Prediction of blood-based biomarkers and subsequent design of bisulfite PCR-LDR-qPCR assay for breast cancer detection

[1]  F. Tang,et al.  Comprehensive DNA methylation analysis of tissue of origin of plasma cell-free DNA by methylated CpG tandem amplification and sequencing (MCTA-Seq) , 2019, Clinical Epigenetics.

[2]  M. Akbari,et al.  Liquid biopsy in breast cancer: A comprehensive review , 2019, Clinical genetics.

[3]  Chiang-Ching Huang,et al.  Bioinformatics Analysis for Circulating Cell-Free DNA in Cancer , 2019, Cancers.

[4]  S. Lippman,et al.  Genomic Assessment of Blood-Derived Circulating Tumor DNA in Patients With Colorectal Cancers: Correlation With Tissue Sequencing, Therapeutic Response, and Survival , 2019, JCO precision oncology.

[5]  Je-Yoel Cho,et al.  Methylation of LINE-1 in cell-free DNA serves as a liquid biopsy biomarker for human breast cancers and dog mammary tumors , 2019, Scientific Reports.

[6]  Ekaterini Chatzaki,et al.  Circulating cell-free DNA in breast cancer: size profiling, levels, and methylation patterns lead to prognostic and predictive classifiers , 2019, Oncogene.

[7]  F. Puglisi,et al.  Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? , 2019, Cancer treatment reviews.

[8]  J. McPherson,et al.  Sensitive tumour detection and classification using plasma cell-free DNA methylomes , 2018, Nature.

[9]  J. Sicklick,et al.  Analysis of Circulating Tumor DNA and Clinical Correlates in Patients with Esophageal, Gastroesophageal Junction, and Gastric Adenocarcinoma , 2018, Clinical Cancer Research.

[10]  Y. Dor,et al.  Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease , 2018, bioRxiv.

[11]  A. Jemal,et al.  Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries , 2018, CA: a cancer journal for clinicians.

[12]  Peilin Huang,et al.  Deletion of long noncoding RNA EFNA3 aggravates hypoxia‐induced injury in PC‐12 cells by upregulation of miR‐101a , 2018, Journal of cellular biochemistry.

[13]  C. Weinberg,et al.  Vitamin D, DNA methylation, and breast cancer , 2018, Breast cancer research : BCR.

[14]  P. Laird,et al.  Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification , 2018, Annals of oncology : official journal of the European Society for Medical Oncology.

[15]  D. Xing,et al.  LRH1 enhances cell resistance to chemotherapy by transcriptionally activating MDC1 expression and attenuating DNA damage in human breast cancer , 2018, Oncogene.

[16]  Ann Siew Gek Lee,et al.  The future of blood-based biomarkers for the early detection of breast cancer. , 2018, European journal of cancer.

[17]  M. Rohanizadegan.  Analysis of circulating tumor DNA in breast cancer as a diagnostic and prognostic biomarker. , 2018, Cancer genetics.

[18]  S. Libutti,et al.  Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model , 2018, Front. Genet..

[19]  V. Georgoulias,et al.  ESR1 Methylation: A Liquid Biopsy–Based Epigenetic Assay for the Follow-up of Patients with Metastatic Breast Cancer Receiving Endocrine Treatment , 2017, Clinical Cancer Research.

[20]  S. Mortimer,et al.  The Landscape of Actionable Genomic Alterations in Cell-Free Circulating Tumor DNA from 21,807 Advanced Cancer Patients , 2017, Clinical Cancer Research.

[21]  M. Nykter,et al.  Concordance of Circulating Tumor DNA and Matched Metastatic Tissue Biopsy in Prostate Cancer , 2017, Journal of the National Cancer Institute.

[22]  M. Gerlinger,et al.  Ultra-Sensitive Mutation Detection and Genome-Wide DNA Copy Number Reconstruction by Error-Corrected Circulating Tumor DNA Sequencing. , 2018, Clinical chemistry.

[23]  Sam Angiuoli,et al.  Direct detection of early-stage cancers using circulating tumor DNA , 2017, Science Translational Medicine.

[24]  Kylie L. Gorringe,et al.  LRH-1 expression patterns in breast cancer tissues are associated with tumour aggressiveness , 2017, Oncotarget.

[25]  Ryan E. Mills,et al.  Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy , 2017, Oncotarget.

