Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

Multi-omics profiling for health

M Babu, M Snyder - Molecular & Cellular Proteomics, 2023 - ASBMB
The world has witnessed a steady rise in both non-infectious and infectious chronic
diseases, prompting a cross-disciplinary approach to understand and treating disease …

Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

AS Nam, N Dusaj, F Izzo, R Murali, RM Myers… - Nature …, 2022 - nature.com
Somatic mutations in cancer genes have been detected in clonal expansions across healthy
human tissue, including in clonal hematopoiesis. However, because mutated and wild-type …

A mammalian methylation array for profiling methylation levels at conserved sequences

A Arneson, A Haghani, MJ Thompson… - Nature …, 2022 - nature.com
Infinium methylation arrays are not available for the vast majority of non-human mammals.
Moreover, even if species-specific arrays were available, probe differences between them …

Simultaneous sequencing of genetic and epigenetic bases in DNA

J Füllgrabe, WS Gosal, P Creed, S Liu, CK Lumby… - Nature …, 2023 - nature.com
DNA comprises molecular information stored in genetic and epigenetic bases, both of which
are vital to our understanding of biology. Most DNA sequencing approaches address either …

Direct enzymatic sequencing of 5-methylcytosine at single-base resolution

T Wang, JM Fowler, L Liu, CE Loo, M Luo… - Nature chemical …, 2023 - nature.com
methylcytosine (5mC) is the most important DNA modification in mammalian genomes. The
ideal method for 5mC localization would be both nondestructive of DNA and direct, without …

Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer

P Li, S Liu, L Du, G Mohseni, Y Zhang, C Wang - Clinical epigenetics, 2022 - Springer
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are
diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is …

Epigenetic analysis of cell-free DNA by fragmentomic profiling

Q Zhou, G Kang, P Jiang, R Qiao… - Proceedings of the …, 2022 - National Acad Sciences
Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information
linked to tissues of origin. We explored the possibility of using fragmentation patterns to …

DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation

Y An, X Zhao, Z Zhang, Z Xia, M Yang, L Ma… - Nature …, 2023 - nature.com
Plasma cell-free DNA (cfDNA) are small molecules generated through a non-random
fragmentation procedure. Despite commendable translational values in cancer liquid biopsy …

Modular oxidation of cytosine modifications and their application in direct and quantitative sequencing of 5-hydroxymethylcytosine

H Xu, J Chen, J Cheng, L Kong, X Chen… - Journal of the …, 2023 - ACS Publications
Selective, efficient, and controllable oxidation of cytosine modifications is valuable for
epigenetic analyses, yet only limited progress has been made. Here, we present two …