Abbreviations DNA: Deoxyribonucleic acid NGS: Next-generation sequencing 5mC: 5-methylCytosine 5hmC: 5-hydroxyMethylcytosine ONT: Oxford Nanopore Technologies SMRT: Single molecule real-time PacBio: Pacific Biosciences A: Adenine C: Cytosine G: Guanine T: Thymine DNMTs: DNA methyltransferase enzymes SAM: S-adenosyl methionine TET: Ten-eleven translocation AID: Activation-induced cytidine deaminase mRNA: Messenger ribonucleic acid APOBEC: Apolipoprotein B messenger ribonucleic acid editing enzyme, catalytic polypeptide MBD: Methyl-CpG-binding domain UHRF: Ubiquitin-like containing PHD and RING finger domains 5hmC: 5-hydroxymethylcytosine P: Phosphate CpG: Cytosine-phosphate-guanine CGI: CpG island 6mA: N6-methyladenine 4mC: N4-methylcytosine 5fC: 5-formylcytosine 5caC: 5-carboxylcytosine ICF syndrome: Immunodeficiency, Centromere instability and Facial anomalies syndrome ATRX syndrome: Alpha thalassemia X-linked intellectual disability PofO: Parent-of-origin DMRs: Differentially methylated regions pRB: Retinoblastoma protein cfDNA: Circulating cell-free DNA miRNA: Micro-ribonucleic acid PCR: Polymerase chain-reaction SNP: Single-nucleotide polymorphisms SMRT: Single-molecule real-time LRS: Long-read sequencing ONT: Oxford Nanopore Technologies MspA: Mycobacterium smegmatis porin A Si 3 N 4 : Silicon nitride SiO 2 : Silicon dioxide Al 2 O 3 : Aluminum oxide BN: Boron nitride HMM: Hidden Markov models MGMT: O 6 -methylguanine-DNA methyltransferase TE: Transposable element nanoNOMe: Nanopore sequencing of Nucleosome Occupancy and Methylome CNN: Convolutional neural network RNN: Recurrent neural network SEPT9: Septin 9 GSTP1: Glutathione S-transferase pi 1 References Xie S, Leung AWS, Zheng Z, et al
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Methylation levels of SFRP1 , SFRP2 , SDC2 , and PRIMA1 were determined using a MethyLight assay after cfDNA isolation and bisulfite conversion of samples ( SOX21 gene promoter methylation, serving as a fecal-based noninvasive biomarker for early diagnosis of colorectal cancer (Moradi et al., 2021)
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