Navigating the pitfalls of mapping DNA and RNA modifications

Y Kong, EA Mead, G Fang - Nature Reviews Genetics, 2023 - nature.com
Chemical modifications to nucleic acids occur across the kingdoms of life and carry
important regulatory information. Reliable high-resolution mapping of these modifications is …

Liquid biopsies beyond mutation calling: genomic and epigenomic features of cell-free DNA in cancer

AK Angeles, F Janke, S Bauer, P Christopoulos… - Cancers, 2021 - mdpi.com
Simple Summary Liquid biopsies provide a non-invasive means to diagnose and profile
tumors when tissue is not available. Sequence-based analysis of cell-free DNA (cfDNA) is …

Detection of early stage pancreatic cancer using 5-hydroxymethylcytosine signatures in circulating cell free DNA

GD Guler, Y Ning, CJ Ku, T Phillips, E McCarthy… - Nature …, 2020 - nature.com
Pancreatic cancer is often detected late, when curative therapies are no longer possible.
Here, we present non-invasive detection of pancreatic ductal adenocarcinoma (PDAC) by 5 …

A human tissue map of 5-hydroxymethylcytosines exhibits tissue specificity through gene and enhancer modulation

XL Cui, J Nie, J Ku, U Dougherty… - Nature …, 2020 - nature.com
Abstract DNA 5-hydroxymethylcytosine (5hmC) modification is known to be associated with
gene transcription and frequently used as a mark to investigate dynamic DNA methylation …

Tissue-specific 5-hydroxymethylcytosine landscape of the human genome

B He, C Zhang, X Zhang, Y Fan, H Zeng, J Liu… - Nature …, 2021 - nature.com
Hydroxymethylcytosine (5hmC) is an important epigenetic mark that regulates gene
expression. Charting the landscape of 5hmC in human tissues is fundamental to …

Copy number variation in plasma as a tool for lung cancer prediction using Extreme Gradient Boosting (XGBoost) classifier

D Yu, Z Liu, C Su, Y Han, XC Duan, R Zhang… - Thoracic …, 2020 - Wiley Online Library
Background The main cause of cancer death is lung cancer (LC) which usually presents at
an advanced stage, but its early detection would increase the benefits of treatment. Blood is …

Bisulfite-free, nanoscale analysis of 5-hydroxymethylcytosine at single base resolution

H Zeng, B He, B Xia, D Bai, X Lu, J Cai… - Journal of the …, 2018 - ACS Publications
High-resolution detection of genome-wide 5-hydroxymethylcytosine (5hmC) sites of small-
scale samples remains challenging. Here, we present hmC-CATCH, a bisulfite-free, base …

Bisulfite-free and single-nucleotide resolution sequencing of DNA epigenetic modification of 5-hydroxymethylcytosine using engineered deaminase

NB Xie, M Wang, TT Ji, X Guo, JH Ding, BF Yuan… - Chemical …, 2022 - pubs.rsc.org
The discovery of 5-hydroxymethylcytosine (5hmC) in mammalian genomes is a landmark in
epigenomics study. Similar to 5-methylcytosine (5mC), 5hmC is viewed as a critical …

Towards precision medicine: advances in 5-hydroxymethylcytosine cancer biomarker discovery in liquid biopsy

C Zeng, EK Stroup, Z Zhang, BCH Chiu… - Cancer …, 2019 - Springer
Robust and clinically convenient biomarkers for cancer diagnosis, early detection, and
prognosis have great potential to improve patient survival and are the key to precision …

Cell-free DNA methylation profiling analysis—technologies and bioinformatics

J Huang, L Wang - Cancers, 2019 - mdpi.com
Analysis of circulating nucleic acids in bodily fluids, referred to as “liquid biopsies”, is rapidly
gaining prominence. Studies have shown that cell-free DNA (cfDNA) has great potential in …