Epigenetic markers of prostate cancer in plasma circulating DNA

2005, Circulating tumour-derived DNA and RNA markers in blood: a tool for early detection, diagnostics, and follow-up?, Lung Cancer, 49, 1, 10.1016/j.lungcan.2004.12.008

2010, American Cancer Society guideline for the early detection of prostate cancer: update 2010, CA Cancer J. Clin., 60, 70, 10.3322/caac.20066

2010, Cancer statistics, 2010, CA Cancer J. Clin., 60, 277, 10.3322/caac.20073

2009, Screening for prostate cancer—the controversy that refuses to die, N. Engl. J. Med., 360, 1351, 10.1056/NEJMe0901166

2009, Mortality results from a randomized prostate-cancer screening trial, N. Engl. J. Med., 360, 1310, 10.1056/NEJMoa0810696

2009, Screening and prostate-cancer mortality in a randomized European study, N. Engl. J. Med., 360, 1320, 10.1056/NEJMoa0810084

2000, Comparison of percent free PSA, PSA density, and age-specific PSA cutoffs for prostate cancer detection and staging, Urology, 56, 255, 10.1016/S0090-4295(00)00637-3

2011, Advances in DNA methylation: 5-hydroxymethylcytosine revisited, Clin. Chim. Acta, 412, 831, 10.1016/j.cca.2011.02.013

2011, Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine, Science, 333, 1300, 10.1126/science.1210597

2003, Gene silencing in cancer in association with promoter hypermethylation, N. Engl. J. Med., 349, 2042, 10.1056/NEJMra023075

2006, DNA methylation profiling of human chromosomes 6, 20 and 22, Nat. Genet., 38, 1378, 10.1038/ng1909

2010, Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA, Biotechniques, 48, 317, 10.2144/000113403

2011, A decade of exploring the cancer epigenome—biological and translational implications, Nat. Rev. Cancer, 11, 726, 10.1038/nrc3130

2008, Epigenetics in cancer, N. Engl. J. Med., 358, 1148, 10.1056/NEJMra072067

2002, Circulating nucleic acids as a tumor marker, Histol. Histopathol., 17, 937

1948, Les acides nucliques du plasma sanguin chez l'homme, C. R. Seances Soc. Biol. Fil., 142, 241

1987, Isolation and characterization of DNA from the plasma of cancer patients, Eur. J. Cancer Clin. Oncol., 23, 707, 10.1016/0277-5379(87)90266-5

2005, Detection and quantification of mutations in the plasma of patients with colorectal tumors, Proc. Natl Acad. Sci. USA, 102, 16368, 10.1073/pnas.0507904102

2008, Circulating mutant DNA to assess tumor dynamics, Nat. Med., 14, 985, 10.1038/nm.1789

2008, Exosome function: from tumor immunology to pathogen biology, Traffic, 9, 871, 10.1111/j.1600-0854.2008.00734.x

2011, Measurement of GSTP1 promoter methylation in body fluids may complement PSA screening: a meta-analysis, Br. J. Cancer, 105, 65, 10.1038/bjc.2011.143

2009, Circulating methylated SEPT9 DNA in plasma is a biomarker for colorectal cancer, Clin. Chem., 55, 1337, 10.1373/clinchem.2008.115808

2002, p16(INK4A) hypermethylation detected by fluorescent methylation-specific PCR in plasmas from non-small cell lung cancer, Clin. Cancer Res., 8, 3782

1999, Detection of aberrant promoter hypermethylation of tumor suppressor genes in serum DNA from non-small cell lung cancer patients, Cancer Res., 59, 67

2002, Detection of p16 hypermethylation in circulating plasma DNA of non-small cell lung cancer patients, Cancer Lett., 188, 109, 10.1016/S0304-3835(02)00496-2

2010, Current and emerging biomarkers in breast cancer: prognosis and prediction, Endocr. Relat. Cancer, 17, R245, 10.1677/ERC-10-0136

2008, DNA methylation changes in ovarian cancer: implications for early diagnosis, prognosis and treatment, Gynecol. Oncol., 109, 129, 10.1016/j.ygyno.2007.12.017

