DNA methylation biomarkers discovered in silico detect cancer in liquid biopsies from non-small cell lung cancer patients

References

• Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424.
   PubMed Web of Science ®Google Scholar
• Mahvi DA, Liu R, Grinstaff MW, et al. Local cancer recurrence: the realities, challenges, and opportunities for new therapies. CA Cancer J Clin. 2018;68:488–505.
   PubMed Web of Science ®Google Scholar
• Schiffman JD, Fisher PG, Gibbs P. Early detection of cancer: past, present, and future. Am Soc Clin Oncol Educ Book. 2015;3:57–65.
   PubMedGoogle Scholar
• Schwarzenbach H, Hoon DSB, Pantel K. Cell-free nucleic acids as biomarkers in cancer patients. Nat Rev Cancer. 2011;11:426–437.
   PubMed Web of Science ®Google Scholar
• Wan JCM, Massie C, Garcia-Corbacho J, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17:223–238.
   PubMed Web of Science ®Google Scholar
• Leon SA, Shapiro B, Sklaroff DM, et al. Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res. 1977;37:646–650.
   PubMed Web of Science ®Google Scholar
• Snyder MW, Kircher M, Hill AJ, et al. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell. 2016;164:57–68.
   PubMed Web of Science ®Google Scholar
• Moss J, Magenheim J, Neiman D, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9:5068.
   PubMed Web of Science ®Google Scholar
• Bettegowda C, Sausen M, Leary RJ, et al. Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med. 2014;6:224ra24.
   PubMed Web of Science ®Google 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 U S A. 2005;102:16368–16373.
   PubMed Web of Science ®Google Scholar
• Jahr S, Hentze H, Englisch S, et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. Cancer Res. 2001;61:1659–1665.
   PubMed Web of Science ®Google Scholar
• Fackler MJ, Lopez Bujanda Z, Umbricht C, et al. Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer Res. 2014;74:2160–2170.
   PubMed Web of Science ®Google Scholar
• Uehiro N, Sato F, Pu F, et al. Circulating cell-free DNA-based epigenetic assay can detect early breast cancer. Breast Cancer Res. 2016;18:129.
   PubMed Web of Science ®Google Scholar
• Shen SY, Singhania R, Fehringer G, et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018;563:579–583.
   PubMed Web of Science ®Google Scholar
• Kulis M, Esteller M. DNA methylation and cancer. Adv Genet. 2010;70:27–56.
   PubMed Web of Science ®Google Scholar
• Feinberg AP, Ohlsson R, Henikoff S. The epigenetic progenitor origin of human cancer. Nat Rev Genet. 2006;7:21–33.
   PubMed Web of Science ®Google Scholar
• Sina AA, Carrascosa LG, Liang Z, et al. Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker. Nat Commun. 2018;9:4915.
   PubMed Web of Science ®Google Scholar
• Esteller M, Herman JG. Cancer as an epigenetic disease: DNA methylation and chromatin alterations in human tumours. J Pathol. 2002;196:1–7.
   PubMed Web of Science ®Google Scholar
• Bird AP. CpG-rich islands and the function of DNA methylation. Nature. 1986;321:209–213.
   PubMed Web of Science ®Google Scholar
• Kim M, Costello J. DNA methylation: an epigenetic mark of cellular memory. Exp Mol Med. 2017;49:e322.
   PubMed Web of Science ®Google Scholar
• Futscher BW, Oshiro MM, Wozniak RJ, et al. Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet. 2002;31:175–179.
   PubMed Web of Science ®Google Scholar
• Vrba L, Garbe JC, Stampfer MR, et al. Epigenetic regulation of normal human mammary cell type-specific miRNAs. Genome Res. 2011;21:2026–2037.
   PubMed Web of Science ®Google Scholar
• Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Genet. 2012;13:679–692.
   PubMed Web of Science ®Google Scholar
• Novak P, Jensen T, Oshiro MM, et al. Agglomerative epigenetic aberrations are a common event in human breast cancer. Cancer Res. 2008;68:8616–8625.
   PubMed Web of Science ®Google Scholar
• Rauch TA, Zhong X, Wu X, et al. High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer. Proc Natl Acad Sci U S A. 2008;105:252–257.
   PubMed Web of Science ®Google Scholar
• Shames DS, Girard L, Gao B, et al. A genome-wide screen for promoter methylation in lung cancer identifies novel methylation markers for multiple malignancies. PLoS Med. 2006;3:e486.
