The promise of methylation on beads for cancer detection and treatment

References

• Heppner GH. Tumor heterogeneity. Cancer Res 1984;44(6):2259-65
   PubMed Web of Science ®Google Scholar
• Sjoblom T, Jones S, Wood LD, et al. The consensus coding sequences of human breast and colorectal cancers. Science 2006;314(5797):268-74
   PubMed Web of Science ®Google Scholar
• Kuebler JP, Wieand HS, O’Connell MJ, et al. Oxaliplatin combined with weekly bolus fluorouracil and leucovorin as surgical adjuvant chemotherapy for stage II and III colon cancer: results from NSABP C-07. JClin Oncol 2007;25(16):2198-204
   PubMed Web of Science ®Google Scholar
• Chin L, Andersen JN, Futreal PA. Cancer genomics: from discovery science to personalized medicine. Nat Med 2011;17(3):297-303
   PubMed Web of Science ®Google Scholar
• Karapetis CS, Khambata-Ford S, Jonker DJ, et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med 2008;359(17):1757-65
   PubMed Web of Science ®Google Scholar
• Shariat SF, Karakiewicz PI, Ashfaq R, et al. Multiple biomarkers improve prediction of bladder cancer recurrence and mortality in patients undergoing cystectomy. Cancer 2008;112(2):315-25
   PubMed Web of Science ®Google Scholar
• Hamburg MA, Collins FS. The path to personalized medicine. N Engl J Med 2010;363(4):301-4
   PubMed Web of Science ®Google Scholar
• Laird PW. Early detection: the power and the promise of DNA methylation markers. Nat Rev Cancer 2003;3(4):253-66
   PubMed Web of Science ®Google Scholar
• Harlan LC, Hankey BF. The surveillance, epidemiology, and end-results program database as a resource for conducting descriptive epidemiologic and clinical studies. J Clin Oncol 2003;21(12):2232-3
   PubMed Web of Science ®Google Scholar
• Catalona WJ, Smith DS, Ratliff TL, Basler JW. Detection of organ-confined prostate cancer is increased through prostate-specific antigen-based screening. JAMA 1993;270(8):948-54
   PubMed Web of Science ®Google Scholar
• Sawyers CL. The cancer biomarker problem. Nature 2008;452(7187):548-52
   PubMed Web of Science ®Google Scholar
• Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer 2005;5(11):845-56
   PubMed Web of Science ®Google Scholar
• Romond EH, Perez EA, Bryant J, et al. Trastuzumab plus adjuvant chemotherapy for operable HER2-positive breast cancer. NEngl J Med 2005;353(16):1673-84
   PubMed Web of Science ®Google Scholar
• Fisher B, Anderson S, Tan-Chiu E, et al. Tamoxifen and chemotherapy for axillary node-negative, estrogen receptor-negative breast cancer: findings from National Surgical Adjuvant Breast and Bowel Project B-23. J Clin Oncol 2001;19(4):931-42
   PubMed Web of Science ®Google Scholar
• Poste G. Bring on the biomarkers. Nature 2011;469(7329):156-7
   PubMed Web of Science ®Google Scholar
• Hu S, Loo JA, Wong DT. Human body fluid proteome analysis. Proteomics 2006;6(23):6326-53
   PubMed Web of Science ®Google Scholar
• Hanash SM, Pitteri SJ, Faca VM. Mining the plasma proteome for cancer biomarkers. Nature 2008;452(7187):571-9
   PubMed Web of Science ®Google Scholar
• Levin B, Lieberman DA, McFarland B, et al. Screening and surveillance for the early detection of colorectal cancer and adenomatous polyps, 2008: a joint guideline from the American Cancer Society, the US Multi-Society Task Force on Colorectal Cancer, and the American College of Radiology. CA Cancer J Clin 2008;58(3):130-60
   PubMed Web of Science ®Google Scholar
• Jemal A, Center MM, DeSantis C, Ward EM. Global patterns of cancer incidence and mortality rates and trends. Cancer Epidemiol Biomarkers Prev 2010;19(8):1893-907
   PubMed Web of Science ®Google Scholar
• Seeff LC, Nadel MR, Klabunde CN, et al. Patterns and predictors of colorectal cancer test use in the adult U.S. population. Cancer 2004;100(10):2093-103
   PubMed Web of Science ®Google Scholar
• Meissner HI, Breen N, Klabunde CN, Vernon SW. Patterns of colorectal cancer screening uptake among men and women in the United States. Cancer Epidemiol Biomarkers Prev 2006;15(2):389-94
