Evaluating liquid biopsies for methylomic profiling of prostate cancer

References

• Wong MC, Goggins WB, Wang HH, et al. Global incidence and mortality for prostate cancer: analysis of temporal patterns and trends in 36 countries. Eur Urol. 2016 Nov;70(5):862–874.
   PubMed Web of Science ®Google Scholar
• Sartor O, de Bono JS. Metastatic prostate cancer. N Engl J Med. 2018 Feb 15;378(7):645–657.
   PubMed Web of Science ®Google Scholar
• Friedlander TW, Roy R, Tomlins SA, et al. Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res. 2012 Feb 1;72(3):616–625.
   PubMed Web of Science ®Google Scholar
• Bardelli A, Pantel K. Liquid biopsies, what we do not know (yet). Cancer Cell. 2017 Feb 13;31(2):172–179.
   PubMed Web of Science ®Google Scholar
• Guttery DS, Blighe K, Page K, et al. Hide and seek: tell-tale signs of breast cancer lurking in the blood. Cancer Metastasis Rev. 2013 Jun;32(1–2):289–302.
   PubMed Web of Science ®Google Scholar
• Dawson SJ, Tsui DW, Murtaza M, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013 Mar 28;368(13):1199–1209.
   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 Feb 19;6(224):224ra24.
   PubMed Web of Science ®Google Scholar
• Heitzer E, Speicher MR. Digital circulating tumor cell analyses for prostate cancer precision oncology. Cancer Discov. 2018 Mar;8(3):269–271.
   PubMed Web of Science ®Google Scholar
• Pantel K, Hille C, Scher HI. Circulating tumor cells in prostate cancer: from discovery to clinical utility. Clin Chem. 2019 Jan;65(1):87–99.
   PubMed Web of Science ®Google Scholar
• Junker K, Heinzelmann J, Beckham C, et al. Extracellular vesicles and their role in urologic malignancies. Eur Urol. 2016 Aug;70(2):323–331.
   PubMed Web of Science ®Google Scholar
• Mahon KL, Qu W, Lin HM, et al. Serum free methylated glutathione S-transferase 1 DNA levels, survival, and response to docetaxel in metastatic, castration-resistant prostate cancer: post hoc analyses of data from a phase 3 trial. Eur Urol. 2018 Nov;76(3):306–312.
   Web of Science ®Google Scholar
• Shen SY, Singhania R, Fehringer G, et al. Sensitive tumor detection and classification using plasma cell-free DNA methylomes. Nature. 2018 Nov;563(7732):579–583.
   PubMed Web of Science ®Google Scholar
• Gordevicius J, Krisciunas A, Groot DE, et al. Cell-free DNA modification dynamics in abiraterone acetate-treated prostate cancer patients. Clin Cancer Res. 2018 Jul 15;24(14):3317–3324.
   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 Nov;67(11):1995–2005.
   PubMed Web of Science ®Google Scholar
• Torres-Ferreira J, Ramalho-Carvalho J, Gomez A, et al. MiR-193b promoter methylation accurately detects prostate cancer in urine sediments and miR-34b/c or miR-129-2 promoter methylation define subsets of clinically aggressive tumors. Mol Cancer. 2017 Jan 31;16(1):26.
   PubMedGoogle Scholar
• Sanda MG, Feng Z, Howard DH, et al. Association between combined TMPRSS2: eRGand PCA3 RNA urinary testing and detection of aggressive prostate cancer. JAMA Oncol. 2017 Aug 1;3(8):1085–1093.
   PubMed Web of Science ®Google Scholar
• Yegnasubramanian SKJ, Gonzalgo ML, Zahurak M, et al. Hypermethylation of CpG islands in primary and metastatic human prostate cancer. Cancer Res. 2004;64(6):1975–1986.
   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 Nov 29;9(1):5068.
   PubMed Web of Science ®Google Scholar
• Gene Ontology C, Blake JA, Dolan M, et al. Gene ontology annotations and resources. Nucleic Acids Res. 2013 Jan;41(Database issue):D530–5.
   PubMedGoogle Scholar
• Jones PA, Issa JP, Baylin S. Targeting the cancer epigenome for therapy. Nat Rev Genet. 2016 Sep 15;17(10):630–641.
   PubMed Web of Science ®Google Scholar
• Aryee MJ, Liu W, Engelmann JC, et al. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013 Jan 23;5(169):169ra10.
