Khoshkar Y, Westerberg M, Adolfsson J, Bill-Axelson A, Olsson H, Eklund M, et al. Mortality in men with castration-resistant prostate cancer—A long-term follow-up of a population-based real-world cohort. BJUI Compass. 2021;3:173–83.
Google Scholar
Le TK, Duong QH, Baylot V, Fargette C, Baboudjian M, Colleaux L, et al. Castration-resistant prostate cancer: from uncovered resistance mechanisms to current treatments. Cancers. 2023;15:5047.
Teo MY, Rathkopf DE, Kantoff P. Treatment of advanced prostate cancer. Annu Rev Med. 2019;70:479–99.
Google Scholar
Chi K, Hotte SJ, Joshua AM, North S, Wyatt AW, Collins LL, et al. Treatment of mCRPC in the AR-axis-targeted therapy-resistant state. Ann Oncol. 2015;26:2044–56.
Google Scholar
Tian S, Lei Z, Gong Z, Sun Z, Xu D, Piao M. Clinical implication of prognostic and predictive biomarkers for castration-resistant prostate cancer: a systematic review. Cancer Cell Int. 2020;20:409.
Google Scholar
Wyatt AW, Annala M, Aggarwal R, Beja K, Feng F, Youngren J, et al. Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer. J Natl Cancer Inst. 2017;109:djx118.
Shen SY, Burgener JM, Bratman SV, De Carvalho DD. Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA. Nat Protoc. 2019;14:2749–80.
Google Scholar
Shen SY, Singhania R, Fehringer G, Chakravarthy A, Roehrl MHA, Chadwick D, et al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature. 2018;563:579–83.
Google Scholar
Chen S, Petricca J, Ye W, Guan J, Zeng Y, Cheng N, et al. The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors. Nat Commun. 2022;13:6467.
Google Scholar
Annala M, Vandekerkhove G, Khalaf D, Taavitsainen S, Beja K, Warner EW, et al. Circulating tumor DNA genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer. Cancer Discov. 2018;8:444–57.
Google Scholar
Lowe R, Rakyan VK. Marmal-aid – a database for Infinium HumanMethylation450. BMC Bioinform. 2013;14:359.
Google Scholar
Hannon E, Dempster EL, Mansell G, Burrage J, Bass N, Bohlken MM, et al. DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia. eLife. 2021;10:e58430.
Google Scholar
Thomas R, Lone VS, Rune T, Heidi T, Søren V, Iver N, et al. Analysis of circulating tumour DNA to monitor disease burden following colorectal cancer surgery. Gut. 2016;65:625.
Google Scholar
Adalsteinsson VA, Ha G, Freeman SS, Choudhury AD, Stover DG, Parsons HA, et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun. 2017;8:1324.
Google Scholar
Lienhard M, Grimm C, Morkel M, Herwig R, Chavez L. MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. Bioinformatics. 2014;30:284–6.
Google Scholar
Lienhard M, Grasse S, Rolff J, Frese S, Schirmer U, Becker M, et al. QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments. Nucleic Acids Res. 2017;45:e44.
Google Scholar
Cavalcante RG, Sartor MA. annotatr: genomic regions in context. Bioinformatics. 2017;33:2381–3.
Google Scholar
Strand SH, Switnicki M, Moller M, Haldrup C, Storebjerg TM, Hedegaard J, et al. RHCG and TCAF1 promoter hypermethylation predicts biochemical recurrence in prostate cancer patients treated by radical prostatectomy. Oncotarget. 2017;8:5774–88.
Google Scholar
Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, et al. The DNA methylation landscape of advanced prostate cancer. Nat Genet. 2020;52:778–89.
Google Scholar
Haldrup C, Mundbjerg K, Vestergaard EM, Lamy P, Wild P, Schulz WA, et al. DNA methylation signatures for prediction of biochemical recurrence after radical prostatectomy of clinically localized prostate cancer. J Clin Oncol. 2013;31:3250–8.
Google Scholar
Lee WH, Morton RA, Epstein JI, Brooks JD, Campbell PA, Bova GS, et al. Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc Natl Acad Sci USA. 1994;91:11733–7.
Google Scholar
Liu L, Yoon J-H, Dammann R, Pfeifer GP. Frequent hypermethylation of the RASSF1A gene in prostate cancer. Oncogene. 2002;21:6835–40.
Google Scholar
Bjerre MT, Nørgaard M, Larsen OH, Jensen SØ, Strand SH, Østergren P, et al. Epigenetic analysis of circulating tumor dna in localized and metastatic prostate cancer: evaluation of clinical biomarker potential. Cells. 2020;9:1362.
Google Scholar
Moss J, Magenheim J, Neiman D, Zemmour H, Loyfer N, Korach A, et al. Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease. Nat Commun. 2018;9:5068.
Google Scholar
Liu MC, Oxnard GR, Klein EA, Swanton C, Seiden MV, Liu MC, et al. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. Ann Oncol. 2020;31:745–59.