   PubMed Web of Science ®Google Scholar
• Traverso G, Shuber A, Levin B, et al. Detection of APC mutations in fecal DNA from patients with colorectal tumors. N Engl J Med 2002;346(5):311-20
   PubMedGoogle Scholar
• Ahlquist DA, Skoletsky JE, Boynton KA, et al. Colorectal cancer screening by detection of altered human DNA in stool: feasibility of a multitarget assay panel. Gastroenterology 2000;119(5):1219-27
   PubMed Web of Science ®Google Scholar
• Palmisano WA, Divine KK, Saccomanno G, et al. Predicting lung cancer by detecting aberrant promoter methylation in sputum. Cancer Res 2000;60(21):5954-8
   PubMed Web of Science ®Google Scholar
• Imperiale TF, Ransohoff DF, Itzkowitz SH, et al. Multitarget stool DNA testing for colorectal-cancer screening. N Engl J Med 2014;370(14):1287-97
   PubMed Web of Science ®Google Scholar
• Tibbe AG, Miller MC, Terstappen LW. Statistical considerations for enumeration of circulating tumor cells. Cytometry A 2007;71(3):154-62
   PubMed Web of Science ®Google Scholar
• Sleijfer S, Gratama JW, Sieuwerts AM, et al. Circulating tumour cell detection on its way to routine diagnostic implementation? Eur J Cancer 2007;43(18):2645-50
   PubMed Web of Science ®Google Scholar
• Gardiner-Garden M, Frommer M. CpG islands in vertebrate genomes. J Mol Biol 1987;196(2):261-82
   PubMed Web of Science ®Google Scholar
• Straussman R, Nejman D, Roberts D, et al. Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 2009;16(5):564-71
   PubMed Web of Science ®Google Scholar
• Schuebel KE, Chen W, Cope L, et al. Comparing the DNA hypermethylome with gene mutations in human colorectal cancer. PLoS Genet 2007;3(9):1709-23
   PubMed Web of Science ®Google Scholar
• Glockner SC, Dhir M, Yi JM, et al. Methylation of TFPI2 in stool DNA: a potential novel biomarker for the detection of colorectal cancer. Cancer Res 2009;69(11):4691-9
   PubMed Web of Science ®Google Scholar
• Yi JM, Guzzetta AA, Bailey VJ, et al. Novel methylation biomarker panel for the early detection of pancreatic cancer. Clin Cancer Res 2013;19(23):6544-55
   PubMed Web of Science ®Google Scholar
• Esteller M, Corn PG, Baylin SB, Herman JG. A gene hypermethylation profile of human cancer. Cancer Res 2001;61(8):3225-9
   PubMed Web of Science ®Google Scholar
• Hughes LA, Melotte V, de Schrijver J, et al. The CpG island methylator phenotype: what’s in a name? Cancer Res 2013;73(19):5858-68
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002;3(6):415-28
   PubMed Web of Science ®Google Scholar
• Swarup V, Rajeswari MR. Circulating (cell-free) nucleic acids – a promising, non-invasive tool for early detection of several human diseases. FEBS Lett 2007;581(5):795-9
   PubMed Web of Science ®Google Scholar
• Viet CT, Schmidt BL. Methylation array analysis of preoperative and postoperative saliva DNA in oral cancer patients. Cancer Epidemiol Biomarkers Prev 2008;17(12):3603-11
   PubMed Web of Science ®Google Scholar
• de Fraipont F, Moro-Sibilot D, Michelland S, et al. Promoter methylation of genes in bronchial lavages: a marker for early diagnosis of primary and relapsing non-small cell lung cancer? Lung Cancer 2005;50(2):199-209
   PubMed Web of Science ®Google Scholar
• Reinert T, Modin C, Castano FM, et al. Comprehensive genome methylation analysis in bladder cancer: identification and validation of novel methylated genes and application of these as urinary tumor markers. Clin Cancer Res 2011;17(17):5582-92
   PubMed Web of Science ®Google Scholar
• Cairns P. Detection of promoter hypermethylation of tumor suppressor genes in urine from kidney cancer patients. Ann N Y Acad Sci 2004;1022:40-3
   PubMed Web of Science ®Google Scholar
• Cairns P, Esteller M, Herman JG, et al. Molecular detection of prostate cancer in urine by GSTP1 hypermethylation. Clin Cancer Res 2001;7(9):2727-30
   PubMed Web of Science ®Google Scholar