[26]  Z. Herceg,et al.  Targeted deep sequencing of plasma circulating cell-free DNA reveals Vimentin and Fibulin 1 as potential epigenetic biomarkers for hepatocellular carcinoma , 2017, PloS one.

[27]  L. Cope,et al.  Monitoring of Serum DNA Methylation as an Early Independent Marker of Response and Survival in Metastatic Breast Cancer: TBCRC 005 Prospective Biomarker Study. , 2017, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[28]  S. Noguchi,et al.  Correlation of Methylated Circulating Tumor DNA With Response to Neoadjuvant Chemotherapy in Breast Cancer Patients , 2017, Clinical breast cancer.

[29]  F. Claret,et al.  Mutual regulation of microRNAs and DNA methylation in human cancers , 2017, Epigenetics.

[30]  R. Tetzner,et al.  Validation of the SHOX2/PTGER4 DNA Methylation Marker Panel for Plasma-Based Discrimination between Patients with Malignant and Nonmalignant Lung Disease , 2017, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[31]  Yijun Sun,et al.  Tracing anti-cancer and cancer-promoting actions of all-trans retinoic acid in breast cancer to a RARa epigenetic mechanism of mammary epithelial cell fate , 2016, Oncotarget.

[32]  B. Burwinkel,et al.  Blood-based DNA methylation as biomarker for breast cancer: a systematic review , 2016, Clinical Epigenetics.

[33]  P. Leung,et al.  Sprouty2 inhibits amphiregulin-induced down-regulation of E-cadherin and cell invasion in human ovarian cancer cells , 2016, Oncotarget.

[34]  P. Meltzer,et al.  Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors , 2016, Genome research.

[35]  A. Robles,et al.  Methylation analyses in liquid biopsy. , 2016, Translational lung cancer research.

[36]  Vincenza Conteduca,et al.  Cell-free DNA as a diagnostic marker for cancer: current insights , 2016, OncoTargets and therapy.

[37]  P. Prorok,et al.  Breast-Cancer Tumor Size, Overdiagnosis, and Mammography Screening Effectiveness. , 2016, The New England journal of medicine.

[38]  E. Lianidou,et al.  Development and validation of a multiplex methylation specific PCR-coupled liquid bead array for liquid biopsy analysis. , 2016, Clinica chimica acta; international journal of clinical chemistry.

[39]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[40]  Amos S Hundert,et al.  Breast cancer subtype dictates DNA methylation and ALDH1A3-mediated expression of tumor suppressor RARRES1 , 2016, Oncotarget.

[41]  G. Sölétormos,et al.  Detection and monitoring of hypermethylated RASSF1A in serum from patients with metastatic breast cancer , 2016, Clinical Epigenetics.

[42]  Dong Wang,et al.  Detection of aberrant methylation of a six-gene panel in serum DNA for diagnosis of breast cancer , 2016, Oncotarget.

[43]  Amy Cantor,et al.  Harms of Breast Cancer Screening: Systematic Review to Update the 2009 U.S. Preventive Services Task Force Recommendation , 2016, Annals of Internal Medicine.

[44]  Shinzaburo Noguchi,et al.  Promoter methylation of TRIM9 as a marker for detection of circulating tumor DNA in breast cancer patients , 2015, SpringerPlus.

[45]  David H. Murray,et al.  Evaluation of an assay for methylated BCAT1 and IKZF1 in plasma for detection of colorectal neoplasia , 2015, BMC Cancer.

[46]  E. Ma,et al.  Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments , 2015, Proceedings of the National Academy of Sciences.

[47]  Z. Herceg,et al.  Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing. , 2015, Epigenomics.

[48]  Joshy George,et al.  Whole–genome characterization of chemoresistant ovarian cancer , 2015, Nature.

[49]  G. Lippi,et al.  Comparison of Genetic and Epigenetic Alterations of Primary Tumors and Matched Plasma Samples in Patients with Colorectal Cancer , 2015, PloS one.

[50]  Jennifer S. Woo,et al.  The cerebellum ages slowly according to the epigenetic clock , 2015, Aging.

[51]  A. Feinberg,et al.  Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin , 2015, Genome Biology.

[52]  D. Neureiter,et al.  Histone deacetylation meets miRNA: epigenetics and post-transcriptional regulation in cancer and chronic diseases , 2015, Expert opinion on biological therapy.