   PubMed Web of Science ®Google Scholar
• Irizarry RA, Ladd-Acosta C, Wen B, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41:178–186.
   PubMed Web of Science ®Google Scholar
• Vrba L, Jensen TJ, Garbe JC, et al. Role for DNA methylation in the regulation of miR-200c and miR-141 expression in normal and cancer cells. PLoS One. 2010;5:e8697.
   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:E32.
   PubMed Web of Science ®Google Scholar
• Hulbert A, Jusue-Torres I, Stark A, et al. Early detection of lung cancer using DNA promoter hypermethylation in plasma and sputum. Clin Cancer Res. 2017;23:1998–2005.
   PubMed Web of Science ®Google Scholar
• Nunes SP, Moreira-Barbosa C, Salta S, et al. Cell-free DNA methylation of selected genes allows for early detection of the major cancers in women. Cancers (Basel). 2018;10:357.
   Web of Science ®Google Scholar
• Ostrow KL, Hoque MO, Loyo M, et al. Molecular analysis of plasma DNA for the early detection of lung cancer by quantitative methylation-specific PCR. Clin Cancer Res. 2010;16:3463–3472.
   PubMed Web of Science ®Google Scholar
• Wielscher M, Vierlinger K, Kegler U, et al. Diagnostic performance of plasma DNA methylation profiles in lung cancer, pulmonary fibrosis and COPD. EBioMedicine. 2015;2:929–936.
   PubMed Web of Science ®Google Scholar
• Ooki A, Maleki Z, Tsay JJ, et al. A panel of novel detection and prognostic methylated DNA markers in primary non-small cell lung cancer and serum DNA. Clin Cancer Res. 2017;23:7141–7152.
   PubMed Web of Science ®Google Scholar
• Weiss G, Schlegel A, Kottwitz D, et al. Validation of the SHOX2/PTGER4 DNA methylation marker panel for plasma-based discrimination between patients with malignant and nonmalignant lung disease. J Thorac Oncol. 2017;12:77–84.
   PubMed Web of Science ®Google Scholar
• Lange CP, Campan M, Hinoue T, et al. Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer. PLoS One. 2012;7:e50266.
   PubMed Web of Science ®Google Scholar
• Barault L, Amatu A, Siravegna G, et al. Discovery of methylated circulating DNA biomarkers for comprehensive non-invasive monitoring of treatment response in metastatic colorectal cancer. Gut. 2018;67:1995–2005.
   PubMed Web of Science ®Google Scholar
• Kisiel JB, Raimondo M, Taylor WR, et al. New DNA methylation markers for pancreatic cancer: discovery, tissue validation, and pilot testing in pancreatic juice. Clin Cancer Res. 2015;21:4473–4481.
   PubMed Web of Science ®Google Scholar
• Grutzmann R, Molnar B, Pilarsky C, et al. Sensitive detection of colorectal cancer in peripheral blood by septin 9 DNA methylation assay. PLoS One. 2008;3:e3759.
   PubMed Web of Science ®Google Scholar
• Lee WH, Isaacs WB, Bova GS, et al. CG island methylation changes near the GSTP1 gene in prostatic carcinoma cells detected using the polymerase chain reaction: a new prostate cancer biomarker. Cancer Epidemiol Biomarkers Prev. 1997;6:443–450.
   PubMed Web of Science ®Google Scholar
• Kang S, Li Q, Chen Q, et al. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol. 2017;18:53.
   PubMed Web of Science ®Google Scholar
• Vrba L, Futscher BW. A suite of DNA methylation markers that can detect most common human cancers. Epigenetics. 2018;13:61–72.
   PubMed Web of Science ®Google Scholar
• Heyn H, Li N, Ferreira HJ, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A. 2012;109:10522–10527.
   PubMed Web of Science ®Google Scholar
• Horvath S, Raj K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet. 2018;19:371–384.
   PubMed Web of Science ®Google Scholar
• Sandoval J, Mendez-Gonzalez J, Nadal E, et al. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. J Clin Oncol. 2013;31:4140–4147.
   PubMed Web of Science ®Google Scholar
• Team RC. R: A Language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2018.
   Google Scholar
• Robin X, Turck N, Hainard A, et al. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics. 2011;12:77.
   PubMed Web of Science ®Google Scholar