   PubMed Web of Science ®Google Scholar
• Hoque MO, Topaloglu O, Begum S, et al. Quantitative methylation-specific polymerase chain reaction gene patterns in urine sediment distinguish prostate cancer patients from control subjects. J Clin Oncol. 2005 Sep 20;23(27):6569–6575.
   PubMed Web of Science ®Google Scholar
• Ellinger J, Haan K, Heukamp LC, et al. CpG island hypermethylation in cell-free serum DNA identifies patients with localized prostate cancer. Prostate. 2008 Jan 1;68(1):42–49.
   PubMed Web of Science ®Google Scholar
• Hendriks RJ, Dijkstra S, Smit FP, et al. Epigenetic markers in circulating cell-free DNA as prognostic markers for survival of castration-resistant prostate cancer patients. Prostate. 2018 Apr;78(5):336–342.
   PubMed Web of Science ®Google Scholar
• Payne SR, Serth J, Schostak M, et al. DNA methylation biomarkers of prostate cancer: confirmation of candidates and evidence urine is the most sensitive body fluid for non-invasive detection. Prostate. 2009 Sep 1;69(12):1257–1269.
   PubMed Web of Science ®Google Scholar
• Brikun I, Nusskern D, Decatus A, et al. A panel of DNA methylation markers for the detection of prostate cancer from FV and DRE urine DNA. Clin Epigenetics. 2018;10:91.
   PubMed Web of Science ®Google Scholar
• Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016 Mar;8(3):389–399.
   PubMed Web of Science ®Google Scholar
• Pidsley R, Zotenko E, Peters TJ, et al. Critical evaluation of the illumina MethylationEPIC beadChip microarray for whole-genome DNA methylation profiling. Genome Biol. 2016 Oct 7;17(1):208.
   PubMed Web of Science ®Google Scholar
• Gallardo-Gomez M, Moran S, Paez de la Cadena M, et al. A new approach to epigenome-wide discovery of non-invasive methylation biomarkers for colorectal cancer screening in circulating cell-free DNA using pooled samples. Clin Epigenetics. 2018;10:53.
   PubMed Web of Science ®Google Scholar
• Vandekerkhove G, Struss WJ, Annala M, et al. Circulating tumor DNA abundance and potential utility in de novo metastatic prostate cancer. Eur Urol. 2019 Apr;75(4):667–675.
   PubMed Web of Science ®Google Scholar
• Mansell G, Gorrie-Stone TJ, Bao Y, et al. Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array. BMC Genomics. 2019 May 14;20(1):366.
   PubMedGoogle Scholar
• Graw S, Henn R, Thompson JA, et al. pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS). BMC Bioinformatics. 2019 Apr 29;20(1):218.
   PubMed Web of Science ®Google Scholar
• van Iterson M, Boer JM, Menezes RX. Filtering, FDR and power. BMC Bioinformatics. 2010 Sep;7(11):450.
   Google Scholar
• Calza S, Raffelsberger W, Ploner A, et al. Filtering genes to improve sensitivity in oligonucleotide microarray data analysis. Nucleic Acids Res. 2007;35(16):e102.
   PubMed Web of Science ®Google Scholar
• Campan M, Weisenberger DJ, Trinh B, et al. MethyLight. Methods Mol Biol. 2009;507:325–337.
   PubMedGoogle Scholar
• Team. RC. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2016. Available from: https://www.r-project.org/
   Google Scholar
• Assenov Y, Muller F, Lutsik P, et al. Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods. 2014;Nov;11(11):1138–1140.
   PubMed Web of Science ®Google Scholar
• Muller F, Scherer M, Assenov Y, et al. RnBeads 2.0: comprehensive analysis of DNA methylation data. Genome Biol. 2019 Mar 14;20(1):55.
   PubMedGoogle Scholar
• Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of infinium DNA methylation beadChip probes. Nucleic Acids Res. 2017 Feb 28;45(4):e22.
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Marabita F, Lechner M, et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics. 2013 Jan 15;29(2):189–196.
   PubMed Web of Science ®Google Scholar
• Liu J, Siegmund KD. An evaluation of processing methods for HumanMethylation450 BeadChip data. BMC Genomics. 2016 Jun 22;17:469.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015 Apr 20;43(7):e47.
   PubMed Web of Science ®Google Scholar