[53]  Chuanli Ren,et al.  Sox17 Promoter Methylation in Plasma DNA Is Associated With Poor Survival and Can Be Used as a Prognostic Factor in Breast Cancer , 2015, Medicine.

[54]  S. Bianco,et al.  LRH-1 controls proliferation in breast tumor cells by regulating CDKN1A gene expression , 2014, Oncogene.

[55]  J. Custódio,et al.  Interplay between estrogen and retinoid signaling in breast cancer--current and future perspectives. , 2014, Cancer letters.

[56]  A. Harris,et al.  EFNA3 long noncoding RNAs induced by hypoxia promote metastatic dissemination , 2014, Oncogene.

[57]  Zhe Zhang,et al.  Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. , 2014, Cancer research.

[58]  Mylène Brunelle,et al.  LRH-1 governs vital transcriptional programs in endocrine-sensitive and -resistant breast cancer cells. , 2014, Cancer research.

[59]  Michael C. Ostrowski,et al.  Protein Kinase C Beta in the Tumor Microenvironment Promotes Mammary Tumorigenesis , 2014, Front. Oncol..

[60]  Peter A. Jones,et al.  Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers , 2014, Oncotarget.

[61]  M. Grce,et al.  Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer , 2013, Epigenetics.

[62]  S. Jeffrey,et al.  Circulating tumor cells versus tumor-derived cell-free DNA: rivals or partners in cancer care in the era of single-cell analysis? , 2013, Genome Medicine.

[63]  H. Fan,et al.  Overexpression of CARM1 in breast cancer is correlated with poorly characterized clinicopathologic parameters and molecular subtypes , 2013, Diagnostic Pathology.

[64]  D. Absher,et al.  Genome-Wide DNA Methylation Analysis of Systemic Lupus Erythematosus Reveals Persistent Hypomethylation of Interferon Genes and Compositional Changes to CD4+ T-cell Populations , 2013, PLoS genetics.

[65]  I. Ellis,et al.  The oestrogen receptor coactivator CARM1 has an oncogenic effect and is associated with poor prognosis in breast cancer , 2013, Breast Cancer Research and Treatment.

[66]  J. Pérez-Ortín,et al.  Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis , 2013, Cell.

[67]  Martin J. Aryee,et al.  Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in Rheumatoid Arthritis , 2013, Nature Biotechnology.

[68]  P. Fasching,et al.  Promoter hypermethylation of the tumor-suppressor genes ITIH5, DKK3, and RASSF1A as novel biomarkers for blood-based breast cancer screening , 2013, Breast Cancer Research.

[69]  Mary Goldman,et al.  The UCSC Cancer Genomics Browser: update 2015 , 2014, Nucleic Acids Res..

[70]  Y. Bignon,et al.  BRCA1 promoter methylation in peripheral blood DNA was identified in sporadic breast cancer and controls. , 2012, Cancer epidemiology.

[71]  A. Chand,et al.  The Orphan Nuclear Receptor LRH-1 and ERα Activate GREB1 Expression to Induce Breast Cancer Cell Proliferation , 2012, PloS one.

[72]  David G. Pisano,et al.  Cdc14b regulates mammalian RNA polymerase II and represses cell cycle transcription , 2011, Scientific reports.

[73]  Ava Kwong,et al.  Quantitative Analysis and Diagnostic Significance of Methylated SLC19A3 DNA in the Plasma of Breast and Gastric Cancer Patients , 2011, PloS one.

[74]  L. Gudas,et al.  Retinoids, retinoic acid receptors, and cancer. , 2011, Annual review of pathology.

[75]  Jennifer D. Brooks,et al.  DNA methylation in pre-diagnostic serum samples of breast cancer cases: results of a nested case-control study. , 2010, Cancer epidemiology.

[76]  Mary Goldman,et al.  The UCSC cancer genomics browser: update 2011 , 2010, Nucleic Acids Res..

[77]  Ting Wang,et al.  The UCSC Cancer Genomics Browser , 2009, Nature Methods.

[78]  Harikrishna Nakshatri,et al.  FOXA1 in breast cancer , 2009, Expert Reviews in Molecular Medicine.

[79]  M. Kazanietz,et al.  Opposite effects of protein kinase C beta1 (PKCβ1) and PKCε in the metastatic potential of a breast cancer murine model , 2009, Breast Cancer Research and Treatment.

