffman JD, Graff RE, Emami NC, Tai CG, Passarelli MN, Hu D, et al. Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. PLoS Genet. 2017;13(3):e1006690.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu L, Shi W, Long J, Guo X, Michailidou K, Beesley J, et al. A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer. Nat Genet. 2018;50(7):968–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kothari C, Ouellette G, Labrie Y, Jacob S, Diorio C, Durocher F. Identification of a gene signature for different stages of breast cancer development that could be used for early diagnosis and specific therapy. Oncotarget. 2018;9(100):37407–20.
Article
PubMed
PubMed Central
Google Scholar
Cantone I, Fisher AG. Epigenetic programming and reprogramming during development. Nat Struct Mol Biol. 2013;20(3):282–9.
Article
CAS
PubMed
Google Scholar
Hansmann T, Pliushch G, Leubner M, Kroll P, Endt D, Gehrig A, et al. Constitutive promoter methylation of BRCA1 and RAD51C in patients with familial ovarian cancer and early-onset sporadic breast cancer. Hum Mol Genet. 2012;21(21):4669–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones PA, Baylin SB. The epigenomics of cancer. Cell. 2007;128(4):683–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Marino N, German R, Rao X, Simpson E, Liu S, Wan J, et al. Upregulation of lipid metabolism genes in the breast prior to cancer diagnosis. NPJ Breast Cancer. 2020;6:50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Latimer JJ, Johnson JM, Kelly CM, Miles TD, Beaudry-Rodgers KA, Lalanne NA, et al. Nucleotide excision repair deficiency is intrinsic in sporadic stage I breast cancer. Proc Natl Acad Sci USA. 2010;107(50):21725–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ziegler Y, Laws MJ, Sanabria Guillen V, Kim SH, Dey P, Smith BP, et al. Suppression of FOXM1 activities and breast cancer growth in vitro and in vivo by a new class of compounds. NPJ Breast Cancer. 2019;5:45.
Article
PubMed
PubMed Central
Google Scholar
Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012;486(7403):346–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, et al. The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun. 2016;7:11479.
Article
CAS
PubMed
PubMed Central
Google Scholar
Piazza R, Ramazzotti D, Spinelli R, Pirola A, De Sano L, Ferrari P, et al. OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes. Sci Rep. 2017;7:46290.
Article
PubMed
Google Scholar
Kumar B, Prasad M, Bhat-Nakshatri P, Anjanappa M, Kalra M, Marino N, et al. Normal breast-derived epithelial cells with luminal and intrinsic subtype-enriched gene expression document interindividual differences in their differentiation cascade. Cancer Res. 2018;78(17):5107–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Neri F, Rapelli S, Krepelova A, Incarnato D, Parlato C, Basile G, et al. Intragenic DNA methylation prevents spurious transcription initiation. Nature. 2017;543(7643):72–7.
Article
CAS
PubMed
Google Scholar
Kulis M, Heath S, Bibikova M, Queiros AC, Navarro A, Clot G, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet. 2012;44(11):1236–42.
Article
CAS
PubMed
Google Scholar
Kufe DW. MUC1-C oncoprotein as a target in breast cancer: activation of signaling pathways and therapeutic approaches. Oncogene. 2013;32(9):1073–81.
Article
CAS
PubMed
Google Scholar
Jing X, Liang H, Hao C, Yang X, Cui X. Overexpression of MUC1 predicts poor prognosis in patients with breast cancer. Oncol Rep. 2019;41(2):801–10.
CAS
PubMed
Google Scholar
Saghafinia S, Mina M, Riggi N, Hanahan D, Ciriello G. Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Rep. 2018;25(4):1066–80 e8.
Chen X, Zhang J, Dai X. DNA methylation profiles capturing breast cancer heterogeneity. BMC Genomics. 2019;20(1):823.
Article
PubMed
PubMed Central
CAS
Google Scholar
de Almeida BP, Apolonio JD, Binnie A, Castelo-Branco P. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer. 2019;19(1):219.
Article
PubMed
PubMed Central
Google Scholar
Xu Z, Sandler DP, Taylor JA. Blood DNA methylation and breast cancer: a prospective case-cohort analysis in the sister study. J Natl Cancer Inst. 2020;112(1):87–94.
Article
PubMed
CAS
Google Scholar
Johnson KC, Houseman EA, King JE, Christensen BC. Normal breast tissue DNA methylation differences at regulatory elements are associated with the cancer risk factor age. Breast Cancer Res. 2017;19(1):81.
Article
PubMed
PubMed Central
CAS
Google Scholar
Sehl ME, Henry JE, Storniolo AM, Ganz PA, Horvath S. DNA methylation age is elevated in breast tissue of healthy women. Breast Cancer Res Treat. 2017;164(1):209–19.