• Bird AP. Use of restriction enzymes to study eukaryotic DNA methylation: II. The symmetry of methylated sites supports semi-conservative copying of the methylation pattern. J Mol Biol 1978;118(1):49-60
   PubMed Web of Science ®Google Scholar
• Eads CA, Danenberg KD, Kawakami K, et al. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res 2000;28(8):E32
   PubMed Web of Science ®Google Scholar
• Herman JG, Graff JR, Myohanen S, et al. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996;93(18):9821-6
   PubMed Web of Science ®Google Scholar
• Grunau C, Clark SJ, Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 2001;29(13):E65-5
   PubMedGoogle Scholar
• Ahuja N, Li Q, Mohan AL, et al. Aging and DNA methylation in colorectal mucosa and cancer. Cancer Res 1998;58(23):5489-94
   PubMed Web of Science ®Google Scholar
• Khanna A, Czyz A, Syed F. EpiGnome[trade] Methyl-Seq Kit: a novel post-bisulfite conversion library prep method for methylation analysis. Nat Meth 2013;10:10
   Google Scholar
• Bailey VJ, Zhang Y, Keeley BP, et al. Single-tube analysis of DNA. methylation with silica superparamagnetic beads. Clin Chem 2010;56(6):1022-5
   PubMedGoogle Scholar
• Keeley B, Stark A, Pisanic Ii TR, et al. Extraction and processing of circulating DNA from large sample volumes using methylation on beads for the detection of rare epigenetic events. Clin Chim Acta 2013;425(0):169-75
   PubMedGoogle Scholar
• Diehl F, Li M, Dressman D, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci USA 2005;102(45):16368-73
   PubMed Web of Science ®Google Scholar
• Jung K, Fleischhacker M, Rabien A. Cell-free DNA in the blood as a solid tumor biomarker-A critical appraisal of the literature. Clin Chim Acta 2010;411(21-22):1611-24
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H, Hoon DSB, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011;11(6):426-37
   PubMed Web of Science ®Google Scholar
• Zeerleder S. The struggle to detect circulating DNA. Crit Care 2006;10(3):142
   PubMedGoogle Scholar
• Kirby KS. New method for the isolation of deoxyribonucleic acids - evidence on the nature of bonds between deoxyribonucleic acid and protein. Biochem J 1957;66(3):495-504
   PubMedGoogle Scholar
• Kirby KS, Cook EA. Isolation of deoxyribonucleic acid from mammalian tissues. Biochem J 1967;104(1):254-7
   PubMedGoogle Scholar
• Daimon K, Komai S, Takarada Y. Method of extracting nucleic acids using particulate carrier. Toyo Boseki Kabushiki Kaisha; Japan: 2003
   Google Scholar
• Otto P. MagneSil™ paramagnetic particles: magnetics for DNA purification. J Assoc Lab Autom 2002;7(3):34-7
   Google Scholar
• Tan WH, Wang KM, He XX, et al. Bionanotechnology based on silica nanoparticles. Med Res Rev 2004;24(5):621-38
   PubMed Web of Science ®Google Scholar
• Gallagher ML, Burke WF, Orzech K. Carrier RNA enhancement of recovery of DNA from dilute-solutions. Biochem Biophys Res Commun 1987;144(1):271-6
   PubMedGoogle Scholar
• Wang RYH, Gehrke CW, Ehrlich M. Comparison of bisulfite modification of 5-methyldeoxycytidine and deoxycytidine residues. Nucleic Acids Res 1980;8(20):4777-90
   PubMed Web of Science ®Google Scholar
• Herman JG, Graff JR, Myöhänen S, et al. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad Sci USA 1996;93(18):9821-6
   PubMed Web of Science ®Google Scholar
• Schrader C, Schielke A, Ellerbroek L, Johne R. PCR inhibitors - occurrence, properties and removal. J Appl Microbiol 2012;113(5):1014-26
   PubMed Web of Science ®Google Scholar
• Dominitz JA, Eisen GM, Baron TH, et al. Complications of colonoscopy. Gastrointest Endosc 2003;57(4):441-5
   PubMedGoogle Scholar
• Bowles CJ, Leicester R, Romaya C, et al. A prospective study of colonoscopy practice in the UK today: are we adequately prepared for national colorectal cancer screening tomorrow? Gut 2004;53(2):277-83
   PubMed Web of Science ®Google Scholar
