86549d6f6adca1f64442261a2452f555 cancers-14-00349-v3.pdf 415b0cfa177b908a2a5b54bcf1a76485d103bbaf cancers-14-00349-v3.pdf 7e3642b27e4c414448176e7ed86231cab2aea68f70203ebdf9b1d623ec62f515 cancers-14-00349-v3.pdf Title: Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer Subject: DNA methylation is an essential epigenetic mark. Alterations of normal DNA methylation are a defining feature of cancer. Here, we review experimental and bioinformatic approaches to showcase the breadth and depth of information that this epigenetic mark provides for cancer research. First, we describe classical approaches for interrogating bulk DNA from cell populations as well as more recently developed approaches for single cells and multi-Omics. Second, we focus on the computational analysis from primary data processing to the identification of unique methylation signatures. Additionally, we discuss challenges such as sparse data and cellular heterogeneity. Keywords: DNA methylation; cancer; methods; software; computational analysis Author: Angelika Merkel and Manel Esteller Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Thu Jan 13 05:23:37 2022 CET ModDate: Thu Jan 13 05:36:06 2022 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 14 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 588710 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- YWQWLZ+VnURWPalladioL Type 1 Custom yes yes no 10 0 TSAZHF+URWPalladioL-Bold Type 1 Custom yes yes no 15 0 TXQGDI+URWPalladioL-Roma Type 1 Custom yes yes no 20 0 TFSIVH+URWPalladioL-Ital Type 1 Custom yes yes no 24 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 32 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 36 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 40 0 LCJEVJ+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 53 0 DVCMRV+CMSY10 Type 1 Builtin yes yes no 75 0 LWLIVD+EURM10 Type 1 Builtin yes yes no 83 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-07-01 02:41:47 CEST RepresentationInformation: cancers-14-00349-v3.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-02-09 17:22:05 CET Size: 588710 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 451 FreeObjects: 3 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@44c8afef Item: Title: DNA Methylation Assays Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Children: Item: Title: Single-Cell and Single-Cell Multi-Omics Approaches Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Item: Title: Cell-Free Circulating Tumour DNA (ct) from Liquid Biopsies Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: Processing of DNA Methylation Data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: Analysis of DNA Methylation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Children: Item: Title: Exploratory Data Analysis and Sparse Data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Deconvolution of Cellular Heterogeneity and Estimating Tumour Purity Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: DNA Methylation Signatures Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Children: Item: Title: Differential Methylation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Methylome Segmentation and the DNA Methylation Landscape Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Item: Title: Downstream Analysis: Interpretation and Application of DNA Methylation Signatures for Research and Clinics Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Conclusion and Remaining Challenges Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Info: Title: Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer Author: Angelika Merkel and Manel Esteller Subject: DNA methylation is an essential epigenetic mark. Alterations of normal DNA methylation are a defining feature of cancer. Here, we review experimental and bioinformatic approaches to showcase the breadth and depth of information that this epigenetic mark provides for cancer research. First, we describe classical approaches for interrogating bulk DNA from cell populations as well as more recently developed approaches for single cells and multi-Omics. Second, we focus on the computational analysis from primary data processing to the identification of unique methylation signatures. Additionally, we discuss challenges such as sparse data and cellular heterogeneity. 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