Article
CAS
PubMed
PubMed Central
Google Scholar
Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):R115.
Article
PubMed
PubMed Central
Google Scholar
Tyrer J, Duffy SW, Cuzick J. A breast cancer prediction model incorporating familial and personal risk factors. Stat Med. 2004;23(7):1111–30.
Article
PubMed
Google Scholar
Branigan TB, Kozono D, Schade AE, Deraska P, Rivas HG, Sambel L, et al. MMB-FOXM1-driven premature mitosis is required for CHK1 inhibitor sensitivity. Cell Rep. 2021;34(9):108808.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fulcher LJ, Bozatzi P, Tachie-Menson T, Wu KZL, Cummins TD, Bufton JC, et al. The DUF1669 domain of FAM83 family proteins anchor casein kinase 1 isoforms. Sci Signal. 2018;11:531.
Article
CAS
Google Scholar
Cipriano R, Graham J, Miskimen KL, Bryson BL, Bruntz RC, Scott SA, et al. FAM83B mediates EGFR- and RAS-driven oncogenic transformation. J Clin Invest. 2012;122(9):3197–210.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cipriano R, Miskimen KL, Bryson BL, Foy CR, Bartel CA, Jackson MW. Conserved oncogenic behavior of the FAM83 family regulates MAPK signaling in human cancer. Mol Cancer Res. 2014;12(8):1156–65.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parameswaran N, Bartel CA, Hernandez-Sanchez W, Miskimen KL, Smigiel JM, Khalil AM, et al. A FAM83A positive feed-back loop drives survival and tumorigenicity of pancreatic ductal adenocarcinomas. Sci Rep. 2019;9(1):13396.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bartel CA, Jackson MW. HER2-positive breast cancer cells expressing elevated FAM83A are sensitive to FAM83A loss. PLoS ONE. 2017;12(5):e0176778.
Article
PubMed
PubMed Central
CAS
Google Scholar
Richtmann S, Wilkens D, Warth A, Lasitschka F, Winter H, Christopoulos P, et al. FAM83A and FAM83B as prognostic biomarkers and potential new therapeutic targets in NSCLC. Cancers (Basel). 2019;11(5).
Zheng YW, Li ZH, Lei L, Liu CC, Wang Z, Fei LR, et al. FAM83A promotes lung cancer progression by regulating the wnt and hippo signaling pathways and indicates poor prognosis. Front Oncol. 2020;10:180.
Article
PubMed
PubMed Central
Google Scholar
Snijders AM, Lee SY, Hang B, Hao W, Bissell MJ, Mao JH. FAM83 family oncogenes are broadly involved in human cancers: an integrative multi-omics approach. Mol Oncol. 2017;11(2):167–79.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang J, Sun G, Mei X. Elevated FAM83A expression predicts poorer clincal outcome in lung adenocarcinoma. Cancer Biomark. 2019;26(3):367–73.
Article
CAS
PubMed
Google Scholar
Rong L, Li H, Li Z, Ouyang J, Ma Y, Song F, et al. FAM83A as a potential biological marker is regulated by miR-206 to promote cervical cancer progression through PI3K/AKT/mTOR pathway. Front Med (Lausanne). 2020;7:608441.
Article
Google Scholar
Pawitan Y, Bjohle J, Amler L, Borg AL, Egyhazi S, Hall P, et al. Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts. Breast Cancer Res. 2005;7(6):R953–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee SY, Meier R, Furuta S, Lenburg ME, Kenny PA, Xu R, et al. FAM83A confers EGFR-TKI resistance in breast cancer cells and in mice. J Clin Invest. 2012;122(9):3211–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Grant S. FAM83A and FAM83B: candidate oncogenes and TKI resistance mediators. J Clin Invest. 2012;122(9):3048–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hayward DG, Fry AM. Nek2 kinase in chromosome instability and cancer. Cancer Lett. 2006;237(2):155–66.
Article
CAS
PubMed
Google Scholar
Chen S, Huang J, Liu Z, Liang Q, Zhang N, Jin Y. FAM83A is amplified and promotes cancer stem cell-like traits and chemoresistance in pancreatic cancer. Oncogenesis. 2017;6(3):e300.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fry AM, O’Regan L, Sabir SR, Bayliss R. Cell cycle regulation by the NEK family of protein kinases. J Cell Sci. 2012;125(Pt 19):4423–33.
CAS
PubMed
PubMed Central
Google Scholar
Hayward DG, Clarke RB, Faragher AJ, Pillai MR, Hagan IM, Fry AM. The centrosomal kinase Nek2 displays elevated levels of protein expression in human breast cancer. Cancer Res. 2004;64(20):7370–6.