Google Scholar
Bronkhorst AJ, Ungerer V, Holdenrieder S. The emerging role of cell-free DNA as a molecular marker for cancer management. Biomol Detect Quantif. 2019;17:100087.
Google Scholar
Sharma M, Verma RK, Kumar S, Kumar V. Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J. 2022;20:26–39.
Google Scholar
Burgener JM, Zou J, Zhao Z, Zheng Y, Shen SY, Huang SH, et al. Tumor-naïve multimodal profiling of circulating tumor dna in head and neck squamous cell carcinoma. Clin Cancer Res. 2021;27:4230–44.
Google Scholar
Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, et al. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res. 2011;21:1028–41.
Google Scholar
Kron K, Trudel D, Pethe V, Briollais L, Fleshner N, van der Kwast T, et al. Altered DNA methylation landscapes of polycomb-repressed loci are associated with prostate cancer progression and ERG oncogene expression in prostate cancer. Clin Cancer Res. 2013;19:3450–61.
Google Scholar
Massie CE, Mills IG, Lynch AG. The importance of DNA methylation in prostate cancer development. J Steroid Biochem Mol Biol. 2017;166:1–15.
Google Scholar
Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, et al. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013;5:169ra10–ra10.
Google Scholar
Fonseca NM, Maurice-Dror C, Herberts C, Tu W, Fan W, Murtha AJ, et al. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun. 2024;15:1828.
Google Scholar
Sweeney CJ, Petry R, Xu C, Childress M, He J, Fabrizio D, et al. Circulating tumor DNA assessment for treatment monitoring adds value to PSA in metastatic castration-resistant prostate cancer. Clin Cancer Res. 2024;30:4115–22.
Google Scholar
Nørgaard M, Bjerre MT, Fredsøe J, Vang S, Jensen JB, De Laere B, et al. Prognostic value of low-pass whole genome sequencing of circulating tumor DNA in metastatic castration-resistant prostate cancer. Clin Chem. 2023;69:386–98.
Google Scholar
Sumanasuriya S, Seed G, Parr H, Christova R, Pope L, Bertan C, et al. Elucidating prostate cancer behaviour during treatment via low-pass whole-genome sequencing of circulating tumour DNA. Eur Urol. 2021;80:243–53.
Google Scholar
Wu A, Cremaschi P, Wetterskog D, Conteduca V, Franceschini GM, Kleftogiannis D, et al. Genome-wide plasma DNA methylation features of metastatic prostate cancer. J Clin Investig. 2020;130:1991–2000.
Google Scholar
Kluge K, Lotz V, Einspieler H, Haberl D, Spielvogel C, Amereller D, et al. Imaging and outcome correlates of ctDNA methylation markers in prostate cancer: a comparative, cross-sectional [⁶⁸Ga]Ga-PSMA-11 PET/CT study. Clin Epigenetics. 2025;17:36.
Google Scholar
Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku S-Y, et al. Noninvasive detection of neuroendocrine prostate cancer through targeted cell-free DNA methylation. Cancer Discov. 2024;14:424–45.
Google Scholar
Xu R-h, Wei W, Krawczyk M, Wang W, Luo H, Flagg K, et al. Circulating tumour DNA methylation markers for diagnosis and prognosis of hepatocellular carcinoma. Nat Mater. 2017;16:1155–61.
Google Scholar
Frank MS, Andersen CSA, Ahlborn LB, Pallisgaard N, Bodtger U, Gehl J. Circulating Tumor DNA monitoring reveals molecular progression before radiologic progression in a real-life cohort of patients with advanced non–small cell lung cancer. Cancer Res Commun. 2022;2:1174–87.
Google Scholar
Scher HI, Beer TM, Higano CS, Anand A, Taplin M-E, Efstathiou E, et al. Antitumour activity of MDV3100 in castration-resistant prostate cancer: a phase 1–2 study. Lancet. 2010;375:1437–46.
Google Scholar
Scher HI, Fizazi K, Saad F, Taplin M-E, Sternberg CN, Miller K, et al. Increased survival with enzalutamide in prostate cancer after chemotherapy. N Engl J Med. 2012;367:1187–97.
Google Scholar
Ryan CJ, Smith MR, Bono JSD, Molina A, Logothetis CJ, Souza PD, et al. Abiraterone in metastatic prostate cancer without previous chemotherapy. N Engl J Med. 2013;368:138–48.
Google Scholar
Hennigan ST, Trostel SY, Terrigino NT, Voznesensky OS, Schaefer RJ, Whitlock NC, et al. Low abundance of circulating tumor DNA in localized prostate cancer. JCO Precis Oncol. 2019;3:1–13.
Lau E, McCoy P, Reeves F, Chow K, Clarkson M, Kwan EM, et al. Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression. Genome Med. 2020;12:72.
Google Scholar

