Thesis

231 Summary and general discussion 71. Mouliere F, Smith CG, Heider K, Su J, van der Pol Y, Thompson M, et al. Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients. EMBO Molecular Medicine. 2021;13(8):e12881. 72. Hudecova I, Smith CG, Hänsel-Hertsch R, Chilamakuri CS, Morris JA, Vijayaraghavan A, et al. Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA. Genome Res. 2022;32(2):215-27. 73. Lee EY, Lee EJ, Yoon H, Lee DH, Kim KH. Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions. Diagnostics (Basel). 2020;10(4). 74. Bach S, Paulis I, Sluiter NR, Tibbesma M, Martin I, van de Wiel MA, et al. Detection of colorectal cancer in urine using DNA methylation analysis. Sci Rep. 2021;11(1):2363. 75. Shen SY, Burgener JM, Bratman SV, De Carvalho DD. Preparation of cfMeDIP-seq libraries for methylome profiling of plasma cell-free DNA. Nature protocols. 2019;14(10):2749-80. 76. Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic acids research. 2010;38(2):391-9. 77. Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, Stunnenberg HG. Whole-genome DNA methylation profiling using MethylCap-seq. Methods. 2010;52(3):232-6. 78. Kolkman RW, Segerink LI, Huskens J. Selective Enrichment of Hypermethylated DNA by a Multivalent Binding Platform. Advanced Materials Interfaces. 2022;9(35):2201557. 79. Wang Y, Douville C, Cohen JD, Mattox A, Curtis S, Silliman N, et al. Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules. Proceedings of the National Academy of Sciences. 2023;120(15):e2220704120. 80. Cheng THT, Jiang P, Teoh JYC, Heung MMS, Tam JCW, Sun X, et al. Noninvasive Detection of Bladder Cancer by Shallow-Depth Genome-Wide Bisulfite Sequencing of Urinary Cell-Free DNA for Methylation and Copy Number Profiling. Clin Chem. 2019;65(7):927-36. 81. Sangtani A, Wang C, Weaver A, Hoppman NL, Kerr SE, Abyzov A, et al. Combining copy number, methylation markers, and mutations as a panel for endometrial cancer detection via intravaginal tampon collection. Gynecologic Oncology. 2020;156(2):387-92. 82. Füllgrabe J, Gosal WS, Creed P, Liu S, Lumby CK, Morley DJ, et al. Simultaneous sequencing of genetic and epigenetic bases in DNA. Nature Biotechnology. 2023. 83. Li W, Zhang X, Lu X, You L, Song Y, Luo Z, et al. 5-Hydroxymethylcytosine signatures in circulating cell-free DNA as diagnostic biomarkers for human cancers. Cell Research. 2017;27(10):1243-57. 84. Cao F, Wei A, Hu X, He Y, Zhang J, Xia L, et al. Integrated epigenetic biomarkers in circulating cell-free DNA as a robust classifier for pancreatic cancer. Clinical Epigenetics. 2020;12(1):112. 85. Markus H, Zhao J, Contente-Cuomo T, Stephens MD, Raupach E, Odenheimer-Bergman A, et al. Analysis of recurrently protected genomic regions in cell-free DNA found in urine. Science Translational Medicine. 2021;13(581):eaaz3088. 86. Zhou Z, Ma M-JL, Chan RWY, Lam WKJ, Peng W, Gai W, et al. Fragmentation landscape of cellfree DNA revealed by deconvolutional analysis of end motifs. Proceedings of the National Academy of Sciences. 2023;120(17):e2220982120. 8

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