Article
CAS
PubMed
Google Scholar
Kokuryo T, Yokoyama Y, Yamaguchi J, Tsunoda N, Ebata T, Nagino M. NEK2 Is an effective target for cancer therapy with potential to induce regression of multiple human malignancies. Anticancer Res. 2019;39(5):2251–8.
Article
CAS
PubMed
Google Scholar
Fang Y, Zhang X. Targeting NEK2 as a promising therapeutic approach for cancer treatment. Cell Cycle. 2016;15(7):895–907.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gormally MV, Dexheimer TS, Marsico G, Sanders DA, Lowe C, Matak-Vinkovic D, et al. Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition. Nat Commun. 2014;5:5165.
Article
CAS
PubMed
Google Scholar
Cho YH, Yazici H, Wu HC, Terry MB, Gonzalez K, Qu M, et al. Aberrant promoter hypermethylation and genomic hypomethylation in tumor, adjacent normal tissues and blood from breast cancer patients. Anticancer Res. 2010;30(7):2489–96.
CAS
PubMed
PubMed Central
Google Scholar
Esteller M, Silva JM, Dominguez G, Bonilla F, Matias-Guiu X, Lerma E, et al. Promoter hypermethylation and BRCA1 inactivation in sporadic breast and ovarian tumors. J Natl Cancer Inst. 2000;92(7):564–9.
Article
CAS
PubMed
Google Scholar
Flanagan JM, Munoz-Alegre M, Henderson S, Tang T, Sun P, Johnson N, et al. Gene-body hypermethylation of ATM in peripheral blood DNA of bilateral breast cancer patients. Hum Mol Genet. 2009;18(7):1332–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Potapova A, Hoffman AM, Godwin AK, Al-Saleem T, Cairns P. Promoter hypermethylation of the PALB2 susceptibility gene in inherited and sporadic breast and ovarian cancer. Cancer Res. 2008;68(4):998–1002.
Article
CAS
PubMed
Google Scholar
Eswaran J, Patnaik D, Filippakopoulos P, Wang F, Stein RL, Murray JW, et al. Structure and functional characterization of the atypical human kinase haspin. Proc Natl Acad Sci U S A. 2009;106(48):20198–203.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin. 2020;70(1):7–30.
Article
PubMed
Google Scholar
Teschendorff AE, Zhu T, Breeze CE, Beck S. EPISCORE: cell type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data. Genome Biol. 2020;21(1):221.
Article
CAS
PubMed
PubMed Central
Google Scholar
Newman AM, Steen CB, Liu CL, Gentles AJ, Chaudhuri AA, Scherer F, et al. Determining cell type abundance and expression from bulk tissues with digital cytometry. Nat Biotechnol. 2019;37(7):773–82.
Article
CAS
PubMed
PubMed Central
Google Scholar
McClintock AH, Golob AL, Laya MB. Breast cancer risk assessment: a step-wise approach for primary care providers on the front lines of shared decision Making. Mayo Clin Proc. 2020;95(6):1268–75.
Article
PubMed
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21.
Article
CAS
PubMed
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maiuri AR, Peng M, Podicheti R, Sriramkumar S, Kamplain CM, Rusch DB, et al. Mismatch repair proteins initiate epigenetic alterations during inflammation-driven tumorigenesis. Cancer Res. 2017;77(13):3467–78.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maiuri AR, Savant SS, Podicheti R, Rusch DB, O’Hagan HM. DNA methyltransferase inhibition reduces inflammation-induced colon tumorigenesis. Epigenetics. 2019;14(12):1209–23.
Article
PubMed
PubMed Central
Google Scholar
Cheadle C, Vawter MP, Freed WJ, Becker KG. Analysis of microarray data using Z score transformation. J Mol Diagn. 2003;5(2):73–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kramer A, Green J, Pollard J Jr, Tugendreich S. Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics. 2014;30(4):523–30.
Article
PubMed
CAS
Google Scholar
Chandrashekar DS, Bashel B, Balasubramanya SAH, Creighton CJ, Ponce-Rodriguez I, Chakravarthi B, et al. UALCAN: a portal for facilitating tumor subgroup gene expression and survival analyses. Neoplasia. 2017;19(8):649–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nakshatri H, Kumar B, Burney HN, Cox ML, Jacobsen M, Sandusky GE, et al. Genetic ancestry-dependent differences in breast cancer-induced field defects in the tumor-adjacent normal breast. Clin Cancer Res. 2019;25(9):2848–59.
Article
CAS
PubMed
Google Scholar
Sandusky GE, Mintze KS, Pratt SE, Dantzig AH. Expression of multidrug resistance-associated protein 2 (MRP2) in normal human tissues and carcinomas using tissue microarrays. Histopathology. 2002;41(1):65–74.
Article
CAS
PubMed
Google Scholar