Bridging biological cfDNA features and machine learning approaches

T Moser, S Kühberger, I Lazzeri, G Vlachos, E Heitzer - Trends in Genetics, 2023 - cell.com
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to
revolutionize precision oncology and blood-based cancer screening. Recent technological …

A clinician's handbook for using ctDNA throughout the patient journey

SO Hasenleithner, MR Speicher - Molecular cancer, 2022 - Springer
Background The promise of precision cancer medicine presently centers around the
genomic sequence of a patient's tumor being translated into timely, actionable information to …

Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing

E Katsman, S Orlanski, F Martignano, I Fox-Fisher… - Genome Biology, 2022 - Springer
Abstract The Oxford Nanopore (ONT) platform provides portable and rapid genome
sequencing, and its ability to natively profile DNA methylation without complex sample …

[HTML][HTML] Formation of memory assemblies through the DNA-sensing TLR9 pathway

V Jovasevic, EM Wood, A Cicvaric, H Zhang, Z Petrovic… - Nature, 2024 - nature.com
As hippocampal neurons respond to diverse types of information, a subset assembles into
microcircuits representing a memory. Those neurons typically undergo energy-intensive …

Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation

GM Franceschini, O Quaini, K Mizuno, F Orlando… - Cancer discovery, 2024 - AACR
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with
phenotypic subtypes that drive therapy response and outcome differences. Histologic …

Chronic graft-versus-host disease detected by tissue-specific cell-free DNA methylation biomarkers

B Avni, D Neiman, E Shaked… - The Journal of …, 2024 - Am Soc Clin Investig
BACKGROUND. Accurate detection of graft-versus-host disease (GVHD) is a major
challenge in the management of patients undergoing hematopoietic stem cell …

Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology

KE Stanley, T Jatsenko, S Tuveri, D Sudhakaran… - Nature …, 2024 - nature.com
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell
types that release them. Current methods for cfDNA deconvolution typically use disease …

Megakaryocyte-and erythroblast-specific cell-free DNA patterns in plasma and platelets reflect thrombopoiesis and erythropoiesis levels

J Moss, R Ben-Ami, E Shai, O Gal-Rosenberg… - Nature …, 2023 - nature.com
Circulating cell-free DNA (cfDNA) fragments are a biological analyte with extensive utility in
diagnostic medicine. Understanding the source of cfDNA and mechanisms of release is …

[HTML][HTML] Circulating cell-free methylated DNA reveals tissue-specific, cellular damage from radiation treatment

ME McNamara, N Loyfer, AJ Kiliti, MO Schmidt… - JCI insight, 2023 - ncbi.nlm.nih.gov
Radiation therapy is an effective cancer treatment, although damage to healthy tissues is
common. Here we analyzed cell-free, methylated DNA released from dying cells into the …

Epigenetic liquid biopsies: a novel putative biomarker in immunology and inflammation

I Fox-Fisher, R Shemer, Y Dor - Trends in Immunology, 2023 - cell.com
Immune and inflammatory processes occurring within tissues are often undetectable by
blood cell counts, standard circulating biomarkers, or imaging, representing an unmet …