[80]  M. Villalobos,et al.  Quantitative detection of methylated ESR1 and 14-3-3-σ gene promoters in serum as candidate biomarkers for diagnosis of breast cancer and evaluation of treatment efficacy , 2008, Cancer biology & therapy.

[81]  Bela Molnar,et al.  DNA methylation biomarkers for blood-based colorectal cancer screening. , 2008, Clinical chemistry.

[82]  S. Turcotte,et al.  Prostate-derived Ets transcription factor overexpression is associated with nodal metastasis and hormone receptor positivity in invasive breast cancer. , 2007, Neoplasia.

[83]  Jérôme Eeckhoute,et al.  Positive Cross-Regulatory Loop Ties GATA-3 to Estrogen Receptor α Expression in Breast Cancer , 2007 .

[84]  Anurag Srivastava,et al.  Promoter hypermethylation of p16INK4A, p14ARF, CyclinD2 and Slit2 in serum and tumor DNA from breast cancer patients. , 2007, Life sciences.

[85]  J. Issa,et al.  DNA Methylation as a Therapeutic Target in Cancer , 2007, Clinical Cancer Research.

[86]  I. Weinstein,et al.  Protein Kinase C β Enhances Growth and Expression of Cyclin D1 in Human Breast Cancer Cells , 2006 .

[87]  G. Sledge,et al.  Protein Kinase C- as a Therapeutic Target in Breast Cancer , 2006 .

[88]  S. Mirza,et al.  Detection of RASSF1A and RAR? Hypermethylation in Serum DNA from Breast Cancer Patients , 2006, Epigenetics.

[89]  E. Williamson,et al.  BRCA1 and FOXA1 proteins coregulate the expression of the cell cycle-dependent kinase inhibitor p27Kip1 , 2006, Oncogene.

[90]  J. O’Shaughnessy.  Extending survival with chemotherapy in metastatic breast cancer. , 2005, The oncologist.

[91]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Jocelyn Kaiser,et al.  NCI Gears Up for Cancer Genome Project , 2005, Science.

[93]  Lincoln Stein,et al.  Reactome: a knowledgebase of biological pathways , 2004, Nucleic Acids Res..

[94]  T. Putti,et al.  The Ras/Mitogen-Activated Protein Kinase Pathway Inhibitor and Likely Tumor Suppressor Proteins, Sprouty 1 and Sprouty 2 Are Deregulated in Breast Cancer , 2004, Cancer Research.

[95]  F. Maurer,et al.  The ErbB2/ErbB3 heterodimer functions as an oncogenic unit: ErbB2 requires ErbB3 to drive breast tumor cell proliferation , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[96]  J. Hopper,et al.  Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies. , 2003, American journal of human genetics.

[97]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[98]  Christoph Grunau,et al.  Bisulfite genomic sequencing: systematic investigation of critical experimental parameters , 2001, Nucleic Acids Res..

[99]  J. Hartley,et al.  Use of uracil DNA glycosylase to control carry-over contamination in polymerase chain reactions. , 1990, Gene.

[100]  B. Shapiro,et al.  Free DNA in the serum of cancer patients and the effect of therapy. , 1977, Cancer research.

[101]  E. Perlin,et al.  Serum DNA levels in patients with malignant disease. , 1972, American journal of clinical pathology.

[102]  A. Jemal,et al.  Cancer statistics, 2019 , 2019, CA: a cancer journal for clinicians.

[103]  E. Lianidou,et al.  SOX17 promoter methylation in circulating tumor cells and matched cell-free DNA isolated from plasma of patients with breast cancer. , 2013, Clinical chemistry.

[104]  M. Agostini,et al.  Circulating cell-free DNA: a promising marker of regional lymphonode metastasis in breast cancer patients. , 2012, Cancer biomarkers : section A of Disease markers.

[105]  J. Eeckhoute,et al.  Positive cross-regulatory loop ties GATA-3 to estrogen receptor alpha expression in breast cancer. , 2007, Cancer research.

[106]  I. Weinstein,et al.  Protein kinase C beta enhances growth and expression of cyclin D1 in human breast cancer cells. , 2006, Cancer research.

[107]  G. Sledge,et al.  Protein kinase C-beta as a therapeutic target in breast cancer. , 2006, Seminars in oncology.

[108]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[109]  N. Dubrawsky.  Cancer statistics , 1989, CA: a cancer journal for clinicians.