• Lofton-Day C, Model F, Devos T, et al. DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem 2008;54(2):414-23
   PubMed Web of Science ®Google Scholar
• Imperiale TF, Ransohoff DF, Itzkowitz SH, et al. Fecal DNA versus fecal occult blood for colorectal-cancer screening in an average-risk population. N Engl J Med 2004;351(26):2704-14
   PubMed Web of Science ®Google Scholar
• Ahlquist DA, Wieand HS, Moertel CG, et al. Accuracy of fecal occult blood screening for colorectal neoplasia. A prospective study using Hemoccult and HemoQuant tests. JAMA 1993;269(10):1262-7
   PubMedGoogle Scholar
• Rockey DC, Paulson E, Niedzwiecki D, et al. Analysis of air contrast barium enema, computed tomographic colonography, and colonoscopy: prospective comparison. Lancet 2005;365(9456):305-11
   PubMed Web of Science ®Google Scholar
• Schwarzenbach H, Hoon DS, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer 2011;11(6):426-37
   PubMed Web of Science ®Google Scholar
• Fleischhacker M, Schmidt B. Circulating nucleic acids (CNAs) and cancer – a survey. Biochim Biophys Acta 2007;1775(1):181-232
   PubMed Web of Science ®Google Scholar
• Gemmel C, Eickhoff A, Helmstadter L, Riemann JF. Pancreatic cancer screening: state of the art. Expert Rev Gastroenterol Hepatol 2009;3(1):89-96
   PubMedGoogle Scholar
• Fry LC, Monkemuller K, Malfertheiner P. Molecular markers of pancreatic cancer: development and clinical relevance. Langenbecks Arch Surg 2008;393(6):883-90
   PubMedGoogle Scholar
• Siegel R, DeSantis C, Virgo K, et al. Cancer treatment and survivorship statistics, 2012. CA Cancer J Clin 2012;62(4):220-41
   PubMed Web of Science ®Google Scholar
• Klapman J, Malafa MP. Early detection of pancreatic cancer: why, who, and how to screen. Cancer Contr 2008;15(4):280-7
   PubMedGoogle Scholar
• Erkan M, Hausmann S, Michalski CW, et al. The role of stroma in pancreatic cancer: diagnostic and therapeutic implications. Nat Rev Gastroenterol Hepatol 2012;9(8):454-67
   PubMed Web of Science ®Google Scholar
• Erkan M, Hausmann S, Michalski CW, et al. How fibrosis influences imaging and surgical decisions in pancreatic cancer. Front Physiol 2012;3:389
   PubMed Web of Science ®Google Scholar
• Wu J, Matthaei H, Maitra A, et al. Recurrent GNAS mutations define an unexpected pathway for pancreatic cyst development. Sci Transl Med 2011;3(92):92ra66
   PubMed Web of Science ®Google Scholar
• Brune K, Hong SM, Li A, et al. Genetic and epigenetic alterations of familial pancreatic cancers. Cancer Epidemiol Biomarkers Prev 2008;17(12):3536-42
   PubMedGoogle Scholar
• Jones S, Hruban RH, Kamiyama M, et al. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science 2009;324(5924):217
   PubMed Web of Science ®Google Scholar
• Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003;349(21):2042-54
   PubMed Web of Science ®Google Scholar
• Kaminskas E, Farrell AT, Wang YC, et al. FDA drug approval summary: azacitidine (5-azacytidine, Vidaza) for injectable suspension. Oncologist 2005;10(3):176-82
   PubMed Web of Science ®Google Scholar
• Wijermans P, Lubbert M, Verhoef G, et al. Low-dose 5-aza-2’-deoxycytidine, a DNA hypomethylating agent, for the treatment of high-risk myelodysplastic syndrome: a multicenter phase II study in elderly patients. J Clin Oncol 2000;18(5):956-62
   PubMed Web of Science ®Google Scholar
• Juergens RA, Wrangle J, Vendetti FP, et al. Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. Cancer Discov 2011;1(7):598-607
   PubMed Web of Science ®Google Scholar
• Fu S, Hu W, Iyer R, et al. Phase 1b-2a study to reverse platinum resistance through use of a hypomethylating agent, azacitidine, in patients with platinum-resistant or platinum-refractory epithelial ovarian cancer. Cancer 2011;117(8):1661-9
   PubMed Web of Science ®Google Scholar
• Matei D, Fang F, Shen C, et al. Epigenetic resensitization to platinum in ovarian cancer. Cancer Res 2012;72(9):2197-205
   PubMed Web of Science ®Google Scholar