2007, Progress in the development of prognostic and predictive markers for gastrointestinal malignancies, Curr. Treat. Options Oncol., 8, 339, 10.1007/s11864-007-0045-x

2010, Differential methylation of cell-free circulating DNA among patients with pancreatic cancer versus chronic pancreatitis, Cancer, 116, 1674, 10.1002/cncr.24893

2011, Methylation patterns in cell-free plasma DNA reflect removal of the primary tumor and drug treatment of breast cancer patients, Int. J. Cancer, 128, 492, 10.1002/ijc.25363

2009, Differential methylation profile of ovarian cancer in tissues and plasma, J. Mol. Diagn., 11, 60, 10.2353/jmoldx.2009.080072

1999, Methylation profiling of CpG islands in human breast cancer cells, Hum. Mol. Genet., 8, 459, 10.1093/hmg/8.3.459

2007, Circulating nucleic acids (CNAs) and cancer—a survey, Biochim. Biophys. Acta, 1775, 181

2005, CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome, Nucleic Acids Res., 33, 2952, 10.1093/nar/gki582

2005, Molecular alterations in primary prostate cancer after androgen ablation therapy, Clin. Cancer Res., 11, 6823, 10.1158/1078-0432.CCR-05-0585

2010, Integrative genomic profiling of human prostate cancer, Cancer Cell, 18, 11, 10.1016/j.ccr.2010.05.026

2010, In silico estimates of tissue components in surgical samples based on expression profiling data, Cancer Res., 70, 6448, 10.1158/0008-5472.CAN-10-0021

2011, DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer, Genome Res., 21, 1017, 10.1101/gr.119487.110

2003, Scanning human gene deserts for long-range enhancers, Science, 302, 413, 10.1126/science.1088328

2009, Finding distal regulatory elements in the human genome, Curr. Opin. Genet. Dev., 19, 541, 10.1016/j.gde.2009.09.006

2009, Biomarkers for prostate cancer, J. Cell. Biochem., 108, 3, 10.1002/jcb.22227

2010, DNA methylation based biomarkers in non-invasive cancer screening, Curr. Mol. Med., 10, 123, 10.2174/156652410790963303

2010, Circulating nucleic acids as a potential source for cancer biomarkers, Curr. Mol. Med., 10, 142, 10.2174/156652410790963295

2008, Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer, Mol. Cancer, 7, 62, 10.1186/1476-4598-7-62

2005, Preoperative serum DNA GSTP1 CpG island hypermethylation and the risk of early prostate-specific antigen recurrence following radical prostatectomy, Clin. Cancer Res., 11, 4037, 10.1158/1078-0432.CCR-04-2446

2008, CpG island hypermethylation profile in the serum of men with clinically localized and hormone refractory metastatic prostate cancer, J. Urol., 179, 529, 10.1016/j.juro.2007.09.038

2008, Noncancerous PTGS2 DNA fragments of apoptotic origin in sera of prostate cancer patients qualify as diagnostic and prognostic indicators, Int. J. Cancer, 122, 138, 10.1002/ijc.23057

2004, Detection of GSTP1 methylation in prostatic secretions using combinatorial MSP analysis, Urology, 63, 414, 10.1016/j.urology.2003.08.039

2009, DNA methylation biomarkers of prostate cancer: confirmation of candidates and evidence urine is the most sensitive body fluid for non-invasive detection, Prostate, 69, 1257, 10.1002/pros.20967

2002, Quantitative adenomatous polyposis coli promoter methylation analysis in tumor tissue, serum, and plasma DNA of patients with lung cancer, Cancer Res., 62, 371

2009, Is there evidence of a relationship between benign prostatic hyperplasia and prostate cancer? Findings of a literature review, Eur. Urol., 55, 864, 10.1016/j.eururo.2008.11.011

2007, Prostate volume and adverse prostate cancer features: fact not artifact, Eur. J. Cancer, 43, 2669, 10.1016/j.ejca.2007.09.022

1992, The association of benign prostatic hyperplasia and cancer of the prostate, Cancer, 70, 291, 10.1002/1097-0142(19920701)70:1+<291::AID-CNCR2820701317>3.0.CO;2-4

2002, Calculated fast-growing benign prostatic hyperplasia—a risk factor for developing clinical prostate cancer, Scand. J. Urol. Nephrol., 36, 330, 10.1080/003655902320783827

2006, BPH: epidemiology and comorbidities, Am. J. Manag. Care, 12, S122

2009, The role of epigenetics in aging and age-related diseases, Ageing Res. Rev., 8, 268, 10.1016/j.arr.2009.03.004

2003, Age-related epigenetic changes and the immune system, Clin. Immunol., 109, 103, 10.1016/S1521-6616(03)00203-1

1994, Management of cancer of the prostate, N. Engl. J. Med., 331, 996, 10.1056/NEJM199410133311507

2006, Translating microarray data for diagnostic testing in childhood leukaemia, BMC Cancer, 6, 229, 10.1186/1471-2407-6-229

2009, Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival, PLoS One, 4, e7850, 10.1371/journal.pone.0007850

2007, A five-gene signature and clinical outcome in non-small-cell lung cancer, N. Engl. J. Med., 356, 11, 10.1056/NEJMoa060096

2009, Convergent Random Forest predictor: methodology for predicting drug response from genome-scale data applied to anti-TNF response, Genomics, 94, 423, 10.1016/j.ygeno.2009.08.008

2003, Clinical significance of chromosome 8p, 10q, and 16q deletions in prostate cancer, Prostate, 54, 103, 10.1002/pros.10173

2008, Deletion at chromosome arms 6q16–22 and 10q22.3–23.1 associated with initiation of prostate cancer, Prostate Cancer Prostatic Dis., 11, 357, 10.1038/pcan.2008.4

1994, Loss of heterozygosity of the retinoblastoma and adenomatous polyposis susceptibility gene loci and in chromosomes 10p, 10q and 16q in human prostate cancer, Br. J. Urol., 73, 390, 10.1111/j.1464-410X.1994.tb07602.x

2009, Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer, Hum. Genet., 126, 743, 10.1007/s00439-009-0723-9

2011, Genomic profiling of cell-free DNA in blood and bone marrow of prostate cancer patients, J. Cancer Res. Clin. Oncol., 137, 811, 10.1007/s00432-010-0941-5

2011, High sensitivity 5-hydroxymethylcytosine detection in Balb/C brain tissue, J. Vis. Exp., 48, 2661

2011, Detection of 5-hydroxymethylcytosine in a combined glycosylation restriction analysis (CGRA) using restriction enzyme Taq(alpha)I, Bioorg. Med. Chem. Lett., 17, 5075

1996, Levels of 5-hydroxymethyl-2′-deoxyuridine in DNA from blood as a marker of breast cancer, Cancer, 77, 691, 10.1002/(SICI)1097-0142(19960215)77:4<691::AID-CNCR15>3.0.CO;2-W

2006, Microarray-based DNA methylation profiling: technology and applications, Nucleic Acids Res., 34, 528, 10.1093/nar/gkj461

2008, Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies, Nucleic Acids Res., 36, e144, 10.1093/nar/gkn735

2002, Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics, 18, S96

2004, Linear models and empirical Bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 3, Article 3

2003, Statistical significance for genomewide studies, Proc. Natl Acad. Sci. USA, 100, 9440, 10.1073/pnas.1530509100

2007, Linear mixed effects models, Methods Mol. Biol., 404, 213, 10.1007/978-1-59745-530-5_11

2001, Random Forests, Mach. Learn., 45, 5, 10.1023/A:1010933404324

2002, Classification and regression by Random Forest, R News, 2, 18

2007, Adjusting batch effects in microarray expression data using empirical Bayes methods, Biostatistics, 8, 118, 10.1093/biostatistics/kxj037

2005, Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data, Nucleic Acids Res., 33, e175, 10.1093/nar/gni179

2003, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19, 185, 10.1093/bioinformatics/19.2.185